AMBER Archive (2004) - By Author

Starting: Thu Jan 01 2004 - 04:51:48 CST
Ending: Thu May 05 2005 - 14:26:38 CDT

• ::©¾¸Û::
  • AMBER: A Question about RESP (Sat Mar 06 2004 - 06:39:22 CST)
• a b
  • AMBER: a general question about the mmpbsa method (Wed Apr 28 2004 - 22:51:00 CDT)
  • AMBER: amber98 with amberffc+INSIGHT II (Wed Mar 17 2004 - 08:28:58 CST)
  • AMBER: adding ions to nucleic acids (Sun Feb 08 2004 - 04:47:19 CST)
  • AMBER: the uses for Amber FFs (Tue Feb 03 2004 - 08:48:24 CST)
  • AMBER: references? (Sun Jan 11 2004 - 08:40:50 CST)
  • AMBER: .crg file for Delphi (Wed Jan 07 2004 - 12:22:34 CST)
• A. Hungie
  • AMBER: free energy (Fri Jun 04 2004 - 12:21:59 CDT)
  • AMBER: gibbs in amber8 (Fri Jun 04 2004 - 12:13:12 CDT)
  • AMBER: Amber 8 compilation (Wed May 26 2004 - 11:23:07 CDT)
  • AMBER: Installation AMber 8: "cannot find -lU77" (Tue May 25 2004 - 08:21:09 CDT)
  • AMBER: force field (Fri Jan 02 2004 - 06:28:59 CST)
  • AMBER: algorithm used in AMBER (Fri Jan 02 2004 - 04:07:11 CST)
• A.B.S.M Osman gani
  • AMBER: Re: ANAL problem (Wed Feb 04 2004 - 13:31:18 CST)
  • Re: AMBER: CYS, CYX and CYM (Thu Jan 29 2004 - 09:50:35 CST)
  • Re: AMBER: XLEAP (Thu Jan 29 2004 - 09:19:04 CST)
  • AMBER: ANAL problem. (Thu Jan 29 2004 - 06:24:19 CST)
• A.Madhumalar
  • Re: AMBER: Parm98 Vs 02 (Wed Jan 21 2004 - 11:01:31 CST)
  • AMBER: Parm98 Vs 02 (Tue Jan 20 2004 - 10:27:03 CST)
• Abd Ghani Abd Aziz
  • Re: AMBER: ptraj problem (Thu Nov 04 2004 - 20:39:37 CST)
  • AMBER: ptraj problem (Thu Nov 04 2004 - 19:53:39 CST)
  • AMBER: amber 8 error (Tue Oct 19 2004 - 03:14:24 CDT)
  • AMBER: amber 8 parallel problem (Sat Oct 16 2004 - 05:47:44 CDT)
  • AMBER: amber 8 error (Sat Oct 16 2004 - 04:19:38 CDT)
• Abd Ghani Bin Abd Aziz
  • AMBER: mdinfo on amber6 (Mon Oct 04 2004 - 00:26:41 CDT)
  • Re: AMBER: amber 8 error (Sat Oct 02 2004 - 04:26:10 CDT)
  • AMBER: amber 8 error (Sat Oct 02 2004 - 02:25:30 CDT)
  • Re: AMBER: amber 8 error on installation (Sun Sep 26 2004 - 08:47:04 CDT)
  • AMBER: amber 8 error on installation (Sun Sep 26 2004 - 07:55:07 CDT)
  • AMBER: (Sat Sep 25 2004 - 05:16:39 CDT)
  • Re: AMBER: make install error (Tue Sep 14 2004 - 10:23:37 CDT)
  • RE: AMBER: amber 8 (Tue Sep 14 2004 - 10:28:47 CDT)
  • AMBER: amber 8 (Tue Sep 14 2004 - 08:17:56 CDT)
  • Re: AMBER: make install error (Sun Sep 12 2004 - 07:53:52 CDT)
  • Re: AMBER: make install error (Sun Sep 12 2004 - 07:40:42 CDT)
  • RE: AMBER: make install error (Sun Sep 12 2004 - 06:25:19 CDT)
  • AMBER: make install error (Sat Sep 11 2004 - 04:56:40 CDT)
  • AMBER: MPICH problem (Fri Sep 10 2004 - 07:33:45 CDT)
  • AMBER: make install error (Fri Sep 10 2004 - 06:21:15 CDT)
  • AMBER: simulated annealing.. (Wed Jul 28 2004 - 08:45:55 CDT)
  • Re: AMBER: simulated annealing (Wed Jul 28 2004 - 08:22:37 CDT)
  • AMBER: simulated annealing (Wed Jul 28 2004 - 07:08:48 CDT)
• Adrian E. Roitberg
  • AMBER: TFE parameters (Tue Dec 21 2004 - 14:34:29 CST)
  • Re: AMBER: Trajectory corruption (Fri Oct 15 2004 - 12:06:23 CDT)
  • Re: AMBER: amber 8 under windows XP (Thu May 27 2004 - 08:09:51 CDT)
  • AMBER: amber 8 under windows XP (Wed May 26 2004 - 13:50:02 CDT)
  • Re: AMBER: parameters for neutral Arg (Fri Apr 23 2004 - 16:05:03 CDT)
• Ahammadunny Pathiaseril
  • AMBER: (Tue Sep 28 2004 - 13:05:44 CDT)
  • AMBER: [Fwd: KLAMBDA in amber7] (Mon Mar 22 2004 - 12:44:11 CST)
• aini_at_UMDNJ.EDU
  • AMBER: question about mm-pbsa (Mon May 10 2004 - 19:10:05 CDT)
  • AMBER: atom type for GBSA (Wed Feb 11 2004 - 09:13:04 CST)
  • AMBER: question about the average structure from ptraj (Sun Feb 08 2004 - 13:33:23 CST)
  • Re: AMBER: A general question (Tue Feb 03 2004 - 19:39:44 CST)
  • AMBER: A general question (Tue Feb 03 2004 - 17:49:06 CST)
  • Re: AMBER: Do I need to repeat MD simulation? (Wed Jan 21 2004 - 12:42:30 CST)
  • AMBER: Do I need to repeat MD simulation? (Tue Jan 20 2004 - 17:43:00 CST)
• ajakalian_at_lav.Boehringer-Ingelheim.com
  • RE: AMBER: RESP vs. AM1-BCC charges for isoprene (Mon Jul 26 2004 - 10:09:31 CDT)
  • RE: AMBER: RESP vs. AM1-BCC charges for isoprene (Thu Jul 22 2004 - 07:43:16 CDT)
• Alberto p
  • AMBER: NSCM (Wed Dec 29 2004 - 06:07:48 CST)
• Alberto Perez
  • AMBER: principal axis (Wed Sep 15 2004 - 08:36:37 CDT)
• aldo jongejan
  • Re: AMBER: animation? (Wed Jul 28 2004 - 07:36:21 CDT)
  • Re: AMBER: cluster MD conformations from sander (Fri Jun 11 2004 - 03:22:40 CDT)
  • Re: AMBER: Aldo's PMEMD bug (Mon Feb 09 2004 - 09:44:39 CST)
  • AMBER: PMEMD and nmropt=1 (Thu Feb 05 2004 - 05:52:29 CST)
• Alena Shmygelska
  • Re: AMBER: increasing the maximum value of NPHB parameter (Thu Dec 02 2004 - 01:42:44 CST)
  • AMBER: increasing the maximum value of NPHB parameter (Mon Nov 29 2004 - 23:05:08 CST)
  • AMBER: GO lie Amber simulation (Sat Nov 27 2004 - 15:48:53 CST)
• Alessio Comisso
  • AMBER: Error message while testing (Wed Apr 07 2004 - 06:53:24 CDT)
• Alexey Onufriev
  • Re: AMBER: modeling GPCR in lipid environment (Thu Jan 08 2004 - 13:08:01 CST)
  • Re: AMBER: Radius of gyration (Tue Jan 06 2004 - 12:59:24 CST)
• Amber admin
  • AMBER: ptraj questions (Sun Oct 31 2004 - 08:59:51 CST)
  • AMBER: Question Amber8 install errer with Windows (Fri Sep 24 2004 - 14:46:06 CDT)
  • AMBER: building parameters with Amber (Wed Sep 22 2004 - 11:41:38 CDT)
  • Re: AMBER: AMBPDB command requires libcxa.so.5 (Mon Jun 28 2004 - 10:12:45 CDT)
  • AMBER: problems with mpich (Fri May 28 2004 - 09:55:25 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 12:25:03 CDT)
  • Re: AMBER: antechamber (Wed May 05 2004 - 15:51:22 CDT)
• Amber Administration
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 16:15:14 CDT)
  • Re: AMBER: water hole (Wed Apr 14 2004 - 18:59:31 CDT)
  • AMBER: multiple messages on the amber reflector (Tue Feb 17 2004 - 16:27:52 CST)
• Andre Farias de Moura
  • Re: AMBER: resp error message (Thu Sep 30 2004 - 08:58:38 CDT)
  • Re: AMBER: resp error message (Wed Sep 29 2004 - 12:41:05 CDT)
  • AMBER: resp error message (Wed Sep 29 2004 - 11:25:07 CDT)
• Andrea Tafi
  • AMBER: Fifth European Workshop in Drug Design (Thu Nov 18 2004 - 06:35:02 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: Kinetics energy (Mon Dec 20 2004 - 04:11:10 CST)
  • Re: AMBER: nanotube parameters (Mon Dec 20 2004 - 04:02:56 CST)
  • Re: AMBER: ptraj hbond memory allocation on opteron (Mon Dec 13 2004 - 10:07:25 CST)
  • Re: AMBER: Compiling Antechamber/Amber8 with ia64_ifort (Mon Dec 06 2004 - 02:56:34 CST)
  • Re: AMBER: SUSE 9.1 and AMBER 8 (Tue Nov 16 2004 - 07:10:44 CST)
  • Re: AMBER: translational and rotational entropy (Fri Nov 05 2004 - 01:43:00 CST)
  • Re: AMBER: amber 8 error (Tue Oct 19 2004 - 04:00:59 CDT)
  • Re: AMBER: Problem with installing Amber8: Where are the MK libraries? (Thu Oct 14 2004 - 12:42:35 CDT)
  • Re: AMBER: Hot solvent/cold solute reference (Mon Oct 11 2004 - 08:16:18 CDT)
  • Re: AMBER: amber8 installation (Wed Sep 22 2004 - 06:05:02 CDT)
  • Re: AMBER: amber8 performance problem on Itanium II's (Fri Sep 17 2004 - 03:52:53 CDT)
  • Re: AMBER: Spike in energy and RMS (Thu Sep 09 2004 - 04:37:57 CDT)
  • Re: AMBER: Temperature Regulation (Tue Jul 27 2004 - 09:09:51 CDT)
  • Re: AMBER: sander on multiprocessors (Tue Jul 06 2004 - 06:15:48 CDT)
  • Re: AMBER: best PC laptop system to run Amber 8 (Sun Jul 04 2004 - 07:24:07 CDT)
  • Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander (Wed Jun 16 2004 - 09:58:33 CDT)
  • Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? (Fri Jun 04 2004 - 10:15:03 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:21:40 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 07:13:56 CDT)
  • Re: AMBER: any program or tool (Mon May 03 2004 - 07:11:50 CDT)
  • Re: Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 09:44:21 CDT)
  • Re: AMBER: WHICH LINUX (Tue Apr 13 2004 - 10:30:20 CDT)
  • Re: AMBER: water hole (Tue Apr 13 2004 - 05:02:12 CDT)
  • Re: AMBER: Compiling Amber 8 (Tue Apr 13 2004 - 04:57:29 CDT)
  • Re: AMBER: understanding SANDER source code (Mon Mar 22 2004 - 06:15:42 CST)
  • Re: AMBER: Do I need to repeat MD simulation? (Wed Jan 21 2004 - 04:40:17 CST)
  • Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning (Wed Jan 07 2004 - 06:12:30 CST)
• Andrew Box
  • AMBER: NMR constraint problem (Tue Dec 07 2004 - 21:06:02 CST)
  • AMBER: (no subject) (Mon Dec 06 2004 - 21:32:52 CST)
  • RE: AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 01:30:46 CDT)
  • AMBER: (no subject) (Sun Jun 27 2004 - 22:29:34 CDT)
• Andrew M K Law
  • AMBER: Unknown Amber Nomeclature (Sat Jan 31 2004 - 16:17:47 CST)
• Andy Purkiss
  • AMBER: Bug and Patch in ANAL (Wed Aug 04 2004 - 10:38:30 CDT)
  • RE: AMBER: Molecular dynamic (Tue Jul 13 2004 - 04:21:02 CDT)
  • Re: AMBER: image and restart problems (Tue Jun 29 2004 - 08:05:48 CDT)
  • Re: AMBER: trajectory file (Mon Mar 29 2004 - 10:54:24 CST)
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Thu Jan 29 2004 - 08:19:22 CST)
• anita pachaimuthu
  • AMBER: VDWAALS error during minimisation (Thu Sep 16 2004 - 09:42:34 CDT)
  • Re: AMBER: lib file (Mon Aug 02 2004 - 09:27:51 CDT)
  • Re: AMBER: lib file (Fri Jul 30 2004 - 16:08:18 CDT)
  • AMBER: lib file (Fri Jul 30 2004 - 15:09:19 CDT)
  • AMBER: Co-ordination error while running tleap (Wed Jul 21 2004 - 10:12:12 CDT)
  • AMBER: .lib file error in tleap (Mon Jul 19 2004 - 12:19:19 CDT)
• Ann P
  • AMBER: Errors when running tleap (Wed Feb 25 2004 - 15:13:53 CST)
• Ann P
  • RE: AMBER: Errors when running tleap (Thu Feb 26 2004 - 13:21:03 CST)
• Anna Schrey
  • Re: AMBER: minimization output (Fri Feb 20 2004 - 03:07:40 CST)
  • Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd (Fri Jan 23 2004 - 04:39:47 CST)
  • AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd (Thu Jan 08 2004 - 04:30:37 CST)
• Annette Ho
  • Re: AMBER: about FEP (Tue Nov 02 2004 - 04:44:03 CST)
• Annette Höglund
  • AMBER: Why the charge is not an integer? (Tue Dec 14 2004 - 01:39:11 CST)
  • AMBER: FEP - GIBBS of charged sidechains using IELPER (Sun Nov 28 2004 - 11:26:06 CST)
  • AMBER: FEP and charges (Wed Nov 03 2004 - 05:59:16 CST)
  • Re: AMBER: about FEP (Tue Nov 02 2004 - 05:58:27 CST)
  • AMBER: questions regarding JTREE (Wed Oct 27 2004 - 10:37:06 CDT)
  • Re: AMBER: FEP error/early termination - why? (Tue Jun 01 2004 - 09:34:53 CDT)
  • AMBER: FEP error/early termination - why? (Mon May 31 2004 - 08:23:27 CDT)
  • AMBER: HIV-RT Nevirapin (Wed Mar 03 2004 - 09:37:40 CST)
• Anselm Horn
  • Re: AMBER: (no subject) (Wed Sep 29 2004 - 10:00:43 CDT)
  • Re: AMBER: NMODE COMPILATION (Mon Mar 15 2004 - 05:34:50 CST)
  • AMBER: MM-PBSA: molecular charges and active site water (Thu Feb 12 2004 - 09:23:05 CST)
• Anshul Awasthi
  • AMBER: Pasrameters for MAI (Wed Mar 31 2004 - 15:46:18 CST)
  • AMBER: erreo in sander (Sat Mar 27 2004 - 07:15:54 CST)
• anshul_at_imtech.res.in
  • Re: AMBER: amber7 on digital unix (Thu Dec 23 2004 - 21:15:47 CST)
  • AMBER: amber7 on digital unix (Thu Dec 23 2004 - 16:23:15 CST)
  • AMBER: Protein with maximum hydrogen bonds (Sat Nov 27 2004 - 11:23:43 CST)
  • AMBER: Fluctuation in temperature (Thu Nov 04 2004 - 16:09:58 CST)
  • AMBER: H bond calculation of CHARMM trajactory using PTRAJ (Fri Oct 15 2004 - 23:59:33 CDT)
  • AMBER: Comparison of simulation results on amber7 and amber 8 (Wed Oct 06 2004 - 15:28:04 CDT)
  • Re: AMBER: error in installing amber8 (Wed Sep 08 2004 - 16:39:27 CDT)
  • AMBER: error in installing amber8 (Thu Sep 02 2004 - 17:37:12 CDT)
  • AMBER: problem loading molecule in leap (Thu Aug 26 2004 - 15:38:44 CDT)
  • RE: AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 11:34:58 CDT)
  • AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 09:52:05 CDT)
  • AMBER: peoblemwith RED II (Tue Aug 17 2004 - 14:15:30 CDT)
  • Re: AMBER: charge not zero (Wed Aug 04 2004 - 22:48:11 CDT)
  • AMBER: charge not zero (Tue Aug 03 2004 - 12:29:12 CDT)
  • AMBER: erroe in installing amber8 (Sat Jul 24 2004 - 12:11:02 CDT)
  • AMBER: atoms not in residue templates (Sat Jul 24 2004 - 10:19:42 CDT)
  • Re: AMBER: vdw energy in minimization (Mon Jul 19 2004 - 22:44:30 CDT)
  • AMBER: vdw energy in minimization (Mon Jul 19 2004 - 10:11:17 CDT)
  • AMBER: Parameter generation from RESP charges (Tue Jul 13 2004 - 23:02:07 CDT)
  • AMBER: (no subject) (Tue Jul 13 2004 - 22:40:08 CDT)
  • Re: AMBER: segmentation fault in leap (Thu Jul 08 2004 - 20:17:40 CDT)
  • AMBER: segmentation fault in leap (Thu Jul 08 2004 - 16:40:42 CDT)
  • Re: AMBER: Simulated anealling (Wed Jun 09 2004 - 09:41:56 CDT)
  • Re: AMBER: Simulated anealling (Fri Jun 04 2004 - 15:56:50 CDT)
  • Re: AMBER: simulated anealling (Thu Jun 03 2004 - 11:56:58 CDT)
  • AMBER: Simulated anealling (Thu Jun 03 2004 - 09:30:42 CDT)
  • AMBER: simulated anealling (Thu Jun 03 2004 - 09:12:55 CDT)
  • AMBER: instalation of RES (Thu May 20 2004 - 13:22:08 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Sun May 16 2004 - 15:01:55 CDT)
  • AMBER: antechamber (Sat May 15 2004 - 11:43:48 CDT)
  • Re: AMBER: MD with NTR + NMROPT (Wed May 12 2004 - 10:07:49 CDT)
  • AMBER: Charges and atom type (Sat May 08 2004 - 16:06:25 CDT)
  • Re: AMBER: xleap don't recognize formaldehyde? (Sat May 08 2004 - 14:44:33 CDT)
  • Re: AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 18:14:53 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 18:01:33 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 17:51:32 CDT)
  • AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 16:50:35 CDT)
  • AMBER: Implicit solvents (Wed May 05 2004 - 15:10:20 CDT)
  • AMBER: H Bonds (Wed May 05 2004 - 15:07:01 CDT)
  • AMBER: methane box (Wed May 05 2004 - 13:57:16 CDT)
  • AMBER: energy criteria. (Fri Apr 30 2004 - 15:51:04 CDT)
  • AMBER: Bond type in leap (Thu Apr 22 2004 - 14:22:31 CDT)
  • Re: AMBER: instalation of amber7 on SUN (Thu Apr 22 2004 - 11:35:37 CDT)
  • AMBER: distance dependent dielectric (Wed Apr 21 2004 - 10:30:49 CDT)
  • AMBER: instalation of amber7 on SUN (Tue Apr 20 2004 - 21:53:20 CDT)
  • AMBER: distance measurement in carnal and ptraj (Fri Apr 16 2004 - 15:56:33 CDT)
  • Re: AMBER: error in antechamber (Thu Apr 08 2004 - 12:36:57 CDT)
  • AMBER: unique atom names (Wed Apr 07 2004 - 18:00:31 CDT)
  • AMBER: error in antechamber (Wed Apr 07 2004 - 17:49:47 CDT)
  • AMBER: (Tue Apr 06 2004 - 16:58:07 CDT)
  • AMBER: Error in building a molecule (Mon Apr 05 2004 - 17:01:54 CDT)
• Anthony Fejes
  • AMBER: gaff parameter ambiguities (Wed Nov 03 2004 - 17:16:07 CST)
• apw397_at_soton.ac.uk
  • Re: AMBER: question about replica exchange in amber8 (Wed Jun 02 2004 - 04:43:21 CDT)
• arubin_at_unmc.edu
  • AMBER: Electrolyte concentrations in MD (Fri Nov 19 2004 - 14:56:09 CST)
• Arvid Soderhall
  • AMBER: [Fwd: No timings from jac test on opteron quad] (Mon Mar 15 2004 - 07:28:02 CST)
• Arvind
  • Re: AMBER: RNA sequence with DNA backbone? (Wed Jul 14 2004 - 05:50:29 CDT)
  • AMBER: RNA sequence with DNA backbone? (Mon Jul 12 2004 - 06:26:36 CDT)
  • Re: AMBER: Amber8 compilation error (Fri Apr 30 2004 - 14:50:38 CDT)
  • AMBER: Amber8 compilation error (Fri Apr 30 2004 - 12:04:02 CDT)
  • Re: AMBER: nucgen generated RNA duplex: leap problems (Wed Apr 21 2004 - 15:23:28 CDT)
  • AMBER: nucgen generated RNA duplex: leap problems (Tue Apr 20 2004 - 06:44:37 CDT)
  • AMBER: Antechamber compilation: leap error (Mon Apr 12 2004 - 06:05:58 CDT)
  • AMBER: Antechamber compilation error (Mon Apr 05 2004 - 11:22:21 CDT)
• arvind_at_mbu.iisc.ernet.in
  • AMBER: How to make leap recognise inosine? (Tue Mar 23 2004 - 11:33:40 CST)
• Asim Okur
  • Re: AMBER: imin=5 in sander (Tue Dec 07 2004 - 14:44:52 CST)
  • Re: AMBER: imin=5 in sander (Tue Dec 07 2004 - 14:47:38 CST)
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 08:12:58 CDT)
• astrid.maass
  • AMBER: gaff: hydrogen atom types (Tue Mar 30 2004 - 01:37:58 CST)
  • AMBER: downloading antechamber (Tue Mar 23 2004 - 01:53:56 CST)
• atchara_at_mercury.hec.utah.edu
  • AMBER: antechamber: frcmod parameter need revision (Mon Apr 05 2004 - 16:11:12 CDT)
  • AMBER: eedmeth (Thu Mar 25 2004 - 12:53:23 CST)
  • AMBER: error in minimization (Tue Mar 02 2004 - 11:47:14 CST)
• Atilio Anzellotti
  • Re: AMBER: metal atoms in Xleap (Fri Aug 20 2004 - 15:25:47 CDT)
  • Re: AMBER: metal atoms in Xleap (Fri Aug 20 2004 - 13:43:51 CDT)
  • AMBER: metal atoms in Xleap (Thu Aug 19 2004 - 10:05:23 CDT)
• atobak_at_eden.rutgers.edu
  • AMBER: ligand minimization (Sat May 08 2004 - 16:13:21 CDT)
• Atro Tossavainen
  • Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F (Tue Oct 19 2004 - 07:39:21 CDT)
  • Re: AMBER: amber 8 error (Tue Oct 19 2004 - 05:23:23 CDT)
  • Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F (Tue Oct 19 2004 - 01:21:57 CDT)
  • AMBER: More AMBER 8 compilation problems on OSF1 4.0F (Mon Oct 18 2004 - 03:08:30 CDT)
  • Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! (Fri Oct 15 2004 - 07:38:59 CDT)
  • Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! (Fri Oct 15 2004 - 05:55:27 CDT)
  • Re: AMBER: Problem with installing Amber8: Where are the MK libraries? (Fri Oct 15 2004 - 04:59:29 CDT)
  • Re: AMBER: AMBER 8 installation trouble (Fri Oct 15 2004 - 02:20:54 CDT)
  • Re: AMBER: Problem with installing Amber8: Where are the MK libraries? (Fri Oct 15 2004 - 02:13:55 CDT)
  • Re: AMBER: Problem with installing Amber8: Where are the MK libraries? (Fri Oct 15 2004 - 01:24:13 CDT)
  • Re: AMBER: AMBER 8 installation trouble (Wed Oct 13 2004 - 01:56:19 CDT)
  • AMBER: More installation problems on Solaris 8 (Tue Oct 12 2004 - 02:44:01 CDT)
  • Re: AMBER: AMBER 8 installation - continued (Tue Oct 12 2004 - 02:37:24 CDT)
  • Re: AMBER: AMBER 8 installation trouble (Tue Oct 12 2004 - 02:29:23 CDT)
  • AMBER: AMBER 8 installation - continued (Mon Oct 11 2004 - 03:57:45 CDT)
  • AMBER: AMBER 8 installation trouble (Mon Oct 11 2004 - 03:36:44 CDT)
• Austin B. Yongye
  • Re: AMBER: tleap: automatically identify and connect disulfide bonds? (Thu Jul 29 2004 - 08:13:46 CDT)
• ayongye_at_sunchem.chem.uga.edu
  • Re: AMBER: ptraj (Tue Apr 13 2004 - 10:48:54 CDT)
• b86203054_at_ntu.edu.tw
  • Re: AMBER: An question about PTRAJ (Mon Sep 13 2004 - 12:35:51 CDT)
  • Re: AMBER: An question about PTRAJ (Mon Sep 13 2004 - 12:37:00 CDT)
  • AMBER: An question about PTRAJ (Fri Sep 10 2004 - 20:29:17 CDT)
• Balvinder Singh
  • AMBER: atoms out of bounds (Thu Oct 07 2004 - 16:27:45 CDT)
  • AMBER: Spike in energy and RMS (Wed Sep 08 2004 - 17:49:04 CDT)
• Beale, John
  • AMBER: dihedral driver (Wed May 12 2004 - 08:58:35 CDT)
  • AMBER: compiling Amber 8 (Fri Apr 16 2004 - 12:23:23 CDT)
  • AMBER: Compiling Amber 8 (Mon Apr 12 2004 - 08:44:25 CDT)
  • AMBER: (Thu Apr 08 2004 - 08:04:04 CDT)
  • AMBER: Antechamber MOPAC (Thu Mar 25 2004 - 09:24:56 CST)
  • AMBER: Cadmium (Wed Mar 24 2004 - 07:10:36 CST)
  • AMBER: compiling on SGI (Thu Mar 11 2004 - 15:26:22 CST)
  • AMBER: PGA (Wed Feb 25 2004 - 07:09:46 CST)
  • AMBER: DNA (Mon Feb 02 2004 - 07:31:51 CST)
  • AMBER: mopac.sh (Mon Jan 26 2004 - 08:31:46 CST)
  • AMBER: PDB files (Tue Jan 20 2004 - 10:43:36 CST)
• Ben Cossins
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Wed Dec 15 2004 - 06:04:50 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Tue Dec 14 2004 - 07:41:08 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Fri Dec 10 2004 - 07:05:33 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Thu Dec 09 2004 - 09:19:20 CST)
  • AMBER: pbsa error in mm_pbsa amber 8 (Thu Dec 09 2004 - 08:58:19 CST)
  • AMBER: MM binding energy with ANAL (Tue Sep 14 2004 - 07:56:37 CDT)
  • Re: AMBER: nmanal problem (Mon Jun 21 2004 - 11:40:50 CDT)
  • AMBER: nmanal problem (Mon Jun 21 2004 - 10:45:20 CDT)
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Thu May 13 2004 - 04:22:21 CDT)
  • Re: AMBER: How to add ACE and NME groups? (Tue Feb 24 2004 - 10:47:43 CST)
  • AMBER: The charge given by xleap from amber 5 (Fri Feb 20 2004 - 06:25:55 CST)
• berry1027 Eric
  • AMBER: add charge error message: Number of electrons is odd (Fri Oct 22 2004 - 03:45:30 CDT)
• Bill Ross
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Tue Dec 21 2004 - 16:57:13 CST)
  • Re: AMBER: nanotube parameters (Fri Dec 17 2004 - 15:52:13 CST)
  • Re: AMBER: Dielectric Constant (Sat Dec 04 2004 - 14:22:33 CST)
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 17:25:58 CST)
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 16:31:54 CST)
  • Re: AMBER: nucgen problem (Thu Nov 25 2004 - 11:08:14 CST)
  • Re: AMBER: build a cyclic peptide (Wed Nov 24 2004 - 15:56:44 CST)
  • Re: AMBER: extracting energy from trajector? (Wed Nov 24 2004 - 13:33:29 CST)
  • Re: AMBER: extracting energy from trajector? (Wed Nov 24 2004 - 12:50:30 CST)
  • Re: AMBER: build a cyclic peptide (Wed Nov 24 2004 - 12:39:15 CST)
  • Re: AMBER: build a cyclic peptide (Tue Nov 23 2004 - 20:33:04 CST)
  • Re: AMBER: Problem with converting AMBER PREP to MOL2 (Tue Nov 23 2004 - 12:00:31 CST)
  • Re: AMBER: problem solved: leap compiling problem on a 64-bit machine (Mon Nov 22 2004 - 16:37:58 CST)
  • Re: AMBER: LEaP compilation error on Solaris 9 (Mon Nov 22 2004 - 16:16:10 CST)
  • Re: AMBER: New problem on our 64bit box: xleap Segmentation fault (Mon Nov 22 2004 - 15:27:21 CST)
  • Re: AMBER: calcium van der Waals parameters (Mon Nov 22 2004 - 12:57:09 CST)
  • Re: AMBER: ambpdb segmentation fault (Sun Nov 21 2004 - 23:34:13 CST)
  • Re: AMBER: leap compiling problem on a 64-bit machine (Fri Nov 19 2004 - 15:14:07 CST)
  • Re: AMBER: calcium van der Waals parameters (Thu Nov 18 2004 - 12:25:49 CST)
  • Re: AMBER: a quick question about carnal (Fri Nov 12 2004 - 15:53:41 CST)
  • Re: AMBER: parameter set (Wed Nov 10 2004 - 14:17:25 CST)
  • Re: AMBER: Problem with Water solute during MD (Wed Nov 10 2004 - 09:20:23 CST)
  • Re: AMBER: Problem with Water solute during MD (Tue Nov 09 2004 - 11:36:22 CST)
  • Re: AMBER: Minimization failure: 1cbn (Fri Nov 05 2004 - 16:32:41 CST)
  • Re: AMBER: Settings about frozen atoms in sander (Fri Oct 29 2004 - 13:44:41 CDT)
  • Re: AMBER: questions regarding JTREE (Wed Oct 27 2004 - 12:53:39 CDT)
  • Re: AMBER: long minimization in sander (Mon Oct 25 2004 - 15:30:32 CDT)
  • Re: AMBER: long minimization in sander (Mon Oct 25 2004 - 10:09:49 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 14:16:26 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 13:26:26 CDT)
  • Re: AMBER: problems with dihedrals - extended information (Mon Oct 18 2004 - 13:04:33 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 12:47:58 CDT)
  • Re: AMBER: Trajectory corruption (Fri Oct 15 2004 - 13:00:59 CDT)
  • Re: AMBER: distance between images (Thu Oct 14 2004 - 10:09:11 CDT)
  • RE: AMBER: A question on AMBER8 installation (Wed Oct 13 2004 - 12:13:48 CDT)
  • Re: Re: AMBER: Running on MPI (Wed Oct 13 2004 - 12:02:42 CDT)
  • Re: AMBER: Carnal & Radius of gyration (Tue Oct 12 2004 - 16:51:30 CDT)
  • Re: AMBER: AddIons (Thu Oct 07 2004 - 14:36:24 CDT)
  • Re: AMBER: radius of gyration (Sun Sep 26 2004 - 22:49:40 CDT)
  • Re: AMBER: radius of gyration (Sun Sep 26 2004 - 22:41:58 CDT)
  • Re: AMBER: Amber 8 installation error on Xeon 2-CPU (Thu Sep 23 2004 - 19:17:17 CDT)
  • RE: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 14:18:37 CDT)
  • Re: AMBER: error in installing amber8 (Wed Sep 08 2004 - 09:49:11 CDT)
  • Re: AMBER: loading frcmod.mod_phipsi.1 (Thu Sep 02 2004 - 17:07:44 CDT)
  • Re: AMBER: (Mon Aug 30 2004 - 16:33:38 CDT)
  • Re: AMBER: Biotin/streptavidin tutorial. (Fri Aug 27 2004 - 12:57:47 CDT)
  • Re: AMBER: One more question about the tree structure of looping residues (Thu Aug 26 2004 - 13:31:23 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 19:56:13 CDT)
  • Re: AMBER: How to test the used parameters. (Wed Aug 11 2004 - 12:31:28 CDT)
  • Re: AMBER: unknown residue: ABA (Tue Aug 10 2004 - 14:20:36 CDT)
  • Re: AMBER: Adding residues (Mon Aug 09 2004 - 14:23:08 CDT)
  • Re: AMBER: Problems with Carnal coordinate average (Mon Aug 09 2004 - 12:12:04 CDT)
  • RE: AMBER: Xleap crash, problem with residue bonding (Thu Jul 22 2004 - 16:55:58 CDT)
  • Re: AMBER: user force (Thu Jul 22 2004 - 16:57:24 CDT)
  • Re: AMBER: antechamber (Fri Jul 16 2004 - 12:48:07 CDT)
  • RE: AMBER: How to apply OPLS force field? (Thu Jul 15 2004 - 11:08:22 CDT)
  • Re: AMBER: MD & running time (Tue Jun 22 2004 - 20:48:03 CDT)
  • Re: AMBER: leap.log warnings (Mon Jun 21 2004 - 14:25:35 CDT)
  • Re: AMBER: leap.log warnings (Mon Jun 21 2004 - 12:40:13 CDT)
  • Re: AMBER: leap.log warnings (Sun Jun 20 2004 - 21:52:17 CDT)
  • Re: AMBER: The first and second derivatives (Fri Jun 18 2004 - 16:02:22 CDT)
  • Re: AMBER: Z-DNA (Thu Jun 17 2004 - 15:00:55 CDT)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Tue Jun 15 2004 - 15:55:31 CDT)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Tue Jun 15 2004 - 14:23:40 CDT)
  • Re: AMBER: Trajectory file (Wed Jun 09 2004 - 16:19:36 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Tue Jun 08 2004 - 13:16:35 CDT)
  • Re: AMBER: Bad contacts (Mon Jun 07 2004 - 20:37:16 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 16:06:04 CDT)
  • Re: AMBER: CARNAL- movement of an axis (Thu Jun 03 2004 - 15:53:47 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 15:44:39 CDT)
  • RE: AMBER: Amber force field for protein-DNA system (Tue Jun 01 2004 - 13:32:52 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 17:16:56 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 16:28:27 CDT)
  • Re: Re[4]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 16:15:01 CDT)
  • Re: Re[2]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 13:34:08 CDT)
  • Re: AMBER: rmsd over residues using ptraj (Tue May 18 2004 - 19:57:54 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Tue May 18 2004 - 14:08:13 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 19:10:36 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 18:42:25 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 17:47:24 CDT)
  • Re: AMBER: reference with ptraj (Thu May 06 2004 - 17:05:55 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 13:16:11 CDT)
  • Re: AMBER: H Bonds (Wed May 05 2004 - 16:18:22 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:35:49 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:24:41 CDT)
  • Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 11:44:16 CDT)
  • Re: AMBER: ptraj: radius of gyration (Sun May 02 2004 - 15:12:23 CDT)
  • Re: AMBER: Amber8 compilation error (Fri Apr 30 2004 - 15:50:28 CDT)
  • Re: AMBER: protein-carbohydrate complex (Thu Apr 22 2004 - 17:39:16 CDT)
  • Re: AMBER: MD for protein-carbohydrate complex (Thu Apr 22 2004 - 15:03:54 CDT)
  • Re: AMBER: Bond type in leap (Thu Apr 22 2004 - 11:53:33 CDT)
  • Re: AMBER: Euclidean distances (Thu Apr 22 2004 - 11:34:37 CDT)
  • Re: AMBER: nucgen generated RNA duplex: leap problems (Wed Apr 21 2004 - 15:34:40 CDT)
  • Re: AMBER: nucgen generated RNA duplex: leap problems (Wed Apr 21 2004 - 13:33:00 CDT)
  • Re: AMBER: How to solve these warnings? (Wed Apr 21 2004 - 13:21:30 CDT)
  • RE: AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 13:09:44 CDT)
  • Re: AMBER: xleap console message (Mon Apr 19 2004 - 15:58:05 CDT)
  • Re: AMBER: xleap console message (Mon Apr 19 2004 - 12:28:17 CDT)
  • Re: AMBER: Problem in loading a PDB file in Leap - Please help me (Sat Apr 17 2004 - 14:40:06 CDT)
  • Re: AMBER: Problem in loading a PDB file in Leap - Please help me (Sat Apr 17 2004 - 00:55:43 CDT)
  • RE: AMBER: compiling Amber 8 (Fri Apr 16 2004 - 14:45:06 CDT)
  • RE: AMBER: compiling Amber 8 (Fri Apr 16 2004 - 14:36:44 CDT)
  • Re: AMBER: distance measurement in carnal and ptraj (Fri Apr 16 2004 - 13:32:07 CDT)
  • Re: AMBER: water hole (Thu Apr 15 2004 - 13:49:02 CDT)
  • Re: AMBER: gibbs termination (Wed Apr 14 2004 - 15:16:50 CDT)
  • Re: AMBER: how to check metal ion bonding ? (Tue Apr 13 2004 - 16:34:52 CDT)
  • Re: AMBER: Compiling Amber 8 (Tue Apr 13 2004 - 11:38:58 CDT)
  • Re: AMBER: water hole (Mon Apr 12 2004 - 20:58:47 CDT)
  • Re: AMBER: Carnal in Amber7 (Thu Apr 08 2004 - 13:16:02 CDT)
  • Re: AMBER: which atoms are H's for SHAKE? (Tue Apr 06 2004 - 15:11:41 CDT)
  • Re: AMBER: HBOND calculation (Mon Mar 29 2004 - 12:24:59 CST)
  • Re: AMBER: fix two groups (Sun Mar 28 2004 - 23:35:00 CST)
  • Re: AMBER: INtel Fortran 90 compiler (Wed Mar 24 2004 - 15:41:30 CST)
  • Re: AMBER: vlimit and vmax problem (Wed Mar 24 2004 - 15:17:32 CST)
  • Re: AMBER: trajectory file (Tue Mar 23 2004 - 16:20:31 CST)
  • Re: AMBER: How to make leap recognise inosine? (Tue Mar 23 2004 - 11:57:27 CST)
  • Re: AMBER: segmentation fault (Thu Mar 18 2004 - 12:22:24 CST)
  • Re: AMBER: trajectory file (Tue Mar 16 2004 - 14:54:10 CST)
  • Re: AMBER: Anal module on PDBs (Sat Mar 13 2004 - 18:17:25 CST)
  • Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file (Thu Mar 04 2004 - 07:11:45 CST)
  • Re: AMBER: Leap atom removal bug? (Thu Mar 04 2004 - 07:06:44 CST)
  • Re: AMBER: compiling xleap on MAC OS X.3 (Wed Mar 03 2004 - 17:16:53 CST)
  • Re: AMBER: compiling xleap on MAC OS X.3 (Wed Mar 03 2004 - 16:37:50 CST)
  • Re: AMBER: A question about RMSD calculation (Tue Mar 02 2004 - 13:53:11 CST)
  • RE: AMBER: Errors when running tleap (Thu Feb 26 2004 - 13:47:05 CST)
  • Re: AMBER: averaged structure with unknown elements (Wed Feb 25 2004 - 15:49:40 CST)
  • Re: AMBER: Errors when running tleap (Wed Feb 25 2004 - 15:31:54 CST)
  • RE: AMBER: add Na+ (Wed Feb 25 2004 - 12:31:43 CST)
  • Re: AMBER: Star like (branching) molecule (Tue Feb 24 2004 - 17:51:10 CST)
  • Re: AMBER: Star like (branching) molecule (Tue Feb 24 2004 - 17:40:13 CST)
  • RE: AMBER: add Na+ (Tue Feb 24 2004 - 13:33:34 CST)
  • RE: AMBER: add Na+ (Tue Feb 24 2004 - 13:07:07 CST)
  • Re: AMBER: carnal (Tue Feb 24 2004 - 11:49:16 CST)
  • Re: AMBER: problem with frcmod file (Mon Feb 23 2004 - 16:44:08 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 16:39:48 CST)
  • RE: AMBER: how to use prep file (Mon Feb 23 2004 - 14:30:37 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 14:14:46 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 12:04:33 CST)
  • Re: AMBER: Build a H+ ion in Leap? (Thu Feb 19 2004 - 15:22:08 CST)
  • Re: AMBER: Build a H+ ion in Leap? (Thu Feb 19 2004 - 14:00:38 CST)
  • Re: AMBER: distance-aromatic ring (Thu Feb 19 2004 - 13:41:32 CST)
  • RE: AMBER: Close contact warnings (Thu Feb 19 2004 - 13:25:33 CST)
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 13:29:19 CST)
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 12:20:38 CST)
  • Re: AMBER: (no subject) (Tue Feb 17 2004 - 15:17:39 CST)
  • Re: AMBER: How to add H+ ion in leap? (Tue Feb 17 2004 - 15:09:01 CST)
  • Re: AMBER: How to add H+ ion in leap? (Tue Feb 17 2004 - 14:29:17 CST)
  • Re: AMBER: center of mass in CARNAL (Tue Feb 17 2004 - 14:25:43 CST)
  • Re: AMBER: bad crd file (Mon Feb 16 2004 - 12:51:57 CST)
  • Re: AMBER: carnal (Mon Feb 16 2004 - 12:37:54 CST)
  • Re: AMBER: question about the average structure from ptraj (Sun Feb 08 2004 - 13:47:11 CST)
  • Re: AMBER: adding ions to nucleic acids (Sun Feb 08 2004 - 13:40:50 CST)
  • Re: Fwd: Re: AMBER: Lattice structures in xleap (Fri Feb 06 2004 - 16:21:12 CST)
  • Re: AMBER: How to remove Cl- ions (Fri Feb 06 2004 - 10:35:27 CST)
  • Re: AMBER: Re: ANAL problem (Thu Feb 05 2004 - 12:07:58 CST)
  • Re: AMBER: ptraj (Thu Feb 05 2004 - 03:43:59 CST)
  • Re: AMBER: carnal (Wed Feb 04 2004 - 13:40:31 CST)
  • Re: AMBER: What does this error message mean? (Tue Feb 03 2004 - 12:40:15 CST)
  • Re: AMBER: Carnal (Tue Feb 03 2004 - 12:14:02 CST)
  • Re: AMBER: conversion of amber trajectories to gromos /(xtc) (Thu Jan 29 2004 - 14:43:45 CST)
  • RE: AMBER: A few questions in the protein unfolding simulations using GB model (Wed Jan 28 2004 - 12:22:55 CST)
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Wed Jan 28 2004 - 12:21:10 CST)
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Tue Jan 27 2004 - 15:19:10 CST)
  • Re: AMBER: trajectory file corruption (Tue Jan 27 2004 - 12:54:30 CST)
  • Re: AMBER: Lattice structures in xleap (Tue Jan 27 2004 - 01:52:38 CST)
  • Re: AMBER: ambpdb in AMBER7 (Mon Jan 26 2004 - 16:40:12 CST)
  • Re: AMBER: Cartitian Restraint Error (Sun Jan 25 2004 - 13:39:58 CST)
  • Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 (Fri Jan 23 2004 - 13:26:15 CST)
  • Re: AMBER: segmentation fault in Leap (Thu Jan 22 2004 - 11:37:09 CST)
  • Re: AMBER: restrt (Thu Jan 22 2004 - 11:15:58 CST)
  • Re: AMBER: How does LEaP place Na+ ions? (Thu Jan 22 2004 - 11:17:32 CST)
  • Re: AMBER: How does LEaP place Na+ ions? (Thu Jan 22 2004 - 11:12:07 CST)
  • Re: AMBER: Do I need to repeat MD simulation? (Wed Jan 21 2004 - 10:01:54 CST)
  • Re: AMBER: segmentation fault in Leap (Wed Jan 21 2004 - 03:47:58 CST)
  • Re: AMBER: atom type CM (Fri Jan 16 2004 - 15:17:29 CST)
  • Re: AMBER: LEAP - Error loading units (Wed Jan 14 2004 - 13:45:19 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 13:52:53 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 13:23:44 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 12:21:03 CST)
  • Re: AMBER: strange output of MD (Wed Jan 07 2004 - 12:39:35 CST)
  • Re: AMBER: strange output of MD (Wed Jan 07 2004 - 11:57:13 CST)
  • Re: AMBER: prep file (Mon Jan 05 2004 - 17:49:14 CST)
  • Re: AMBER: Molecular Frame (Fri Jan 02 2004 - 17:40:54 CST)
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Thu Jan 01 2004 - 16:26:55 CST)
• Bimo Ario Tejo
  • AMBER: input conversion error [Amber8] (Tue Dec 28 2004 - 23:15:58 CST)
  • Re: AMBER: Minimization failure: 1cbn (Fri Nov 05 2004 - 16:12:03 CST)
  • Re: AMBER: MD & folding (Tue Nov 02 2004 - 01:26:09 CST)
  • Re: AMBER: How to covalently bind a ligand to a residue? (Fri Aug 06 2004 - 00:06:02 CDT)
  • Re: AMBER: pH effect on protein folding (Thu Jul 15 2004 - 22:34:39 CDT)
  • AMBER: Correl in Amber8: Diagonal elements not 1? (Thu Jul 15 2004 - 06:47:43 CDT)
  • AMBER: correlation in Amber 8 (Thu Jul 08 2004 - 03:14:34 CDT)
  • Re: AMBER: factor used in b-factor calculation (Wed Mar 10 2004 - 05:02:46 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 07:31:51 CST)
  • Re: AMBER: MD at different pH !! (Sat Mar 06 2004 - 06:18:15 CST)
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 22:58:39 CST)
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 20:43:36 CST)
  • Re: AMBER: Memory for AMBER 6 simulation (Mon Jan 26 2004 - 04:39:25 CST)
  • Re: AMBER: Problem using GLYCAM with sander (Sat Jan 24 2004 - 09:28:15 CST)
  • AMBER: Radius of gyration (Tue Jan 06 2004 - 00:14:37 CST)
• Binbin Liu
  • AMBER: The convergence of energy minimisation (Tue Sep 28 2004 - 14:10:56 CDT)
• bishop
  • Re: AMBER: Normal modes of protein-ligand (Wed Jan 28 2004 - 08:44:20 CST)
  • Re: AMBER: Do I need to repeat MD simulation? (Wed Jan 21 2004 - 09:14:45 CST)
  • Re: AMBER: disulfide bonds/ Engineered (Tue Jan 13 2004 - 08:20:19 CST)
• box_twin2_at_hotmail.com
  • AMBER: From Andrew Box: Invitation and new email address (Tue Aug 10 2004 - 19:39:25 CDT)
• Brandon Tefft
  • Fwd: Re: AMBER: Lattice structures in xleap (Fri Feb 06 2004 - 15:27:50 CST)
  • AMBER: Lattice structures in xleap (Mon Jan 26 2004 - 23:11:46 CST)
• Brent Krueger
  • AMBER: octavalent metal (Fri Jun 25 2004 - 16:17:01 CDT)
• by way of riccardo nifosi
  • AMBER: SHAKE in thermodynamic integration (Thu May 20 2004 - 05:38:21 CDT)
• bybaker_at_itsa.ucsf.edu
  • AMBER: cut-off & MD (Mon Dec 06 2004 - 14:49:04 CST)
  • Re: AMBER: MD run: frozen (Sun Nov 28 2004 - 18:39:30 CST)
  • AMBER: MD run: frozen (Sun Nov 28 2004 - 00:17:36 CST)
  • AMBER: combine crd files (Fri Nov 26 2004 - 16:54:43 CST)
  • AMBER: Re: md.out & plot (Wed Nov 24 2004 - 00:21:10 CST)
  • AMBER: Re: md.out & plot (Tue Nov 23 2004 - 19:26:36 CST)
  • AMBER: md.out & plot (Tue Nov 23 2004 - 16:23:41 CST)
  • AMBER: Babel (Sun Nov 14 2004 - 01:29:40 CST)
  • AMBER: convert .pdb to .mol2 (Sat Nov 13 2004 - 22:35:45 CST)
  • AMBER: MD & folding (Tue Nov 02 2004 - 18:05:00 CST)
  • AMBER: MD & folding (Tue Nov 02 2004 - 15:31:31 CST)
  • AMBER: MD & folding (Tue Nov 02 2004 - 01:03:42 CST)
  • AMBER: Re: RSM & ptraj (Sun Oct 31 2004 - 12:43:41 CST)
  • AMBER: RSM fluctuation by residues (Sun Oct 31 2004 - 01:22:53 CDT)
  • AMBER: RSM & ptraj (Sun Oct 31 2004 - 01:13:10 CDT)
  • AMBER: RSM fluctuation & residues (Fri Oct 29 2004 - 15:21:42 CDT)
  • AMBER: Re: process_mdout.perl (Tue Oct 12 2004 - 20:36:45 CDT)
  • AMBER: process_mdout.perl: work now (Tue Oct 12 2004 - 20:32:49 CDT)
  • AMBER: process_mdout.perl (Tue Oct 12 2004 - 01:08:06 CDT)
  • AMBER: Re: Amber (Tue Sep 28 2004 - 16:35:01 CDT)
  • AMBER: Amber (Tue Sep 28 2004 - 14:28:32 CDT)
  • AMBER: Re: Atom distance (Mon Sep 27 2004 - 20:21:20 CDT)
  • Re: AMBER: Atom distance (Mon Sep 27 2004 - 15:39:49 CDT)
  • AMBER: Atom distance (Mon Sep 27 2004 - 01:59:05 CDT)
  • Re: AMBER: loading frcmod.mod_phipsi.1 (Thu Sep 02 2004 - 17:18:07 CDT)
  • AMBER: Water Box & MD (Thu Sep 02 2004 - 16:48:00 CDT)
  • AMBER: loading frcmod.mod_phipsi.1 (Thu Sep 02 2004 - 16:12:04 CDT)
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 20:57:39 CDT)
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 17:15:04 CDT)
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 11:21:00 CDT)
  • AMBER: parm94 (Tue Aug 31 2004 - 01:50:09 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 17:02:53 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 15:48:00 CDT)
  • AMBER: MD & net charge (Sun Aug 29 2004 - 01:19:18 CDT)
  • Re: AMBER: Molecular dynamic & Acknowledgement (Tue Jul 13 2004 - 13:20:50 CDT)
  • Re: AMBER: Molecular dynamic (Fri Jul 09 2004 - 17:54:38 CDT)
  • Re: AMBER: Disulfide bond command (Fri Jul 09 2004 - 13:51:46 CDT)
  • AMBER: Disulfide bond command (Fri Jul 09 2004 - 13:16:13 CDT)
  • AMBER: Molecular dynamic (Wed Jul 07 2004 - 16:12:33 CDT)
  • Re: AMBER: MD & running time (Tue Jun 22 2004 - 23:29:58 CDT)
  • Thanks - Re: AMBER: MD & running time (Tue Jun 22 2004 - 18:29:09 CDT)
  • AMBER: MD & running time (Tue Jun 22 2004 - 13:11:58 CDT)
  • Re: AMBER: Amber & mutation (Thu Jun 10 2004 - 11:24:24 CDT)
  • AMBER: Amber & mutation (Wed Jun 09 2004 - 19:53:58 CDT)
  • Re: AMBER: Bad contacts (Wed Jun 09 2004 - 15:30:38 CDT)
  • Re: AMBER: Bad contacts (Wed Jun 09 2004 - 12:02:01 CDT)
  • AMBER: Bad contacts (Mon Jun 07 2004 - 19:44:37 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 17:36:24 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 17:32:53 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 15:59:50 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 15:54:55 CDT)
  • AMBER: Sander & fix atoms (Thu Jun 03 2004 - 11:48:40 CDT)
  • Re: AMBER: Sander went through (Sat May 29 2004 - 06:51:26 CDT)
  • AMBER: Sander went through (Fri May 28 2004 - 19:19:02 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 17:05:22 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 16:22:00 CDT)
  • Re: AMBER: Cannot read in sander (Thu May 27 2004 - 15:56:12 CDT)
  • Re: AMBER: Cannot read in sander (Wed May 26 2004 - 19:47:30 CDT)
  • AMBER: Cannot read in sander (Tue May 25 2004 - 17:51:48 CDT)
• Byungchan Kim
  • Re: AMBER: Ewald calculation using PME for charged system (Tue Mar 09 2004 - 17:09:18 CST)
  • AMBER: Ewald calculation using PME for charged system (Tue Mar 09 2004 - 15:04:31 CST)
  • AMBER: Ewald calculation using PME for charged system (Fri Mar 05 2004 - 12:13:43 CST)
  • Re: AMBER: NVE&polarizable force field (Tue Feb 03 2004 - 11:54:55 CST)
  • AMBER: Nose Hoover chain thermostat (Fri Jan 30 2004 - 19:35:08 CST)
  • Re: AMBER: Fwd: NVE & polarizable force field] (Fri Jan 23 2004 - 20:58:04 CST)
  • Re: AMBER: Molecular Frame (Sat Jan 03 2004 - 13:00:20 CST)
  • Re: AMBER: Molecular Frame (Fri Jan 02 2004 - 17:03:36 CST)
  • AMBER: Molecular Frame (Thu Jan 01 2004 - 21:46:14 CST)
• Cai, Yufeng
  • AMBER: Sander TI (Mon Dec 20 2004 - 12:11:29 CST)
  • AMBER: where is the VDW radius? (Sat Nov 06 2004 - 09:42:29 CST)
  • AMBER: end point contribution in MCTI (Fri Nov 05 2004 - 08:12:11 CST)
  • AMBER: pure aromatic? (Mon Oct 25 2004 - 16:16:06 CDT)
  • AMBER: problem with antechamber (Sun Oct 17 2004 - 21:04:28 CDT)
  • AMBER: changepot (Fri Oct 15 2004 - 13:33:08 CDT)
  • AMBER: from gaussian to antechamber (Fri Oct 15 2004 - 13:14:48 CDT)
• cailliez
  • AMBER: constraints on atoms (Mon Dec 20 2004 - 05:06:19 CST)
  • Re: AMBER: question about mmpbsa (Wed Dec 08 2004 - 12:23:01 CST)
  • AMBER: amber8 parallel installation with mpich (Tue Nov 30 2004 - 06:24:41 CST)
  • Re: AMBER: calcium van der Waals parameters (Mon Nov 22 2004 - 11:10:30 CST)
  • AMBER: calcium van der Waals parameters (Thu Nov 18 2004 - 10:53:23 CST)
  • Re: AMBER: BOND energy during minimisation (Wed Oct 20 2004 - 02:16:26 CDT)
  • Re: AMBER: BOND energy during minimisation (Tue Oct 19 2004 - 11:12:55 CDT)
  • AMBER: BOND energy during minimisation (Tue Oct 19 2004 - 02:53:47 CDT)
  • Re: AMBER: file corruption with ptraj (Mon Oct 18 2004 - 10:32:32 CDT)
  • Re: AMBER: nbflag (Fri Sep 24 2004 - 10:20:13 CDT)
  • AMBER: nbflag (Fri Sep 24 2004 - 01:44:22 CDT)
  • Re: AMBER: RESTARTED DUE TO LINMIN FAILURE ... (Thu Sep 23 2004 - 03:42:31 CDT)
  • AMBER: question on mm-pbsa (Wed Sep 01 2004 - 04:48:54 CDT)
  • Re: AMBER: restart a MD after replacing molecules (Thu Aug 26 2004 - 03:38:55 CDT)
  • AMBER: restart a MD after replacing molecules (Wed Aug 25 2004 - 09:03:41 CDT)
  • AMBER: questions on mm_pbsa (Fri Aug 20 2004 - 07:13:51 CDT)
  • AMBER: execution time (Fri Jul 09 2004 - 04:50:25 CDT)
  • AMBER: sander on multiprocessors (Tue Jul 06 2004 - 02:38:39 CDT)
  • AMBER: jump in temperature + problem in trajectory files (Mon Jun 28 2004 - 09:11:14 CDT)
  • AMBER: GB parameters for Calcium (Wed Jun 23 2004 - 07:39:38 CDT)
  • AMBER: Calcium and GB (Tue Jun 08 2004 - 06:38:58 CDT)
  • AMBER: ptraj-6.5 (Thu Apr 15 2004 - 04:42:36 CDT)
  • AMBER: salt concentration (Wed Apr 14 2004 - 09:45:44 CDT)
  • AMBER: which parameters for Ca2+ ? (Tue Apr 06 2004 - 02:50:03 CDT)
• carlos
  • Re: AMBER: vdw energy in minimization (Mon Jul 19 2004 - 07:13:30 CDT)
• Carlos P. Sosa
  • Re: AMBER: F90 compiler for linux ppc64 (Wed Sep 15 2004 - 10:10:32 CDT)
• Carlos Simmerling
  • Re: AMBER: nrespa=2 (Tue Dec 21 2004 - 09:54:15 CST)
  • Re: AMBER: Kinetics energy (Sat Dec 18 2004 - 13:07:11 CST)
  • Re: AMBER: imin=5 in sander (Mon Dec 06 2004 - 19:52:14 CST)
  • Re: AMBER: strange bond energies (Mon Dec 06 2004 - 08:22:10 CST)
  • Re: AMBER: MD run: frozen (Sun Nov 28 2004 - 09:32:25 CST)
  • Re: AMBER: combine crd files (Fri Nov 26 2004 - 18:03:28 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 13:24:59 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 10:55:48 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 08:02:56 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Thu Nov 25 2004 - 10:45:34 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Thu Nov 25 2004 - 09:50:12 CST)
  • Re: AMBER: build a cyclic peptide (Wed Nov 24 2004 - 14:33:10 CST)
  • Re: AMBER: extracting energy from trajector? (Wed Nov 24 2004 - 13:07:12 CST)
  • Re: AMBER: extracting energy from trajector? (Wed Nov 24 2004 - 12:55:49 CST)
  • Re: AMBER: build a cyclic peptide (Wed Nov 24 2004 - 12:56:57 CST)
  • Re: AMBER: build a cyclic peptide (Tue Nov 23 2004 - 20:43:13 CST)
  • Re: AMBER: restart calculation (Tue Nov 23 2004 - 06:45:28 CST)
  • Re: AMBER: sander, MD problems (Mon Nov 22 2004 - 06:53:29 CST)
  • Re: AMBER: Problem with a single aminoacid as inhibitor (Wed Nov 17 2004 - 06:43:08 CST)
  • Re: AMBER: Babel (Sun Nov 14 2004 - 08:02:17 CST)
  • Re: AMBER: MD & folding (Tue Nov 02 2004 - 17:03:41 CST)
  • Re: AMBER: ptraj questions (Sun Oct 31 2004 - 11:06:54 CST)
  • Re: AMBER: ptraj questions (Sun Oct 31 2004 - 09:45:21 CST)
  • Re: AMBER: RSM & ptraj (Sun Oct 31 2004 - 01:25:14 CDT)
  • Re: AMBER: MD after partially solvated (Sat Oct 30 2004 - 22:11:27 CDT)
  • Re: AMBER: a question on ntwx and ntwr (Thu Oct 28 2004 - 10:50:10 CDT)
  • Re: AMBER: MM_PBSA reproduction of literature values and accuracy (Tue Oct 26 2004 - 17:51:16 CDT)
  • Re: AMBER: MM_PBSA reproduction of literature values and accuracy (Mon Oct 25 2004 - 12:53:50 CDT)
  • Re: AMBER: PMF (Mon Oct 25 2004 - 07:14:19 CDT)
  • Re: AMBER: BOND energy during minimisation (Tue Oct 19 2004 - 12:33:52 CDT)
  • Re: AMBER: BOND energy during minimisation (Tue Oct 19 2004 - 06:21:28 CDT)
  • Re: AMBER: amber 8 error (Tue Oct 19 2004 - 06:22:37 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 13:29:35 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 12:22:48 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 11:25:52 CDT)
  • Re: AMBER: order parameter (Sun Oct 17 2004 - 08:14:43 CDT)
  • Re: AMBER: Trajectory corruption (Fri Oct 15 2004 - 09:54:14 CDT)
  • Re: AMBER: Running on MPI (Wed Oct 13 2004 - 08:59:38 CDT)
  • Re: AMBER: RE:sander8 (Tue Oct 12 2004 - 06:21:02 CDT)
  • Re: AMBER: Question about restart MD (Mon Oct 11 2004 - 13:55:39 CDT)
  • Re: AMBER: Box information from Amber (Sat Oct 09 2004 - 13:00:43 CDT)
  • Re: AMBER: sander8 (Sat Oct 09 2004 - 12:39:34 CDT)
  • Re: AMBER: Box information from Amber (Sat Oct 09 2004 - 07:10:56 CDT)
  • Re: AMBER: restrain one tosion angle (Fri Oct 08 2004 - 15:50:34 CDT)
  • Re: AMBER: restrain one tosion angle (Fri Oct 08 2004 - 14:10:16 CDT)
  • Re: AMBER: sander8 (Fri Oct 08 2004 - 10:07:23 CDT)
  • Re: AMBER: solute leaving PBC box (Fri Oct 08 2004 - 09:02:42 CDT)
  • Re: AMBER: problems with dihedrals (Fri Oct 08 2004 - 08:27:44 CDT)
  • Re: AMBER: solute leaving PBC box (Thu Oct 07 2004 - 17:43:49 CDT)
  • Re: AMBER: solute leaving PBC box (Thu Oct 07 2004 - 16:48:12 CDT)
  • Re: AMBER: atoms out of bounds (Thu Oct 07 2004 - 07:17:15 CDT)
  • Re: AMBER: Comparison of simulation results on amber7 and amber 8 (Wed Oct 06 2004 - 12:21:54 CDT)
  • Re: AMBER: Running on MPI (Wed Oct 06 2004 - 09:33:19 CDT)
  • Re: AMBER: Comparison of simulation results on amber7 and amber 8 (Wed Oct 06 2004 - 08:36:03 CDT)
  • Re: AMBER: Parameters for phosphorylated aminoacids (Tue Oct 05 2004 - 10:58:07 CDT)
  • Re: AMBER: Running on MPI (Tue Oct 05 2004 - 07:16:59 CDT)
  • Re: AMBER: Running on MPI (Mon Oct 04 2004 - 06:37:18 CDT)
  • Re: AMBER: mdinfo on amber6 (Mon Oct 04 2004 - 06:40:03 CDT)
  • Re: AMBER: small molecule simulation (Sun Oct 03 2004 - 07:54:40 CDT)
  • Re: AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 15:46:43 CDT)
  • Re: AMBER: how to visualize modes from PCA (Mon Sep 27 2004 - 11:13:10 CDT)
  • Re: AMBER: amber 8 error on installation (Sun Sep 26 2004 - 08:24:08 CDT)
  • Re: AMBER: Moil-view & Amber trajectory (Tue Sep 21 2004 - 11:17:59 CDT)
  • Re: AMBER: Trajectory file conversion between Amber & Charmm (Mon Sep 20 2004 - 12:59:41 CDT)
  • Re: AMBER: Moil-view & Amber trajectory (Fri Sep 17 2004 - 16:01:37 CDT)
  • Re: AMBER: restraining internal coordinates (Thu Sep 16 2004 - 12:04:14 CDT)
  • Re: AMBER: back interpret (Wed Sep 15 2004 - 17:08:40 CDT)
  • Re: AMBER: target rmsd (Mon Sep 13 2004 - 15:49:30 CDT)
  • Re: AMBER: REM make test (Fri Sep 10 2004 - 08:35:18 CDT)
  • Re: AMBER: Increase lastrst in the &cntrl namelist (Wed Sep 01 2004 - 12:54:37 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 15:57:50 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 08:51:28 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 08:41:21 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 08:21:36 CDT)
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 08:23:20 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 14:44:36 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:36:38 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 09:25:31 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 09:00:52 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 15:06:47 CDT)
  • Re: AMBER: freezing atoms in impliciti solvent (Tue Aug 24 2004 - 12:54:58 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Sat Aug 14 2004 - 07:13:23 CDT)
  • Re: AMBER: simulated annealing (Sat Aug 14 2004 - 07:20:12 CDT)
  • Re: AMBER: AMBER 6 compilation problems! (Fri Jul 30 2004 - 14:03:31 CDT)
  • Re: AMBER: AMBER 6 compilation problems! (Fri Jul 30 2004 - 12:26:59 CDT)
  • Re: AMBER: simulated annealing.. (Wed Jul 28 2004 - 09:06:01 CDT)
  • Re: AMBER: simulated annealing (Wed Jul 28 2004 - 07:17:55 CDT)
  • Re: AMBER: question on simulated annealing (Tue Jul 27 2004 - 13:28:27 CDT)
  • Re: AMBER: sander : constraints to conserve hydrogen bonds (Fri Jul 23 2004 - 07:08:43 CDT)
  • Re: AMBER: user force (Fri Jul 23 2004 - 06:47:17 CDT)
  • Re: AMBER: user force (Thu Jul 22 2004 - 17:28:42 CDT)
  • Re: AMBER: sander tutorial (Thu Jul 22 2004 - 07:33:08 CDT)
  • Re: AMBER: cut offs in amber? (Wed Jul 21 2004 - 16:32:18 CDT)
  • Re: AMBER: vdw energy in minimization (Mon Jul 19 2004 - 13:47:21 CDT)
  • Re: AMBER: Implicit MD problem (Wed Jul 14 2004 - 11:53:31 CDT)
  • Re: AMBER: Implicit MD problem (Wed Jul 14 2004 - 08:42:18 CDT)
  • Re: AMBER: Angle restraint during MD (Wed Jul 14 2004 - 08:39:38 CDT)
  • Re: AMBER: Angle restraint during MD (Tue Jul 13 2004 - 12:47:16 CDT)
  • Re: AMBER: (Tue Jul 13 2004 - 06:59:08 CDT)
  • Re: AMBER: Angle restraint during MD (Tue Jul 13 2004 - 07:00:42 CDT)
  • Re: AMBER: what is averaged RMS fluctuation? (Mon Jul 12 2004 - 15:37:13 CDT)
  • Re: AMBER: peptide-DNA crosslink modeling (Thu Jul 01 2004 - 20:42:48 CDT)
  • Re: AMBER: MAXRMSPT error in MOIL-view (Thu Jul 01 2004 - 17:26:53 CDT)
  • Re: AMBER: Implicit MD simulation (Thu Jul 01 2004 - 07:07:52 CDT)
  • Re: AMBER: traj. analysis (Wed Jun 30 2004 - 14:08:50 CDT)
  • Re: AMBER: GB+LES (Wed Jun 30 2004 - 06:26:59 CDT)
  • Re: AMBER: image and restart problems (Tue Jun 29 2004 - 09:57:42 CDT)
  • Re: AMBER: question about water molecule (Mon Jun 28 2004 - 12:48:11 CDT)
  • Re: AMBER: Octahedron Box (Mon Jun 28 2004 - 10:43:21 CDT)
  • Re: AMBER: free energy (Mon Jun 28 2004 - 08:06:43 CDT)
  • Re: AMBER: restraints error (Fri Jun 25 2004 - 13:19:34 CDT)
  • Re: AMBER: restraints error (Fri Jun 25 2004 - 12:23:26 CDT)
  • Re: AMBER: Units of Charges on Atoms (Thu Jun 24 2004 - 14:49:43 CDT)
  • Re: AMBER: Restrain or freeze molecule question? (Thu Jun 24 2004 - 10:39:58 CDT)
  • Re: AMBER: amber8 parallel jobs (Thu Jun 24 2004 - 07:17:05 CDT)
  • Re: AMBER: TOP file in AMBER7/8 (Mon Jun 21 2004 - 08:52:38 CDT)
  • Re: AMBER: MOIL-View question (Wed Jun 16 2004 - 15:25:45 CDT)
  • Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander (Wed Jun 16 2004 - 10:15:20 CDT)
  • Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander (Wed Jun 16 2004 - 09:42:33 CDT)
  • Re: AMBER: MOIL-View question (Wed Jun 16 2004 - 06:57:27 CDT)
  • Re: AMBER: Improper Torsional Parameters (Mon Jun 14 2004 - 16:54:57 CDT)
  • Re: AMBER: question about force field (Mon Jun 14 2004 - 11:14:18 CDT)
  • Re: AMBER: Bad contacts (Wed Jun 09 2004 - 13:56:09 CDT)
  • Re: AMBER: old trajectory file (amber6) to new trajectory file ? (Tue Jun 08 2004 - 06:37:48 CDT)
  • Re: AMBER: Bad contacts (Mon Jun 07 2004 - 20:26:19 CDT)
  • Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? (Fri Jun 04 2004 - 06:52:40 CDT)
  • Re: AMBER: parallel Sander (amber8): run-time error under Irix (Thu Jun 03 2004 - 10:03:43 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 13:21:41 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 12:56:24 CDT)
  • Re: AMBER: about amber8, replica exchange (Fri May 28 2004 - 22:55:34 CDT)
  • Re: AMBER: Amber 7 (sander) use of PME (Thu May 27 2004 - 14:47:50 CDT)
  • Re: AMBER: Reproducing the energy during restart in MD! (Wed May 19 2004 - 08:41:17 CDT)
  • Re: AMBER: Removal of rotation: Flying ice cube (Tue May 18 2004 - 19:39:59 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Mon May 17 2004 - 12:08:56 CDT)
  • Re: AMBER: tmd questions (Thu May 13 2004 - 06:41:31 CDT)
  • Re: AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 08:24:02 CDT)
  • Re: AMBER: simulated anealing ...vlimit exceed (Thu May 06 2004 - 06:47:48 CDT)
  • Re: AMBER: water hole (Mon Apr 12 2004 - 17:40:13 CDT)
  • Re: AMBER: recovering total force array (Wed Mar 31 2004 - 15:39:18 CST)
  • Re: AMBER: recovering total force array (Tue Mar 30 2004 - 20:11:28 CST)
  • Re: AMBER: fix two groups (Sun Mar 28 2004 - 21:16:17 CST)
  • Re: AMBER: Resizing sizes.h and recompiling problem! (Sat Mar 13 2004 - 13:24:44 CST)
  • Re: AMBER: what's the meaning of parameter NRUN (Tue Mar 09 2004 - 08:04:29 CST)
  • Re: AMBER: Sander problem with different CPU (Mon Mar 08 2004 - 08:45:19 CST)
  • Re: AMBER: Sander problem with different CPU (Fri Mar 05 2004 - 07:27:22 CST)
  • Re: AMBER: Question about RMSD calculation (Wed Mar 03 2004 - 22:43:58 CST)
  • Re: AMBER: LES methodology question (Fri Feb 20 2004 - 07:01:06 CST)
  • Re: AMBER: LES (Thu Feb 19 2004 - 16:13:07 CST)
  • Re: AMBER: LES (Thu Feb 19 2004 - 15:11:58 CST)
  • Re: AMBER: LES (Thu Feb 19 2004 - 14:26:21 CST)
  • Re: AMBER: tmd question (Thu Feb 19 2004 - 10:17:51 CST)
  • Re: AMBER: moil-view question (Tue Feb 17 2004 - 07:38:59 CST)
  • Re: AMBER: Run calculations for protein in Amber (Thu Feb 12 2004 - 07:18:32 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 14:03:44 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 13:43:58 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 11:55:27 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 07:48:48 CST)
  • Re: AMBER: questions parm94/99 ff secondary structure (Fri Feb 06 2004 - 06:58:45 CST)
  • Re: AMBER: A general question (Tue Feb 03 2004 - 18:13:09 CST)
  • Re: AMBER: What does this error message mean? (Tue Feb 03 2004 - 10:30:56 CST)
  • Re: AMBER: nucleic acid bases nonplanar during LES sim (Mon Feb 02 2004 - 15:56:00 CST)
  • Re: AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 13:29:23 CST)
  • Re: AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 13:07:50 CST)
  • Re: AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 08:27:30 CST)
  • Re: AMBER: sander and mpich (which compilers/mpich work) (Fri Jan 30 2004 - 17:09:09 CST)
  • Re: AMBER: LES error (Thu Jan 29 2004 - 14:51:28 CST)
  • Re: AMBER: Moil View on Linux (Thu Jan 29 2004 - 11:21:20 CST)
  • Re: AMBER: LES Simulations (Thu Jan 29 2004 - 11:20:45 CST)
  • Re: AMBER: LES question (Thu Jan 29 2004 - 10:36:04 CST)
  • Re: AMBER: LES question (Wed Jan 28 2004 - 16:28:51 CST)
  • Re: AMBER: LES question (Wed Jan 28 2004 - 13:03:04 CST)
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Wed Jan 28 2004 - 12:26:31 CST)
  • Re: AMBER: SANDER - Abnormal high velocities (Wed Jan 28 2004 - 10:36:45 CST)
• carlsonh_at_umich.edu
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Thu May 13 2004 - 13:40:03 CDT)
• Carsten Detering
  • AMBER: mm_pbsa (Wed Dec 15 2004 - 15:57:13 CST)
  • AMBER: mm_pbsa + vertex atom mismatch (Mon Nov 22 2004 - 21:01:28 CST)
  • Re: AMBER: mm_pbsa +fillratio (Mon Nov 22 2004 - 18:38:13 CST)
  • AMBER: mm_pbsa +fillratio (Mon Nov 22 2004 - 17:14:55 CST)
  • AMBER: nmode (Tue Sep 14 2004 - 17:29:49 CDT)
  • AMBER: mm_pbsa problem (Tue Aug 03 2004 - 15:49:34 CDT)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 10:55:04 CDT)
  • AMBER: recompiling amber8 (Mon Aug 02 2004 - 19:57:19 CDT)
  • Re: AMBER: using ptraj (Thu Jul 29 2004 - 17:11:11 CDT)
  • AMBER: using ptraj (Tue Jul 27 2004 - 16:10:02 CDT)
  • Re: AMBER: parametrization problem (Fri Jul 23 2004 - 15:33:01 CDT)
  • Re: AMBER: parametrization problem (Fri Jul 23 2004 - 15:38:59 CDT)
  • AMBER: parametrization problem (Fri Jul 23 2004 - 13:16:13 CDT)
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 16 2004 - 16:33:51 CDT)
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 16 2004 - 16:37:22 CDT)
  • AMBER: problems with mdcrd (Thu Jul 08 2004 - 12:16:04 CDT)
  • AMBER: bug in leap? (Mon Jun 07 2004 - 18:14:30 CDT)
  • AMBER: address error (Wed May 19 2004 - 12:09:12 CDT)
  • AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 15:37:42 CDT)
  • Re: AMBER: dummy atom other than H (Wed May 12 2004 - 16:18:23 CDT)
  • AMBER: dummy atom other than H (Tue May 11 2004 - 20:12:22 CDT)
  • AMBER: xleap bug? (Wed Apr 14 2004 - 17:28:07 CDT)
  • AMBER: gibbs termination (Wed Apr 14 2004 - 14:17:29 CDT)
  • AMBER: Ti of CH3 -> NH2 (Wed Apr 07 2004 - 17:14:11 CDT)
  • Re: AMBER: new leap with old gibbs (Tue Apr 06 2004 - 16:48:26 CDT)
  • AMBER: new leap with old gibbs (Tue Apr 06 2004 - 14:16:01 CDT)
  • AMBER: gibbs calculation (Tue Apr 06 2004 - 13:11:55 CDT)
  • AMBER: sander + ew_legal.h (Fri Apr 02 2004 - 19:08:07 CST)
  • AMBER: installing amber8 on a dual processor single box (Fri Apr 02 2004 - 12:37:46 CST)
  • AMBER: INtel Fortran 90 compiler (Wed Mar 24 2004 - 13:03:17 CST)
  • AMBER: segmentation fault with sander (Tue Mar 16 2004 - 20:29:55 CST)
  • AMBER: sander + child process died (Tue Mar 09 2004 - 20:18:21 CST)
  • Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file (Fri Mar 05 2004 - 12:19:18 CST)
  • Re: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files (Tue Mar 02 2004 - 13:18:42 CST)
  • Re: AMBER: ptraj (Tue Mar 02 2004 - 12:48:35 CST)
  • AMBER: ptraj (Mon Mar 01 2004 - 11:23:26 CST)
  • AMBER: sander + vlimit exceed... (Thu Feb 26 2004 - 17:16:31 CST)
  • AMBER: check unit + saveamberparm (Wed Feb 18 2004 - 20:21:58 CST)
  • AMBER: sander + ewald bomb (Wed Feb 18 2004 - 13:20:51 CST)
  • Re: AMBER: antechamber + FAILED TO ACHIEVE SCF (Mon Feb 09 2004 - 16:02:10 CST)
  • AMBER: antechamber + FAILED TO ACHIEVE SCF (Mon Feb 09 2004 - 13:17:41 CST)
  • Re: AMBER: antechamber error (Mon Feb 09 2004 - 11:38:41 CST)
  • AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED (Fri Feb 06 2004 - 19:50:46 CST)
  • AMBER: antechamber + mopac +scf failed (Fri Feb 06 2004 - 18:11:22 CST)
  • AMBER: antechamber error in test / differences in prmtop files (Thu Feb 05 2004 - 14:07:07 CST)
  • AMBER: antechamber + mopac error (Wed Feb 04 2004 - 20:57:48 CST)
  • AMBER: TI, angle parameters for nitrogen, frcmod (Mon Feb 02 2004 - 14:38:59 CST)
  • AMBER: compilation under fedora core 1 (Tue Jan 27 2004 - 12:51:26 CST)
• Cenk Andac
  • Re: AMBER: Problem with computing Resp charges using RED (Thu Dec 30 2004 - 11:30:34 CST)
  • AMBER: Problem with computing Resp charges using RED (Sat Dec 25 2004 - 09:54:54 CST)
  • AMBER: mm_gbsa results for charged ligands (Fri Dec 24 2004 - 03:50:10 CST)
  • Re: AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 (Wed Dec 01 2004 - 21:04:31 CST)
  • AMBER: Resend: Problem with converting AMBER8 PREP to MOL2 (Tue Nov 23 2004 - 02:57:55 CST)
  • AMBER: Problem with converting AMBER PREP to MOL2 (Mon Nov 22 2004 - 18:13:39 CST)
  • INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 (Tue Nov 16 2004 - 08:19:03 CST)
  • AMBER: MAXATOM failure in ANTECHAMBER (Fri Oct 08 2004 - 04:31:18 CDT)
  • Re: AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP (Thu Jul 01 2004 - 00:02:17 CDT)
  • AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP (Wed Jun 30 2004 - 10:12:10 CDT)
  • AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP (Wed Jun 30 2004 - 10:14:18 CDT)
  • AMBER: AMBPDB command requires libcxa.so.5 (Sat Jun 26 2004 - 10:16:52 CDT)
  • AMBER: Problem with menu bar in LEAP (Fri Jun 25 2004 - 16:54:47 CDT)
• Charles F. Fisher
  • AMBER: installation test question (antechamber, ash) (Mon Jan 26 2004 - 12:16:30 CST)
• Charlie Laughton
  • AMBER: Parameters for deuterium (Tue Jan 06 2004 - 09:17:46 CST)
• charris5
  • Re: AMBER: (Tue Jan 13 2004 - 13:07:33 CST)
• Chen
  • Re: Re: AMBER: (Fri Jul 30 2004 - 22:55:14 CDT)
  • Re: Re: AMBER: NB pairs exceeds? (Fri Jul 16 2004 - 03:40:42 CDT)
  • AMBER: NB pairs exceeds? (Fri Jul 16 2004 - 02:35:16 CDT)
• Chen Song
  • AMBER: energy unit (Wed Dec 22 2004 - 23:20:00 CST)
  • AMBER: Using AMBER to simulate carbon nanotubes? (Tue Aug 31 2004 - 05:54:26 CDT)
• Chen Yongzhi
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 13:23:48 CDT)
  • AMBER: A problem for compiling amber8 parallel version (Tue May 25 2004 - 15:58:37 CDT)
• Chen, Ya
  • AMBER: Question on Clustering Analysis (Tue Jul 27 2004 - 13:26:30 CDT)
  • AMBER: MCSS (Thu Feb 05 2004 - 22:33:48 CST)
• Chenglong Li
  • Re: AMBER: solvateCap warning (Fri Apr 23 2004 - 12:44:14 CDT)
  • Re: AMBER: Using pbsa (Tue Apr 20 2004 - 18:47:34 CDT)
  • AMBER: pbsa (Thu Apr 15 2004 - 12:26:51 CDT)
• Chris Harrison
  • Re: AMBER: MD & net charge (Mon Aug 30 2004 - 08:28:46 CDT)
• Chris Moth
  • Re: AMBER: how to neutralize the peptide (Wed Oct 27 2004 - 11:57:23 CDT)
  • AMBER 8 default is now HIS->HIE and not HIS->HID - typo? (Tue Oct 26 2004 - 15:24:05 CDT)
  • Re: AMBER: average structure using ptraj (Fri Jul 02 2004 - 12:11:42 CDT)
  • Re: AMBER: energy criteria. (Fri Apr 30 2004 - 13:03:39 CDT)
  • Re: AMBER: NSNB parameter (Sat Apr 24 2004 - 07:31:55 CDT)
  • AMBER: antechamber bcctype.c typo (Thu Apr 22 2004 - 07:07:32 CDT)
  • RE: AMBER: What kind of informations are needed in a .pdb file in order to start using antechamber? (Thu Apr 22 2004 - 07:02:30 CDT)
  • RE: AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 10:58:07 CDT)
  • RE: AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 10:00:14 CDT)
  • RE: AMBER: how to use mm_pbsa_statistics.pl independently (Tue Apr 13 2004 - 10:34:26 CDT)
  • AMBER: Group in sander (Mon Apr 12 2004 - 14:20:37 CDT)
  • Re: AMBER: bug of leap? (Thu Apr 08 2004 - 11:10:06 CDT)
  • AMBER: unique atom names (Wed Apr 07 2004 - 09:20:11 CDT)
  • RE: AMBER: unique atom names (Wed Apr 07 2004 - 09:21:50 CDT)
  • AMBER: question about image - truncated octahedron (Sat Apr 03 2004 - 09:22:14 CST)
  • AMBER: PMEMD and myrinet trouble (Mon Mar 29 2004 - 13:05:07 CST)
  • RE: AMBER: tleap error and warnings (Fri Mar 26 2004 - 09:34:08 CST)
  • RE: AMBER: a question about anal (Thu Mar 25 2004 - 21:54:51 CST)
  • PMEMD and myrinet trouble (Wed Mar 24 2004 - 15:25:57 CST)
  • AMBER: About RESP Calculation (Fri Mar 19 2004 - 15:38:40 CST)
• Chris Page
  • Re: AMBER: question about molsurf (Thu Nov 25 2004 - 12:45:28 CST)
• Chung-Chien Wei
  • Re: AMBER: Some questions in building a new residue (Wed Mar 10 2004 - 13:49:33 CST)
  • AMBER: Some questions in building a new residue (Wed Mar 10 2004 - 11:16:37 CST)
• Chunhu Tan
  • Re: AMBER: cannot load frcmod file properly (Wed Nov 24 2004 - 14:37:46 CST)
  • Re: AMBER: cannot load frcmod file properly (Tue Nov 23 2004 - 20:12:42 CST)
  • Re: AMBER: TI with electrostatic decoupling (Tue Nov 23 2004 - 13:01:48 CST)
  • Re: AMBER: questions on dummy atom types in FEP setup (Mon Nov 22 2004 - 17:37:57 CST)
  • Re: AMBER: <dV/dL> fluctuations in TI (Fri Nov 19 2004 - 13:07:03 CST)
  • Re: AMBER: <dV/dL> fluctuations in TI (Thu Nov 18 2004 - 16:57:05 CST)
  • Re: AMBER: Solvation free energy of a charged molecule. (Fri Nov 12 2004 - 12:43:32 CST)
  • AMBER: Solvation free energy of a charged molecule. (Thu Nov 11 2004 - 19:53:58 CST)
  • Re: AMBER: FEP and charges (Thu Nov 04 2004 - 16:23:16 CST)
  • AMBER: Sander TI with NTR = 1. (Wed Sep 15 2004 - 18:33:47 CDT)
  • Re: AMBER: A question about pheTI in AMBER8 test. (Thu Aug 05 2004 - 17:56:56 CDT)
  • AMBER: A question about pheTI in AMBER8 test. (Wed Aug 04 2004 - 16:35:48 CDT)
  • AMBER: About the free energy difference in vacuum with GIBBS. (Mon Jul 12 2004 - 17:34:35 CDT)
  • AMBER: My strange result of TI. (Wed Jul 07 2004 - 18:35:19 CDT)
  • Re: AMBER: About TI with sander (Sun Jul 04 2004 - 20:18:48 CDT)
  • AMBER: Questions about pert.charge and atom type change. (Wed Jun 30 2004 - 19:20:38 CDT)
  • AMBER: About TI with sander (Mon Jun 28 2004 - 14:35:54 CDT)
• Chutintorn Punwong
  • Re: AMBER: segmentation fault when running parmchk (Tue Jun 08 2004 - 13:07:45 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Wed Jun 02 2004 - 14:11:22 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Wed Jun 02 2004 - 12:57:06 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Fri May 28 2004 - 15:08:56 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 13:37:09 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 13:01:16 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Mon May 24 2004 - 17:34:11 CDT)
• CK Sim
  • RE: AMBER: Trajectory file conversion between Amber & Charmm (Mon Sep 20 2004 - 12:45:09 CDT)
  • AMBER: Trajectory file conversion between Amber & Charmm (Tue Aug 24 2004 - 15:42:19 CDT)
• Craig TOEPFER
  • Re: AMBER: Compiling using pgf90 (Wed Oct 06 2004 - 11:52:06 CDT)
  • Re: AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 14:19:01 CDT)
  • AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 13:21:53 CDT)
• csong_at_mail.sdu.edu.cn
  • AMBER: (Fri Jul 30 2004 - 04:08:40 CDT)
  • Re: Re: AMBER: NB pairs exceeds? (Sun Jul 18 2004 - 03:28:27 CDT)
  • Re: Re: AMBER: NB pairs exceeds? (Sat Jul 17 2004 - 05:10:23 CDT)
• Dalmaris, John
  • AMBER: nonpalar energy contribution-DMSO (Sat Aug 28 2004 - 09:11:43 CDT)
  • AMBER: MMPBSA problem (Sun May 30 2004 - 08:22:55 CDT)
• Daniel Wetzler
  • Re: AMBER: Question concerning ANAL total energy calculation (Mon Dec 20 2004 - 15:15:12 CST)
  • Re: AMBER: Question concerning ANAL total energy calculation (Sat Dec 18 2004 - 03:33:26 CST)
  • AMBER: Question concerning ANAL total energy calculation (Fri Dec 17 2004 - 06:04:05 CST)
  • AMBER: Problem with minimisation of an protein-inhibitor complex (Tue Nov 23 2004 - 06:31:38 CST)
  • AMBER: Problem with minimisation of an protein-inhibitor complex (Tue Nov 23 2004 - 04:31:33 CST)
  • Re: AMBER: Problem with a single aminoacid as inhibitor (Wed Nov 17 2004 - 10:13:50 CST)
  • AMBER: Problem with a single aminoacid as inhibitor (Wed Nov 17 2004 - 05:59:12 CST)
  • AMBER: Problem with a single aminoacid as inhibitor (Wed Nov 17 2004 - 05:54:04 CST)
  • Re: AMBER: Problem with Water solute during MD (Wed Nov 10 2004 - 04:19:11 CST)
  • AMBER: Problem with Water solute during MD (Tue Nov 09 2004 - 07:20:13 CST)
  • AMBER: Problems using mm_pbsa.perl (Fri Nov 05 2004 - 10:28:15 CST)
  • Re: AMBER: MD problem (very long parhabs endless runtime) (Sun Oct 24 2004 - 04:40:09 CDT)
  • Re: AMBER: MD problem (very long parhabs endless runtime) (Sat Oct 23 2004 - 13:16:12 CDT)
  • AMBER: MD problem (very long parhabs endless runtime) (Sat Oct 23 2004 - 08:05:49 CDT)
  • Re: AMBER: Problem with EDIT (AMBER 5) (Thu Oct 14 2004 - 07:23:32 CDT)
  • AMBER: Problem with EDIT (AMBER 5) (Thu Oct 14 2004 - 06:53:45 CDT)
  • AMBER: Problem with AMBER/ANAL (Fri Oct 08 2004 - 03:31:29 CDT)
• darden
  • Re: AMBER: Using AMBER to simulate carbon nanotubes? (Tue Aug 31 2004 - 10:43:56 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 15:57:15 CDT)
  • Re: AMBER: Periodic boundary simulation (Tue Jun 01 2004 - 08:11:54 CDT)
  • Re: AMBER: Nonplanar ring systems in nucleic acid (Wed May 19 2004 - 16:05:59 CDT)
  • Re: AMBER: production input file (Mon Mar 01 2004 - 16:32:35 CST)
  • Re: AMBER: Fwd: NVE & polarizable force field] (Sat Jan 24 2004 - 15:14:55 CST)
• Darian, Eva
  • AMBER: Extracting torsional angles for specific conformation (Wed Nov 03 2004 - 12:12:33 CST)
• Dat H. Nguyen
  • Re: AMBER: Problem with menu bar in LEAP (Fri Jun 25 2004 - 17:09:00 CDT)
  • Re: AMBER: Core Dump ERROR When Using TIP4P (Tue Jun 15 2004 - 16:21:28 CDT)
  • AMBER: Core Dump ERROR When Using TIP4P (Thu Jun 10 2004 - 20:12:06 CDT)
• Dave S Walker
  • Re: AMBER: recovering total force array (Tue Oct 19 2004 - 18:59:00 CDT)
  • Re: AMBER: recovering total force array (Tue Oct 19 2004 - 14:04:16 CDT)
  • AMBER: ntwprt feature in AMBER7 (Thu May 06 2004 - 21:26:51 CDT)
  • Re: AMBER: recovering total force array (Wed Mar 31 2004 - 15:29:13 CST)
  • Re: AMBER: recovering total force array (Tue Mar 30 2004 - 19:51:41 CST)
  • AMBER: recovering total force array (Thu Mar 11 2004 - 20:20:57 CST)
  • Re: AMBER: sander output (Fri Feb 20 2004 - 15:47:24 CST)
  • Re: AMBER: sander output (Thu Feb 19 2004 - 17:55:59 CST)
  • AMBER: cell dimensions (Mon Feb 02 2004 - 15:46:54 CST)
• David A. Case
  • Re: AMBER: Dummy Atoms: How to create them? (Thu Dec 30 2004 - 21:55:59 CST)
  • Re: AMBER: Molecular modelling. (Thu Dec 23 2004 - 20:03:50 CST)
  • Re: AMBER: Output of sander (Thu Dec 23 2004 - 15:35:49 CST)
  • Re: AMBER: amber7 on digital unix (Thu Dec 23 2004 - 12:26:55 CST)
  • Re: AMBER: amber7 on digital unix (Thu Dec 23 2004 - 10:18:46 CST)
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Wed Dec 22 2004 - 18:39:57 CST)
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Wed Dec 22 2004 - 15:50:00 CST)
  • Re: AMBER: Output of sander (Wed Dec 22 2004 - 11:35:27 CST)
  • Re: AMBER: a question (Tue Dec 21 2004 - 16:07:51 CST)
  • Re: AMBER: Ideal bonds and angles (Tue Dec 21 2004 - 12:52:15 CST)
  • Re: AMBER: constraints on atoms (Tue Dec 21 2004 - 11:12:55 CST)
  • Re: AMBER: parameter development (Tue Dec 21 2004 - 10:53:19 CST)
  • Re: AMBER: Sander TI (Tue Dec 21 2004 - 10:15:50 CST)
  • Re: AMBER: nrespa=2 (Tue Dec 21 2004 - 09:52:53 CST)
  • Re: AMBER: Dummy torsion paramters for thermodynamic integration (Tue Dec 21 2004 - 09:49:29 CST)
  • Re: AMBER: Question concerning ANAL total energy calculation (Mon Dec 20 2004 - 16:10:08 CST)
  • Re: AMBER: Question on tleap of amber8 (Mon Dec 20 2004 - 11:27:07 CST)
  • Re: AMBER: Question concerning ANAL total energy calculation (Sat Dec 18 2004 - 10:50:01 CST)
  • Re: AMBER: nanotube parameters (Fri Dec 17 2004 - 17:34:31 CST)
  • Re: AMBER: General Question about AMBER's Free Energy Perturbation Method (Fri Dec 17 2004 - 17:26:34 CST)
  • Re: AMBER: entropy implementation in ptraj (Fri Dec 17 2004 - 10:11:29 CST)
  • Re: AMBER: Question concerning ANAL total energy calculation (Fri Dec 17 2004 - 09:58:49 CST)
  • Re: AMBER: Residue Loading Problem (Thu Dec 16 2004 - 20:10:43 CST)
  • Re: AMBER: About MM/PBSA, PB Calculation (Thu Dec 16 2004 - 11:38:32 CST)
  • Re: Re: Re: AMBER: Why the surface calculations sometimes fail? (Thu Dec 16 2004 - 11:32:29 CST)
  • Re: AMBER: General Question about AMBER's Free Energy Perturbation Method (Thu Dec 16 2004 - 01:03:18 CST)
  • Re: AMBER: Ewald (Wed Dec 15 2004 - 12:17:04 CST)
  • Re: AMBER: entropy implementation in ptraj (Wed Dec 15 2004 - 12:07:50 CST)
  • Re: AMBER: unknown elements (Wed Dec 15 2004 - 12:00:32 CST)
  • Re: AMBER: Compiling question (Tue Dec 14 2004 - 13:33:34 CST)
  • Re: Re: AMBER: Why the surface calculations sometimes fail? (Mon Dec 13 2004 - 20:29:17 CST)
  • Re: AMBER: Why the charge is not an integer? (Sun Dec 12 2004 - 15:05:57 CST)
  • Re: AMBER: Implicit Solvent Models (Fri Dec 10 2004 - 10:51:12 CST)
  • Re: AMBER: Why the surface calculations sometimes fail? (Wed Dec 08 2004 - 13:52:29 CST)
  • Re: AMBER: (Wed Dec 08 2004 - 13:49:41 CST)
  • Re: AMBER: 1-4 EEL (Wed Dec 08 2004 - 12:13:08 CST)
  • Re: AMBER: NMR constraint problem (Wed Dec 08 2004 - 12:08:11 CST)
  • Re: AMBER: some questions.... (Wed Dec 08 2004 - 12:04:13 CST)
  • Re: AMBER: (no subject) (Tue Dec 07 2004 - 07:00:49 CST)
  • Re: AMBER: install problem (Tue Dec 07 2004 - 07:03:12 CST)
  • Re: AMBER: Dielectric Constant (Sat Dec 04 2004 - 17:15:10 CST)
  • Re: AMBER: Implicit 4r md (Fri Dec 03 2004 - 10:48:00 CST)
  • Re: AMBER: restrainted torsion (Thu Dec 02 2004 - 13:12:19 CST)
  • Re: AMBER: ntt parameter (Wed Dec 01 2004 - 18:14:30 CST)
  • Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) (Wed Dec 01 2004 - 11:44:12 CST)
  • Re: AMBER: FEP along a reaction coordinate in sander (Wed Dec 01 2004 - 11:38:45 CST)
  • Re: AMBER: increasing the maximum value of NPHB parameter (Tue Nov 30 2004 - 19:58:59 CST)
  • Re: AMBER: memory prolem of the nmode calculation (Tue Nov 30 2004 - 19:40:29 CST)
  • Re: AMBER: Slowly releasing restraints (Tue Nov 30 2004 - 13:55:40 CST)
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 17:27:41 CST)
  • Re: AMBER: problem in quasih.f diagonalising matrix (Mon Nov 29 2004 - 10:38:46 CST)
  • Re: AMBER: FEP - GIBBS of charged sidechains using IELPER (Sun Nov 28 2004 - 17:28:43 CST)
  • Re: AMBER: GO lie Amber simulation (Sat Nov 27 2004 - 17:37:45 CST)
  • Re: AMBER: About Disulfer bond (Sat Nov 27 2004 - 12:05:28 CST)
  • Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90 (Wed Nov 24 2004 - 01:03:55 CST)
  • Re: AMBER: TI with electrostatic decoupling (Tue Nov 23 2004 - 10:42:16 CST)
  • Re: AMBER: restart calculation (Tue Nov 23 2004 - 10:39:37 CST)
  • Re: AMBER: add dummy atoms (Tue Nov 23 2004 - 10:27:48 CST)
  • Re: AMBER: langevin dynamic in sander (Tue Nov 23 2004 - 10:21:30 CST)
  • Re: AMBER: Problem with converting AMBER PREP to MOL2 (Tue Nov 23 2004 - 10:12:06 CST)
  • Re: AMBER: generating parmfile containing topology and parameter information (Mon Nov 22 2004 - 18:12:20 CST)
  • Re: AMBER: mm_pbsa +fillratio (Mon Nov 22 2004 - 17:20:03 CST)
  • Re: AMBER: LEaP compilation error on Solaris 9 (Mon Nov 22 2004 - 16:02:35 CST)
  • Re: AMBER: Can xleap to handle homology model altogether X-ray structure? (Tue Nov 16 2004 - 10:13:11 CST)
  • Re: AMBER: constant pH simulations reference (Mon Nov 15 2004 - 20:23:42 CST)
  • Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! (Mon Nov 15 2004 - 15:43:15 CST)
  • Re: AMBER: gibbs compilation error (Mon Nov 15 2004 - 12:18:12 CST)
  • Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! (Mon Nov 15 2004 - 10:10:43 CST)
  • Re: AMBER: Parameters for new residue? (Sat Nov 13 2004 - 19:30:39 CST)
  • Re: AMBER: the energy difference between sander and nmode (Fri Nov 12 2004 - 16:43:28 CST)
  • Re: AMBER: glibc version (Fri Nov 12 2004 - 16:17:53 CST)
  • Re: AMBER: AMBER 4 Manual? (Fri Nov 12 2004 - 16:10:42 CST)
  • Re: AMBER: Energy change for isomerization reaction of cyclic peptide (Fri Nov 12 2004 - 16:02:10 CST)
  • Re: AMBER: Solvation free energy of a charged molecule. (Fri Nov 12 2004 - 10:11:15 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Wed Nov 10 2004 - 18:15:32 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Wed Nov 10 2004 - 15:49:47 CST)
  • Re: AMBER: About the parameter names (Wed Nov 10 2004 - 15:50:58 CST)
  • Re: AMBER: parameter set (Wed Nov 10 2004 - 14:10:40 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Wed Nov 10 2004 - 11:07:13 CST)
  • Re: AMBER: Problem with Water solute during MD (Wed Nov 10 2004 - 09:42:50 CST)
  • Re: AMBER: Building the parallel version in AMBER 8 and GIBBS (Tue Nov 09 2004 - 23:07:05 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Tue Nov 09 2004 - 18:57:24 CST)
  • Re: AMBER: Leap (Tue Nov 09 2004 - 11:00:38 CST)
  • Re: AMBER: Problem with Water solute during MD (Tue Nov 09 2004 - 10:06:31 CST)
  • Re: AMBER: Amber7 compilation error (Fri Nov 05 2004 - 10:50:01 CST)
  • Re: AMBER: end point contribution in MCTI (Fri Nov 05 2004 - 10:36:31 CST)
  • Re: AMBER: SANDER BOMB in subroutine nonbond_list (Wed Nov 03 2004 - 12:05:15 CST)
  • Re: AMBER: about FEP (Tue Nov 02 2004 - 10:19:27 CST)
  • Re: AMBER: Amber7 installation error on Solaris 9 (Mon Nov 01 2004 - 15:11:24 CST)
  • Re: AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo? (Thu Oct 28 2004 - 11:50:34 CDT)
  • Re: AMBER: getting new box info (Thu Oct 28 2004 - 09:39:07 CDT)
  • Re: AMBER: parallel of sander_classic (Mon Oct 25 2004 - 08:17:44 CDT)
  • Re: AMBER: Amber: what different? (Sun Oct 24 2004 - 09:17:47 CDT)
  • Re: AMBER: add charge error message: Number of electrons is odd (Fri Oct 22 2004 - 16:12:00 CDT)
  • Re: AMBER: Sander-7 for Win32 (Wed Oct 20 2004 - 18:03:49 CDT)
  • Re: AMBER: A question on AMBER8 installation (Wed Oct 20 2004 - 00:04:36 CDT)
  • Re: AMBER: A question on AMBER8 installation (Tue Oct 19 2004 - 18:27:08 CDT)
  • Re: AMBER: recovering total force array (Tue Oct 19 2004 - 16:26:31 CDT)
  • Re: AMBER: MAXMASK problem (Tue Oct 19 2004 - 16:10:29 CDT)
  • Re: AMBER: question on NAB (Tue Oct 19 2004 - 10:06:50 CDT)
  • Re: AMBER: BOND energy during minimisation (Tue Oct 19 2004 - 09:59:46 CDT)
  • Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F (Tue Oct 19 2004 - 09:48:52 CDT)
  • Re: AMBER: question on NMR restrain (Mon Oct 18 2004 - 20:30:30 CDT)
  • Re: AMBER: problem with antechamber (Mon Oct 18 2004 - 15:14:29 CDT)
  • Re: AMBER: problems with dihedrals - extended information (Mon Oct 18 2004 - 12:42:50 CDT)
  • Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F (Mon Oct 18 2004 - 10:59:58 CDT)
  • Re: AMBER: question about molsurf (Fri Oct 15 2004 - 10:28:10 CDT)
  • Re: AMBER: modes analysis in ptraj (Fri Oct 15 2004 - 10:18:50 CDT)
  • Re: AMBER: difference in GBSOL in amber7 and amber8 (Fri Oct 15 2004 - 10:07:04 CDT)
  • Re: AMBER: A question on AMBER8 installation (Fri Oct 15 2004 - 09:58:29 CDT)
  • Re: AMBER: AMBER 8 installation trouble (Fri Oct 15 2004 - 09:51:59 CDT)
  • Re: AMBER: normal mode analysis after energy minimizaiton using sander (Thu Oct 14 2004 - 18:35:01 CDT)
  • Re: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 13:22:14 CDT)
  • Re: AMBER: Amber8 - Energy Calculations (Thu Oct 14 2004 - 12:55:38 CDT)
  • Re: AMBER: amber8 compilation on AIX (regatta) (Thu Oct 14 2004 - 12:36:28 CDT)
  • Re: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 11:45:30 CDT)
  • Re: Re: AMBER: errors in SGI (Thu Oct 14 2004 - 11:33:32 CDT)
  • Re: AMBER: errors in SGI (Thu Oct 14 2004 - 10:04:24 CDT)
  • Re: Re: AMBER: Running on MPI (Wed Oct 13 2004 - 10:57:24 CDT)
  • Re: AMBER: A question on AMBER8 installation (Wed Oct 13 2004 - 09:58:58 CDT)
  • Re: AMBER: klambdas and Weights for Gaussian Quadrature (Tue Oct 12 2004 - 18:37:11 CDT)
  • Re: AMBER: AMBER 8 installation trouble (Tue Oct 12 2004 - 12:28:14 CDT)
  • Re: AMBER: rms fluct and displacement in modes analysis (Tue Oct 12 2004 - 11:19:48 CDT)
  • Re: AMBER: about antechamber (Mon Oct 11 2004 - 11:13:05 CDT)
  • Re: AMBER: AMBER 8 installation trouble (Mon Oct 11 2004 - 10:43:44 CDT)
  • Re: AMBER: Distance Restraints (Mon Oct 11 2004 - 10:17:39 CDT)
  • Re: AMBER: nmode error (Mon Oct 11 2004 - 10:09:18 CDT)
  • Re: AMBER: A torsion parameter in AMBER2003 force field (Fri Oct 08 2004 - 11:53:21 CDT)
  • Re: AMBER: Problem with AMBER/ANAL (Fri Oct 08 2004 - 11:15:12 CDT)
  • Re: AMBER: generalized Born parameters (Fri Oct 08 2004 - 11:08:02 CDT)
  • Re: AMBER: Antechamber on cluster with queue? (Wed Oct 06 2004 - 11:31:53 CDT)
  • Re: AMBER: Antechamber on cluster with queue? (Wed Oct 06 2004 - 10:24:17 CDT)
  • Re: AMBER: problem with protonate (Tue Oct 05 2004 - 16:31:12 CDT)
  • Re: AMBER: parameter error for a ligand (Tue Oct 05 2004 - 15:23:01 CDT)
  • Re: AMBER: question about nmode (Tue Oct 05 2004 - 14:03:52 CDT)
  • Re: AMBER: Compiling AMBER8 (Thu Sep 30 2004 - 10:59:42 CDT)
  • Re: AMBER: impose: Illegal angle internal definition (Wed Sep 29 2004 - 14:13:36 CDT)
  • Re: AMBER: (no subject) (Wed Sep 29 2004 - 10:39:43 CDT)
  • Re: AMBER: scaling 1-4 NB interaction for rings (Wed Sep 29 2004 - 10:11:02 CDT)
  • Re: AMBER: intramolecular energies (Tue Sep 28 2004 - 12:11:57 CDT)
  • Re: AMBER: intramolecular energies (Tue Sep 28 2004 - 10:43:11 CDT)
  • Re: AMBER: intramolecular energies (Mon Sep 27 2004 - 18:27:25 CDT)
  • Re: AMBER: Amber-7:Bugfix.47 (Mon Sep 27 2004 - 15:20:20 CDT)
  • Re: AMBER: unformatted md problem (Mon Sep 27 2004 - 10:06:05 CDT)
  • Re: AMBER: nmode error (Sat Sep 25 2004 - 13:44:37 CDT)
  • Re: AMBER: minimization problem (Sat Sep 25 2004 - 13:43:49 CDT)
  • Re: AMBER: Question Amber8 install errer with Windows (Fri Sep 24 2004 - 15:41:18 CDT)
  • Re: AMBER: regular ewald sum in Amber8 (Fri Sep 24 2004 - 14:12:30 CDT)
  • Re: AMBER: replica exchange with thermodynamic integration (Fri Sep 24 2004 - 10:44:01 CDT)
  • Re: AMBER: phosphoserine library component (Fri Sep 24 2004 - 10:25:10 CDT)
  • Re: AMBER: nbflag (Fri Sep 24 2004 - 10:15:20 CDT)
  • Re: AMBER: mm_pbsa.pl nmode entropy estimating problem (Wed Sep 22 2004 - 15:29:04 CDT)
  • Re: AMBER: amber8 tests (Wed Sep 22 2004 - 13:28:34 CDT)
  • Re: AMBER: The question about SAS calculation in MM_PBSA (Wed Sep 22 2004 - 13:29:52 CDT)
  • Re: AMBER: all_nucleic02 and all_nucleic94 (Wed Sep 22 2004 - 11:59:01 CDT)
  • Re: AMBER: Question about Parallel Compilation (Wed Sep 22 2004 - 11:49:02 CDT)
  • Re: AMBER: about PARALLEL run on SGI. (Sun Sep 19 2004 - 19:49:30 CDT)
  • Re: AMBER: Amber 7 Compiling Problem (Fri Sep 17 2004 - 12:23:23 CDT)
  • Re: AMBER: Amber 7 Compiling Problem (Fri Sep 17 2004 - 11:29:58 CDT)
  • Re: AMBER: extra points (Thu Sep 16 2004 - 12:26:09 CDT)
  • Re: AMBER: Sander TI with NTR = 1. (Thu Sep 16 2004 - 09:56:48 CDT)
  • Re: AMBER: back interpret (Wed Sep 15 2004 - 17:23:18 CDT)
  • Re: AMBER: GB and langevin dynamics (Wed Sep 15 2004 - 17:01:31 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 11:08:04 CDT)
  • Re: AMBER: bond constraints in nmode (Wed Sep 15 2004 - 11:03:09 CDT)
  • Re: AMBER: nmode (Tue Sep 14 2004 - 18:13:14 CDT)
  • Re: AMBER: MM binding energy with ANAL (Tue Sep 14 2004 - 17:32:48 CDT)
  • Re: AMBER: Restraints in sander.QMMM (Tue Sep 14 2004 - 17:21:07 CDT)
  • Re: AMBER: TI with sander (Tue Sep 14 2004 - 14:20:49 CDT)
  • Re: AMBER: bond between two polypeptides (Tue Sep 14 2004 - 11:20:23 CDT)
  • Re: AMBER: GB and langevin dynamics (Mon Sep 13 2004 - 14:59:31 CDT)
  • Re: AMBER: AMBER7 : update gaff and parm99 force field (Mon Sep 13 2004 - 14:59:12 CDT)
  • Re: AMBER: Monte Carlo simulation (Fri Sep 10 2004 - 16:56:20 CDT)
  • Re: AMBER: REM make test (Thu Sep 09 2004 - 18:40:13 CDT)
  • Re: AMBER: Amber:how to increase the memory allocation? (Thu Sep 09 2004 - 10:38:12 CDT)
  • Re: AMBER: Antechamber Failure (Wed Sep 08 2004 - 17:48:41 CDT)
  • Re: AMBER: error in installing amber8 (Wed Sep 08 2004 - 11:23:04 CDT)
  • Re: AMBER: Amber: BOMB (Wed Sep 08 2004 - 09:55:04 CDT)
  • Re: AMBER: Amber7 tleap problem (Sat Sep 04 2004 - 15:11:39 CDT)
  • Re: AMBER: error in installing amber8 (Thu Sep 02 2004 - 10:31:02 CDT)
  • Re: AMBER: Increase lastrst in the &cntrl namelist (Wed Sep 01 2004 - 13:22:07 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Sep 01 2004 - 12:48:34 CDT)
  • Re: AMBER: Re. HSG Convention (Wed Sep 01 2004 - 11:01:44 CDT)
  • Re: AMBER: Increase lastrst in the &cntrl namelist (Tue Aug 31 2004 - 23:53:20 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Tue Aug 31 2004 - 23:43:01 CDT)
  • Re: AMBER: Updating Amber 7 (Tue Aug 31 2004 - 23:00:46 CDT)
  • Re: AMBER: (Tue Aug 31 2004 - 22:56:27 CDT)
  • Re: AMBER: PBC in sander (Tue Aug 31 2004 - 22:57:49 CDT)
  • Re: AMBER: ANAL memory problem. (Tue Aug 17 2004 - 11:33:03 CDT)
  • Re: AMBER: Amber: Anal program format (Tue Aug 17 2004 - 11:14:31 CDT)
  • Re: AMBER: About the Amber constraint constant (Tue Aug 17 2004 - 10:08:04 CDT)
  • Re: AMBER: ANAL memory problem. (Mon Aug 16 2004 - 20:34:22 CDT)
  • Re: AMBER: About the Amber constraint constant (Sun Aug 15 2004 - 18:07:11 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Sun Aug 15 2004 - 17:59:51 CDT)
  • Re: AMBER: Bug: ptraj adds spurious box information (Fri Aug 13 2004 - 17:13:33 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 17:07:42 CDT)
  • Re: AMBER: Temp control (Fri Aug 13 2004 - 15:13:20 CDT)
  • Re: AMBER: Antechamber and dummy atoms (Fri Aug 13 2004 - 09:49:49 CDT)
  • Re: AMBER: opteron 64 bit workstation (Thu Aug 12 2004 - 14:55:13 CDT)
  • Re: AMBER: bending (Thu Aug 12 2004 - 14:48:30 CDT)
  • Re: AMBER: units (Thu Aug 12 2004 - 09:56:09 CDT)
  • Re: AMBER: different cooling schedules for simulated annealing (Thu Aug 12 2004 - 09:55:45 CDT)
  • Re: AMBER: different cooling schedules for simulated annealing (Wed Aug 11 2004 - 09:41:50 CDT)
  • Re: AMBER: Membrane protein simulation (Tue Aug 10 2004 - 20:06:57 CDT)
  • Re: AMBER: how to correct the charge of oligosaccharides (Tue Aug 10 2004 - 09:31:40 CDT)
  • Re: AMBER: Sander (Mon Aug 09 2004 - 17:21:12 CDT)
  • Re: AMBER: Sander (Mon Aug 09 2004 - 11:57:40 CDT)
  • Re: AMBER: antechamber test (Sun Aug 08 2004 - 11:40:34 CDT)
  • Re: AMBER: AMBER7 plastocyanin tutorial problem. (Fri Aug 06 2004 - 14:09:34 CDT)
  • Re: AMBER: another cpinutil.pl error (Fri Aug 06 2004 - 10:58:46 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Fri Aug 06 2004 - 10:56:46 CDT)
  • Re: AMBER: A question about pheTI in AMBER8 test. (Thu Aug 05 2004 - 19:39:06 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Thu Aug 05 2004 - 17:35:22 CDT)
  • Re: AMBER: Bug and Patch in ANAL (Thu Aug 05 2004 - 10:44:38 CDT)
  • Re: AMBER: intense and spectrum (Wed Aug 04 2004 - 18:41:13 CDT)
  • Re: AMBER: A question about pheTI in AMBER8 test. (Wed Aug 04 2004 - 18:38:52 CDT)
  • Re: AMBER: Problem: Installing Amber8 on PC with Windows XP (Tue Aug 03 2004 - 17:28:25 CDT)
  • AMBER: Re: Phosphoserine residue in AMBER (Tue Aug 03 2004 - 16:23:20 CDT)
  • Re: AMBER: Minimum imaging (Tue Aug 03 2004 - 09:25:47 CDT)
  • Re: AMBER: recompiling amber8 (Mon Aug 02 2004 - 20:18:25 CDT)
  • Re: AMBER: lib file (Fri Jul 30 2004 - 15:48:50 CDT)
  • Re: AMBER: (no subject) (Fri Jul 30 2004 - 15:42:15 CDT)
  • Re: AMBER: WHAM program (Fri Jul 30 2004 - 12:16:02 CDT)
  • Re: AMBER: (Fri Jul 30 2004 - 10:06:56 CDT)
  • Re: AMBER: umbrella sampling (Thu Jul 29 2004 - 13:19:13 CDT)
  • Re: AMBER: NSPSOL in parm file (Thu Jul 29 2004 - 10:07:54 CDT)
  • Re: AMBER: question on simulated annealing (Tue Jul 27 2004 - 14:26:06 CDT)
  • Re: AMBER: Temperature Regulation (Tue Jul 27 2004 - 10:24:31 CDT)
  • Re: AMBER: erroe in installing amber8 (Sat Jul 24 2004 - 03:40:06 CDT)
  • Re: AMBER: Ewald parameter range (Fri Jul 23 2004 - 03:53:50 CDT)
  • Re: AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in) (Wed Jul 21 2004 - 08:32:44 CDT)
  • Re: AMBER: Is it a bug?(in prep file opls_unict.in) (Wed Jul 21 2004 - 03:52:22 CDT)
  • Re: Re: AMBER: NB pairs exceeds? (Sat Jul 17 2004 - 20:09:22 CDT)
  • Re: AMBER: Is it a bug?(in prep file opls_unict.in) (Fri Jul 16 2004 - 11:27:41 CDT)
  • Re: AMBER: Amber8: Vlimit problem again (Fri Jul 16 2004 - 11:26:06 CDT)
  • Re: Re: AMBER: NB pairs exceeds? (Fri Jul 16 2004 - 11:23:22 CDT)
  • Re: AMBER: antechamber (Fri Jul 16 2004 - 11:16:14 CDT)
  • Re: AMBER: antechamber (Thu Jul 15 2004 - 18:30:26 CDT)
  • Re: AMBER: Normal mode calculation with periodic boundary condition (Thu Jul 15 2004 - 12:04:07 CDT)
  • Re: AMBER: How to apply OPLS force field? (Thu Jul 15 2004 - 12:04:22 CDT)
  • Re: AMBER: xleap solvatebox/oct problem (Thu Jul 15 2004 - 12:02:11 CDT)
  • Re: AMBER: About the free energy difference in vacuum with GIBBS. (Wed Jul 14 2004 - 15:51:38 CDT)
  • Re: AMBER: How to apply OPLS force field? (Wed Jul 14 2004 - 11:29:59 CDT)
  • Re: AMBER: Implicit MD problem (Wed Jul 14 2004 - 11:29:47 CDT)
  • Re: AMBER: torsion scan (Tue Jul 13 2004 - 15:47:00 CDT)
  • Re: AMBER: anisotropic scaling (Tue Jul 13 2004 - 15:43:02 CDT)
  • Re: AMBER: Use of ibelly with nmode analysis (Tue Jul 13 2004 - 11:24:27 CDT)
  • Re: AMBER: RNA sequence with DNA backbone? (Mon Jul 12 2004 - 15:35:43 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sat Jul 10 2004 - 22:46:57 CDT)
  • Re: AMBER: how to calculate E-pot from restart file? (Thu Jul 08 2004 - 23:07:49 CDT)
  • Re: AMBER: charge problem in minimization (Thu Jul 08 2004 - 15:54:54 CDT)
  • Re: AMBER: name error (Thu Jul 08 2004 - 15:54:48 CDT)
  • Re: AMBER: Amber7 bugfix1 (Tue Jul 06 2004 - 13:37:04 CDT)
  • Re: AMBER: running MD simulatons (Tue Jul 06 2004 - 13:40:50 CDT)
  • Re: AMBER: idecomp (Tue Jul 06 2004 - 11:37:42 CDT)
  • Re: AMBER: combination rules (Mon Jul 05 2004 - 12:29:04 CDT)
  • Re: AMBER: leap problem in AMBER7 (residue insertion) (Mon Jul 05 2004 - 12:21:50 CDT)
  • Re: AMBER: Amber8 on Digital UNIX (Mon Jul 05 2004 - 11:55:20 CDT)
  • Re: AMBER: About TI with sander (Mon Jul 05 2004 - 10:31:23 CDT)
  • Re: AMBER: Namelist problem (Mon Jul 05 2004 - 10:21:12 CDT)
  • Re: AMBER: Problem to converge minimization (Mon Jul 05 2004 - 10:22:01 CDT)
  • Re: AMBER: question about antechamber program (Fri Jul 02 2004 - 15:26:12 CDT)
  • Re: AMBER: mm_pbsa problem (Fri Jul 02 2004 - 09:52:46 CDT)
  • Re: AMBER: peptide-DNA crosslink modeling (Fri Jul 02 2004 - 00:01:40 CDT)
  • Re: AMBER: tleap input file error (Thu Jul 01 2004 - 19:06:18 CDT)
  • Re: AMBER: N-terminal Arg charges in ff99 not 1.00 (Thu Jul 01 2004 - 14:17:52 CDT)
  • Re: AMBER: Questions about pert.charge and atom type change. (Wed Jun 30 2004 - 20:10:02 CDT)
  • Re: AMBER: Problems with processing SYBYL-Tripos pdb files in LEAP (Wed Jun 30 2004 - 12:50:41 CDT)
  • Re: AMBER: problems in using glycam (Wed Jun 30 2004 - 10:03:07 CDT)
  • Re: AMBER: Amber 8 installation error (Tue Jun 29 2004 - 18:55:18 CDT)
  • Re: AMBER: Atom Labels (Tue Jun 29 2004 - 15:54:37 CDT)
  • Re: AMBER: Question about dummy atoms (Tue Jun 29 2004 - 12:24:56 CDT)
  • Re: AMBER: About TI with sander (Tue Jun 29 2004 - 11:45:52 CDT)
  • Re: AMBER: Test run error in amber8 : IBM-AIX (Tue Jun 29 2004 - 10:00:58 CDT)
  • Re: AMBER: Amber 8 installation error (Tue Jun 29 2004 - 09:56:53 CDT)
  • Re: AMBER: question about building prmtop and inpcrd files in xleap (Mon Jun 28 2004 - 11:02:37 CDT)
  • Re: AMBER: Amber8 compilation in IBM-AIX (Mon Jun 28 2004 - 10:42:20 CDT)
  • Re: AMBER: (no subject) (Mon Jun 28 2004 - 01:12:26 CDT)
  • Re: AMBER: "Total vdw box size" information is gone (Sun Jun 27 2004 - 16:03:39 CDT)
  • Re: AMBER: AMBPDB command requires libcxa.so.5 (Sat Jun 26 2004 - 13:56:09 CDT)
  • Re: AMBER: -p4pg problem (Sat Jun 26 2004 - 13:54:03 CDT)
  • Re: AMBER: restraints error (Fri Jun 25 2004 - 14:26:56 CDT)
  • Re: AMBER: Amber 8 installation (Fri Jun 25 2004 - 14:15:50 CDT)
  • Re: AMBER: restraints error (Fri Jun 25 2004 - 12:32:48 CDT)
  • Re: AMBER: Born radii (Fri Jun 25 2004 - 10:36:20 CDT)
  • Re: RE: AMBER: Amber 8 installation (Fri Jun 25 2004 - 10:33:30 CDT)
  • Re: AMBER: Restrain or freeze molecule question? (Thu Jun 24 2004 - 10:24:37 CDT)
  • Re: AMBER: MD & running time (Wed Jun 23 2004 - 16:02:45 CDT)
  • Re: AMBER: GB parameters for Calcium (Wed Jun 23 2004 - 13:10:23 CDT)
  • Re: AMBER: Problems in Amber MPI version (64 bits machine) (Wed Jun 23 2004 - 12:58:07 CDT)
  • Re: AMBER: Box range in vacuum when restart MD (Wed Jun 23 2004 - 11:06:29 CDT)
  • Re: AMBER: Problems in Amber MPI version (64 bits machine) (Tue Jun 22 2004 - 19:31:25 CDT)
  • Re: AMBER: nmanal problem (Mon Jun 21 2004 - 10:51:59 CDT)
  • Re: AMBER: leap.log warnings (Mon Jun 21 2004 - 10:43:07 CDT)
  • Re: AMBER: solvate proteins in xleap/amber8 (Mon Jun 21 2004 - 10:42:47 CDT)
  • Re: AMBER: Changing MAXPR in Amber 8? (Fri Jun 18 2004 - 15:34:43 CDT)
  • Re: AMBER: The first and second derivatives (Fri Jun 18 2004 - 15:25:29 CDT)
  • Re: AMBER: Could not assign parameters (Fri Jun 18 2004 - 14:04:57 CDT)
  • Re: AMBER: Deeper problem with the energetics of the system (Fri Jun 18 2004 - 13:20:20 CDT)
  • Re: AMBER: The first and second derivatives (Fri Jun 18 2004 - 13:18:34 CDT)
  • Re: AMBER: Using gibbs to calculate free energy (Fri Jun 18 2004 - 10:14:55 CDT)
  • Re: AMBER: Nmode (Thu Jun 17 2004 - 10:14:26 CDT)
  • Re: AMBER: Nmode (Wed Jun 16 2004 - 23:20:10 CDT)
  • Re: AMBER: problems with extra points (Wed Jun 16 2004 - 13:50:05 CDT)
  • Re: AMBER: binary files (Wed Jun 16 2004 - 09:44:39 CDT)
  • Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander (Wed Jun 16 2004 - 09:40:32 CDT)
  • Re: AMBER: DENSITY in constant pressure MD (Tue Jun 15 2004 - 17:50:57 CDT)
  • Re: AMBER: The parallel problem for umbrella sampling in Amber 8 (Tue Jun 15 2004 - 17:55:20 CDT)
  • Re: AMBER: Core Dump ERROR When Using TIP4P (Tue Jun 15 2004 - 17:28:36 CDT)
  • Re: AMBER: About umbrella sampling in Amber 8 (Tue Jun 15 2004 - 11:05:59 CDT)
  • Re: AMBER: Config file for installing Amber 8 on PC with Windows XP (Mon Jun 14 2004 - 20:01:57 CDT)
  • Re: AMBER: Improper Torsional Parameters (Mon Jun 14 2004 - 16:20:21 CDT)
  • Re: AMBER: parmcal problem (Fri Jun 11 2004 - 17:37:53 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Fri Jun 11 2004 - 10:00:13 CDT)
  • Re: AMBER: Core Dump ERROR When Using TIP4P (Fri Jun 11 2004 - 09:08:18 CDT)
  • Re: AMBER: old trajectory file (amber6) to new trajectory file ? (Wed Jun 09 2004 - 21:16:26 CDT)
  • Re: AMBER: Calcium and GB (Wed Jun 09 2004 - 21:10:26 CDT)
  • Re: AMBER: Amber Transition State Output (Wed Jun 09 2004 - 20:54:23 CDT)
  • Re: AMBER: Amber Transition State Output (Wed Jun 09 2004 - 17:55:14 CDT)
  • Re: AMBER: xleap solvatebox problem (Wed Jun 09 2004 - 17:51:06 CDT)
  • Re: AMBER: Constant Pressure Problem of MD (Mon Jun 07 2004 - 21:12:41 CDT)
  • Re: AMBER: gibbs in amber8 (Sat Jun 05 2004 - 22:33:37 CDT)
  • Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? (Fri Jun 04 2004 - 08:00:47 CDT)
  • Re: AMBER: amber8 compile on Lemieux (Thu Jun 03 2004 - 21:39:58 CDT)
  • Re: AMBER: Simulated anealling (Thu Jun 03 2004 - 21:34:17 CDT)
  • Re: AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid (Thu Jun 03 2004 - 21:31:06 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 17:02:07 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Wed Jun 02 2004 - 13:41:56 CDT)
  • Re: AMBER: sander of AMBER 8 doesn't work (Wed Jun 02 2004 - 09:47:20 CDT)
  • Re: AMBER: Free energy in Amber8 (Wed Jun 02 2004 - 09:35:24 CDT)
  • Re: [pradipta_b@mail.jnu.ac.in: AMBER: Software to visualize normal modes!] (Tue Jun 01 2004 - 18:24:54 CDT)
  • Re: AMBER: sander8 performance (Tue Jun 01 2004 - 15:15:50 CDT)
  • Re: AMBER: Amber7: pdb format file (Tue Jun 01 2004 - 14:23:47 CDT)
  • Re: AMBER: sander8 performance (Tue Jun 01 2004 - 14:22:29 CDT)
  • Re: AMBER: Heme parameters (Tue Jun 01 2004 - 14:20:56 CDT)
  • Re: AMBER: Free energy in Amber8 (Tue Jun 01 2004 - 14:17:34 CDT)
  • Re: AMBER: Amber force field for protein-DNA system (Tue Jun 01 2004 - 13:40:15 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 12:33:08 CDT)
  • Re: AMBER: program compatibility (Mon May 31 2004 - 00:05:15 CDT)
  • Re: AMBER: question about NMODE for RNA (Sun May 30 2004 - 18:14:33 CDT)
  • Re: AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file (Fri May 28 2004 - 16:34:45 CDT)
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 13:43:23 CDT)
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 11:52:56 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 18:47:49 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 18:15:37 CDT)
  • Re: AMBER: types of water atom (Thu May 27 2004 - 15:34:59 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Thu May 27 2004 - 13:24:27 CDT)
  • Re: AMBER: xleap solvatebox problem (Thu May 27 2004 - 10:42:48 CDT)
  • Re: AMBER: amber 8 under windows XP (Thu May 27 2004 - 10:34:50 CDT)
  • Re: AMBER: Cannot read in sander (Thu May 27 2004 - 10:11:03 CDT)
  • Re: AMBER: amber 8 under windows XP (Wed May 26 2004 - 15:07:05 CDT)
  • Re: AMBER: A problem for compiling amber8 parallel version (Wed May 26 2004 - 12:08:43 CDT)
  • Re: AMBER: Scaling nb between groups (Tue May 25 2004 - 15:52:30 CDT)
  • Re: AMBER: protein is out of the water box (Wed May 26 2004 - 11:17:00 CDT)
  • Re: AMBER: Cannot read in sander (Wed May 26 2004 - 11:14:52 CDT)
  • Re: AMBER: IOUTFM and binary/unformatted files error (Tue May 25 2004 - 10:01:28 CDT)
  • Re: AMBER: mm_pbsa energy decomposition error (Tue May 25 2004 - 10:20:13 CDT)
  • Re: AMBER: segmentation fault when running parmchk (Mon May 24 2004 - 23:41:14 CDT)
  • Re: AMBER: Free energies using Sander in Amber8 (Mon May 24 2004 - 23:36:22 CDT)
  • Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Mon May 24 2004 - 10:37:29 CDT)
  • Re: AMBER: NHE problem (Sun May 23 2004 - 11:14:34 CDT)
  • Re: AMBER: IGR1/grnam1 problem (Sat May 22 2004 - 23:03:16 CDT)
  • Re: AMBER: NHE problem (Sat May 22 2004 - 18:55:52 CDT)
  • Re: AMBER: Problem compiling amber7 (Fri May 21 2004 - 10:23:09 CDT)
  • Re: AMBER: pbsa calculation on part of the molecule & nmode analysis (Thu May 20 2004 - 20:40:10 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 20:33:14 CDT)
  • Re: AMBER: SHAKE in thermodynamic integration (Thu May 20 2004 - 13:01:17 CDT)
  • Re: AMBER: DEBUG and GB (Thu May 20 2004 - 13:34:38 CDT)
  • Re: AMBER: instalation of RES (Thu May 20 2004 - 12:15:35 CDT)
  • Re: AMBER: (Thu May 20 2004 - 12:14:13 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 10:22:26 CDT)
  • Re: AMBER: Does this warning matter? (about improper torsion parameters) (Wed May 19 2004 - 10:00:59 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 17:47:26 CDT)
  • Re: AMBER: NTT=4 (Tue May 18 2004 - 09:57:19 CDT)
  • Re: AMBER: Clean in RESP (Tue May 18 2004 - 09:55:42 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 18:21:15 CDT)
  • Re: AMBER: sander_classic for cap simulations? (Mon May 17 2004 - 15:18:41 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Mon May 17 2004 - 14:36:41 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Mon May 17 2004 - 14:31:38 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Mon May 17 2004 - 14:27:30 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Sat May 15 2004 - 11:14:06 CDT)
  • Re: AMBER: install RESP (Sat May 15 2004 - 11:03:57 CDT)
  • Re: AMBER: antechamber (Sat May 15 2004 - 11:02:30 CDT)
  • Re: AMBER: solvents reference. (Fri May 14 2004 - 15:16:06 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Fri May 14 2004 - 14:20:24 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Thu May 13 2004 - 13:41:18 CDT)
  • Re: AMBER: dummy atom other than H (Wed May 12 2004 - 14:30:26 CDT)
  • Re: AMBER: shake option in sander (Wed May 12 2004 - 14:11:53 CDT)
  • Re: AMBER: MD with NTR + NMROPT (Wed May 12 2004 - 14:09:24 CDT)
  • Re: AMBER: ptraj and LES (Wed May 12 2004 - 10:19:00 CDT)
  • Re: AMBER: what does EAMBER stand for? (Tue May 11 2004 - 12:30:56 CDT)
  • Re: AMBER: some bugfixes (Mon May 10 2004 - 18:10:08 CDT)
  • Re: AMBER: MD with NTR + NMROPT (Mon May 10 2004 - 10:46:06 CDT)
  • Re: AMBER: Solvent accessible surface area(LCPO) computation (Fri May 07 2004 - 10:23:33 CDT)
  • Re: AMBER: solvent cap and eedmeth (Fri May 07 2004 - 10:20:18 CDT)
  • Re: AMBER: Opteron PMEMD (Thu May 06 2004 - 17:09:47 CDT)
  • Re: AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 14:27:10 CDT)
  • Re: AMBER: Computing psec/day using Amber 8 (Thu May 06 2004 - 13:42:37 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Thu May 06 2004 - 10:29:30 CDT)
  • Re: AMBER: Sander klambda question (Wed May 05 2004 - 18:43:44 CDT)
  • Re: AMBER: How to choose force constant? (Wed May 05 2004 - 17:00:14 CDT)
  • Re: AMBER: H Bonds (Wed May 05 2004 - 11:20:26 CDT)
  • Re: AMBER: Implicit solvents (Wed May 05 2004 - 10:54:56 CDT)
  • Re: AMBER: Normal Mode Analysis possibility (Tue May 04 2004 - 13:25:27 CDT)
  • Re: AMBER: separate the longitudinal and transverse vibrations frequencies (Tue May 04 2004 - 13:15:38 CDT)
  • Re: AMBER: PMF correction factor (Tue May 04 2004 - 13:01:18 CDT)
  • Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 10:10:36 CDT)
  • AMBER: some bugfixes (Mon May 03 2004 - 13:10:47 CDT)
  • Re: AMBER: nmode analysis (Mon May 03 2004 - 12:14:19 CDT)
  • Re: AMBER: nmode analysis (Mon May 03 2004 - 10:50:44 CDT)
  • Re: Re: AMBER: xleap problem (Mon May 03 2004 - 10:45:34 CDT)
  • Re: AMBER: xleap problem (Sun May 02 2004 - 16:07:20 CDT)
  • Re: AMBER: Amber8 compilation error (Fri Apr 30 2004 - 13:31:57 CDT)
  • Re: AMBER: energy criteria. (Fri Apr 30 2004 - 10:36:13 CDT)
  • Re: AMBER: Angle Restraining (Fri Apr 30 2004 - 10:39:27 CDT)
  • Re: AMBER: just sander not run (Fri Apr 30 2004 - 10:34:47 CDT)
  • Re: AMBER: questions about NMODE (Thu Apr 29 2004 - 14:03:54 CDT)
  • Re: AMBER: Redhat install (Thu Apr 29 2004 - 12:32:33 CDT)
  • Re: AMBER: questions about NMODE (Wed Apr 28 2004 - 19:21:41 CDT)
  • Re: AMBER: questions about NMODE (Wed Apr 28 2004 - 17:24:34 CDT)
  • Re: AMBER: antechamber bcctype.c typo (Wed Apr 28 2004 - 16:42:11 CDT)
  • Re: AMBER: questions about NMODE (Wed Apr 28 2004 - 14:06:01 CDT)
  • Re: AMBER: %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of atoms (Wed Apr 28 2004 - 12:56:10 CDT)
  • Re: AMBER: question on simulated annealing (Wed Apr 28 2004 - 11:24:59 CDT)
  • Re: AMBER: AMBER Gibbs Memory problem (Tue Apr 27 2004 - 14:04:15 CDT)
  • Re: AMBER: xleap don't recognize formaldehyde? (Tue Apr 27 2004 - 13:56:30 CDT)
  • Re: AMBER: PMEMD and ifort 8 update (Tue Apr 27 2004 - 13:52:02 CDT)
  • Re: AMBER: Antechamber: problems with bcc correction (Sun Apr 25 2004 - 02:26:59 CDT)
  • Re: AMBER: NSNB parameter (Sat Apr 24 2004 - 15:13:11 CDT)
  • Re: AMBER: tutorial of Biotin/Streptavidin (Sat Apr 24 2004 - 15:08:00 CDT)
  • Re: AMBER: instalation of amber7 on SUN (Sat Apr 24 2004 - 13:00:40 CDT)
  • Re: AMBER: rdparm: a parameter array overflowed (Wed Apr 21 2004 - 12:15:16 CDT)
  • Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 10:57:26 CDT)
  • Re: AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 10:54:54 CDT)
  • Re: AMBER: Using pbsa (Tue Apr 20 2004 - 20:26:08 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Tue Apr 20 2004 - 16:50:42 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Tue Apr 20 2004 - 15:29:47 CDT)
  • Re: AMBER: nucgen generated RNA duplex: leap problems (Tue Apr 20 2004 - 13:26:17 CDT)
  • Re: AMBER: instalation of amber7 on SUN (Tue Apr 20 2004 - 13:14:58 CDT)
  • Re: AMBER: memory problem in NMODE (Mon Apr 19 2004 - 19:56:44 CDT)
  • Re: AMBER: memory problem in NMODE (Mon Apr 19 2004 - 16:54:34 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Mon Apr 19 2004 - 16:45:34 CDT)
  • Re: AMBER: xleap console message (Mon Apr 19 2004 - 11:40:46 CDT)
  • Re: AMBER: distance measurement in carnal and ptraj (Fri Apr 16 2004 - 10:46:04 CDT)
  • Re: AMBER: gibbs termination (Wed Apr 14 2004 - 20:24:10 CDT)
  • Re: AMBER: Time to minimize the energy by NMODE (Wed Apr 14 2004 - 17:54:10 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Wed Apr 14 2004 - 11:56:52 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Wed Apr 14 2004 - 10:36:52 CDT)
  • Re: AMBER: Amber 7 on SGI: Sander MPI problem (Tue Apr 13 2004 - 19:37:04 CDT)
  • Re: AMBER: water hole (Mon Apr 12 2004 - 19:13:37 CDT)
  • Re: AMBER: XLeap: head/tail and frcmod (Mon Apr 12 2004 - 10:15:29 CDT)
  • Re: AMBER: equilibration does not start with SHAKE (Fri Apr 09 2004 - 18:16:09 CDT)
  • Re: AMBER: NMODE (Fri Apr 09 2004 - 17:46:35 CDT)
  • Re: AMBER: warning about improper dihedral in leap!! (Thu Apr 08 2004 - 10:09:11 CDT)
  • Re: AMBER: error in antechamber (Thu Apr 08 2004 - 09:58:42 CDT)
  • Re: AMBER: respgen (Wed Apr 07 2004 - 20:20:36 CDT)
  • Re: AMBER: Ti of CH3 -> NH2 (Wed Apr 07 2004 - 20:17:30 CDT)
  • Re: AMBER: error in antechamber (Wed Apr 07 2004 - 10:27:43 CDT)
  • Re: AMBER: ANAL: how can i buld the anal.in file? (Wed Apr 07 2004 - 10:21:53 CDT)
  • Re: AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly? (Wed Apr 07 2004 - 10:19:27 CDT)
  • Re: AMBER: more vlimit exceeded problems... (Wed Apr 07 2004 - 10:06:31 CDT)
  • Re: AMBER: free energy perturbation (Tue Apr 06 2004 - 20:26:37 CDT)
  • Re: AMBER: Question on Amber7... (Tue Apr 06 2004 - 19:25:37 CDT)
  • Re: AMBER: new leap with old gibbs (Tue Apr 06 2004 - 19:13:57 CDT)
  • Re: AMBER: new leap with old gibbs (Tue Apr 06 2004 - 16:31:10 CDT)
  • Re: AMBER: minimization of GLH (Mon Apr 05 2004 - 12:06:39 CDT)
  • Re: AMBER: Antechamber compilation error (Mon Apr 05 2004 - 12:12:05 CDT)
  • Re: AMBER: minimization of GLH (Mon Apr 05 2004 - 10:26:27 CDT)
  • Re: AMBER: AMBER 7 Installation (Fri Apr 02 2004 - 19:37:57 CST)
  • Re: AMBER: sander + ew_legal.h (Fri Apr 02 2004 - 19:34:32 CST)
  • Re: AMBER: installing amber8 on a dual processor single box (Fri Apr 02 2004 - 13:39:24 CST)
  • Re: AMBER: Alignment tensor for Sander RDCs (Fri Apr 02 2004 - 11:46:24 CST)
  • Re: AMBER: Question on Amber7... (Thu Apr 01 2004 - 19:33:30 CST)
  • Re: AMBER: test output of amber8 (Wed Mar 31 2004 - 19:37:50 CST)
  • Re: AMBER: GIBBS: FEP and TI (Wed Mar 31 2004 - 13:07:17 CST)
  • Re: AMBER: Bad atom symbol, K+ and IB in vacuum (Wed Mar 31 2004 - 12:38:47 CST)
  • Re: AMBER: segmentation fault when running parmchk (Wed Mar 31 2004 - 11:50:54 CST)
  • Re: AMBER: solvation energy (Sun Mar 28 2004 - 23:15:25 CST)
  • Re: AMBER: Error while protonating a PDB file (Sat Mar 27 2004 - 16:46:43 CST)
  • Re: AMBER: erreo in sander (Sat Mar 27 2004 - 03:13:20 CST)
  • Re: Fwd: Re: AMBER: Pang-model of Zn2+ (Fri Mar 26 2004 - 16:18:35 CST)
  • Re: AMBER: (Fri Mar 26 2004 - 15:41:32 CST)
  • Re: AMBER: How to compile antechamber? (Fri Mar 26 2004 - 11:56:10 CST)
  • Re: AMBER: Error while protonating a PDB file (Thu Mar 25 2004 - 19:34:43 CST)
  • Re: AMBER: eedmeth (Thu Mar 25 2004 - 18:46:44 CST)
  • Re: AMBER: undefined loops and protonate (Thu Mar 25 2004 - 18:37:47 CST)
  • Re: AMBER: Antechamber MOPAC (Thu Mar 25 2004 - 18:34:53 CST)
  • Re: AMBER: [Fwd: KLAMBDA in amber7] (Wed Mar 24 2004 - 19:38:10 CST)
  • AMBER: antechamber download files should now be available (Wed Mar 24 2004 - 17:05:19 CST)
  • Re: AMBER: langevin dynamics (Tue Mar 23 2004 - 16:33:01 CST)
  • Re: AMBER: Assignment of parameters, missing parameters (Tue Mar 23 2004 - 16:28:59 CST)
  • Re: AMBER: downloading antechamber (Tue Mar 23 2004 - 16:20:34 CST)
  • Re: AMBER: M7G parameters (Tue Mar 23 2004 - 16:16:24 CST)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 14:15:39 CST)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 10:14:29 CST)
  • Re: AMBER: segmentation fault (Thu Mar 18 2004 - 10:19:04 CST)
  • Re: AMBER: segmentation fault when convert pdb to mol2 (Thu Mar 18 2004 - 10:13:42 CST)
  • Re: AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8 (Wed Mar 17 2004 - 13:26:00 CST)
  • Re: AMBER: Preparing complex in Xleap for Amber calculations (Wed Mar 17 2004 - 10:39:27 CST)
  • Re: AMBER: protein-protein interaction (Wed Mar 17 2004 - 10:37:40 CST)
  • Re: AMBER: MD problem. (Wed Mar 17 2004 - 10:36:04 CST)
  • Re: AMBER: rdparm/ptraj writeparm + leap problem (Wed Mar 17 2004 - 10:33:34 CST)
  • Re: AMBER: description of toplogy file format? (Tue Mar 16 2004 - 19:57:26 CST)
  • Re: AMBER: AMBER6 manual (Tue Mar 16 2004 - 15:30:52 CST)
  • Re: AMBER: antechamber/mopac question (Mon Mar 15 2004 - 19:56:51 CST)
  • Re: AMBER: new wed site for amber tutorials (Mon Mar 15 2004 - 09:35:16 CST)
  • AMBER: Release announcement for Amber 8 (Mon Mar 15 2004 - 00:39:25 CST)
  • Re: AMBER: Resizing sizes.h and recompiling problem! (Sat Mar 13 2004 - 12:03:39 CST)
  • Re: AMBER: recovering total force array (Fri Mar 12 2004 - 11:13:57 CST)
  • Re: AMBER: residue insertion (Thu Mar 11 2004 - 01:00:39 CST)
  • Re: AMBER: Residue question (Wed Mar 10 2004 - 10:10:11 CST)
  • Re: AMBER: Ewald calculation using PME for charged system (Wed Mar 10 2004 - 02:11:54 CST)
  • Re: AMBER: what's the meaning of parameter NRUN (Wed Mar 10 2004 - 00:31:33 CST)
  • Re: AMBER: Ewald calculation using PME for charged system (Tue Mar 09 2004 - 16:58:29 CST)
  • Re: AMBER: what's the meaning of parameter NRUN (Tue Mar 09 2004 - 09:23:56 CST)
  • Re: AMBER: antechamber prepin (Mon Mar 08 2004 - 00:49:48 CST)
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 19:43:19 CST)
  • Re: AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite (Fri Mar 05 2004 - 12:20:26 CST)
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 10:23:27 CST)
  • Re: AMBER: conversion of Amber 7 .pdb file to .bgf file (Fri Mar 05 2004 - 10:16:19 CST)
  • Re: AMBER: conversion of Amber 7 .pdb file to .bgf file (Thu Mar 04 2004 - 16:59:21 CST)
  • Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file (Thu Mar 04 2004 - 10:47:10 CST)
  • Re: AMBER: Leap atom removal bug? (Thu Mar 04 2004 - 10:00:08 CST)
  • Re: AMBER: General Questions (Wed Mar 03 2004 - 07:22:14 CST)
  • Re: AMBER: How to use tleap convert *.pdb file to *.crd and *.top files (Tue Mar 02 2004 - 13:53:31 CST)
  • Re: AMBER: A question about RMSD calculation (Tue Mar 02 2004 - 13:52:05 CST)
  • Re: AMBER: error in minimization (Tue Mar 02 2004 - 13:41:36 CST)
  • Re: AMBER: sander + vlimit exceed... (Mon Mar 01 2004 - 08:50:23 CST)
  • Re: AMBER: size.h error (Thu Feb 26 2004 - 16:48:29 CST)
  • Re: AMBER: averaged structure with unknown elements (Wed Feb 25 2004 - 16:15:25 CST)
  • Re: AMBER: NMR restraints-Floating point exception (Wed Feb 25 2004 - 10:17:46 CST)
  • Re: AMBER: add Na+ (Tue Feb 24 2004 - 13:35:06 CST)
  • Re: AMBER: problem with frcmod file (Mon Feb 23 2004 - 16:43:59 CST)
  • Re: AMBER: how to use prep file (Mon Feb 23 2004 - 14:19:30 CST)
  • Re: AMBER: LCPO parameters in gbsa (Mon Feb 23 2004 - 12:51:46 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 10:49:58 CST)
  • Re: AMBER: How to add ACE and NME groups? (Mon Feb 23 2004 - 10:47:05 CST)
  • Re: AMBER: sander output (Thu Feb 19 2004 - 23:54:32 CST)
  • Re: AMBER: prep files for modified bases (Thu Feb 19 2004 - 14:23:41 CST)
  • Re: AMBER: compiling software(RESP) on MAC G5 (Thu Feb 19 2004 - 14:21:39 CST)
  • Re: AMBER: Close contact warnings (Thu Feb 19 2004 - 10:30:15 CST)
  • Re: AMBER: pmf calculation using gibbs. (Thu Feb 19 2004 - 10:27:33 CST)
  • Re: AMBER: pmf calculation using gibbs. (Wed Feb 18 2004 - 22:45:57 CST)
  • Re: AMBER: MD simulations with 2 molecules (Wed Feb 18 2004 - 16:15:04 CST)
  • Re: AMBER: sander + ewald bomb (Wed Feb 18 2004 - 16:00:40 CST)
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 13:34:24 CST)
  • Re: AMBER: histidine and its various forms (Wed Feb 18 2004 - 09:58:44 CST)
  • Re: AMBER: Close contact warnings (Tue Feb 17 2004 - 12:37:06 CST)
  • Re: AMBER: Close contact warnings (Tue Feb 17 2004 - 10:39:22 CST)
  • Re: AMBER: saveamberparm warning in leap? (Mon Feb 16 2004 - 19:04:17 CST)
  • AMBER: multiple messages on the amber reflector (Mon Feb 16 2004 - 17:33:40 CST)
  • Re: AMBER: TIP4P extended (Mon Feb 16 2004 - 11:37:32 CST)
  • Re: AMBER: TIP4P (Mon Feb 16 2004 - 10:36:37 CST)
  • Re: AMBER: SIGSEGV (Mon Feb 16 2004 - 10:30:18 CST)
  • Re: AMBER: minimizating complex-protein with AMBER (Sun Feb 15 2004 - 23:14:02 CST)
  • Re: AMBER: problem with tleap in Amber (Sun Feb 15 2004 - 23:10:31 CST)
  • Re: AMBER: neutrality of charge in AMBER 7 (Sat Feb 14 2004 - 14:10:22 CST)
  • Re: AMBER: MM-PBSA: molecular charges and active site water (Thu Feb 12 2004 - 22:06:56 CST)
  • Re: AMBER: TER in amber (Thu Feb 12 2004 - 10:56:45 CST)
  • Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function (Thu Feb 12 2004 - 10:41:16 CST)
  • Re: AMBER: GBSA frequency update (Thu Feb 12 2004 - 00:09:34 CST)
  • Re: AMBER: atom type for GBSA (Wed Feb 11 2004 - 11:33:04 CST)
  • Re: AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. (Tue Feb 10 2004 - 17:54:45 CST)
  • Re: AMBER: minimization output (Tue Feb 10 2004 - 15:05:59 CST)
  • Re: AMBER: Temperature in Nmode (Tue Feb 10 2004 - 10:42:06 CST)
  • Re: AMBER: Nmode convergence (Tue Feb 10 2004 - 10:34:17 CST)
  • Re: AMBER: antechamber + FAILED TO ACHIEVE SCF (Mon Feb 09 2004 - 16:17:49 CST)
  • Re: AMBER: antechamber error (Mon Feb 09 2004 - 10:22:07 CST)
  • Re: AMBER: antechamber + mopac + MAXIMUM NUMBER OF ATOMIC ORBITALS EXCEEDED (Sat Feb 07 2004 - 10:33:48 CST)
  • Re: Fwd: Re: AMBER: Lattice structures in xleap (Fri Feb 06 2004 - 15:54:07 CST)
  • Re: AMBER: ptraj and dipoles (Fri Feb 06 2004 - 01:11:50 CST)
  • Re: AMBER: MCSS (Fri Feb 06 2004 - 01:12:47 CST)
  • Re: AMBER: PMEMD and nmropt=1 (Thu Feb 05 2004 - 19:29:41 CST)
  • Re: AMBER: antechamber error in test / differences in prmtop files (Thu Feb 05 2004 - 15:11:53 CST)
  • Re: AMBER: cell dimensions (Thu Feb 05 2004 - 12:00:41 CST)
  • Re: AMBER: TI, angle parameters for nitrogen, frcmod (Thu Feb 05 2004 - 11:51:39 CST)
  • Re: AMBER: xleap & antechamber (Thu Feb 05 2004 - 11:46:02 CST)
  • Re: AMBER: Re: ANAL problem (Thu Feb 05 2004 - 11:36:05 CST)
  • Re: AMBER: antechamber + mopac error (Thu Feb 05 2004 - 11:21:11 CST)
  • Re: AMBER: NMODE for protein via MM-PBSA-cntd (Wed Feb 04 2004 - 10:32:37 CST)
  • Re: AMBER: leap - orientation of sequenced residues (Tue Feb 03 2004 - 11:44:50 CST)
  • Re: AMBER: What does this error message mean? (Tue Feb 03 2004 - 10:12:48 CST)
  • Re: AMBER: ANAL problem. (Mon Feb 02 2004 - 12:51:02 CST)
  • Re: AMBER: LEaP- Error reading frcmod parameters. (Mon Feb 02 2004 - 12:20:43 CST)
  • Re: AMBER: DNA (Mon Feb 02 2004 - 10:58:26 CST)
  • Re: AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 13:02:01 CST)
  • Re: AMBER: (No subject) (Thu Jan 29 2004 - 22:20:43 CST)
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Thu Jan 29 2004 - 21:59:24 CST)
  • Re: AMBER: SANDER - Abnormal high velocities (Wed Jan 28 2004 - 10:31:18 CST)
  • Re: AMBER: installation test question (antechamber, ash) (Mon Jan 26 2004 - 14:24:26 CST)
  • Re: FW: AMBER: Segmentation fault (core dumped) error of antechamber program (Mon Jan 26 2004 - 12:26:38 CST)
  • Re: AMBER: how to correctly change frcmod? (Sun Jan 25 2004 - 19:17:47 CST)
  • Re: AMBER: Fwd: NVE & polarizable force field] (Sat Jan 24 2004 - 19:18:45 CST)
  • Re: AMBER: Problem using GLYCAM with sander (Fri Jan 23 2004 - 15:41:22 CST)
  • Re: AMBER: Segmentation fault (core dumped) error of antechamber program (Thu Jan 22 2004 - 19:21:40 CST)
  • Re: AMBER: remove rotational motion (Thu Jan 22 2004 - 19:21:03 CST)
  • Re: AMBER: crystal lattice determination (Thu Jan 22 2004 - 19:20:42 CST)
  • Re: AMBER: antechamber and mopac5010mn (Wed Jan 21 2004 - 10:41:53 CST)
  • Re: AMBER: PDB files (Tue Jan 20 2004 - 17:12:04 CST)
  • Re: AMBER: Parm98 Vs 02 (Tue Jan 20 2004 - 17:08:57 CST)
  • Re: AMBER: restraint (Tue Jan 20 2004 - 17:05:59 CST)
  • Re: AMBER: GB and Atom Type (Tue Jan 20 2004 - 17:03:52 CST)
  • Re: AMBER: NTF (Fri Jan 16 2004 - 10:09:27 CST)
  • Re: AMBER: free energy profile calculation (Thu Jan 15 2004 - 10:32:17 CST)
  • Re: AMBER: disulfide bonds (Tue Jan 13 2004 - 12:57:25 CST)
  • Re: AMBER: error in minimization (Tue Jan 13 2004 - 10:48:50 CST)
  • Re: AMBER: disulfide bonds (Mon Jan 12 2004 - 19:54:48 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 14:14:22 CST)
  • Re: AMBER: Amber compilation in IBM-SP4 (Sat Jan 10 2004 - 12:43:06 CST)
  • Re: AMBER: running on Itanium machines (Fri Jan 09 2004 - 10:43:48 CST)
  • Re: AMBER: Vlimit problem (Thu Jan 08 2004 - 18:31:00 CST)
  • Re: AMBER: Minimiation (AMBER5/AMBER7) does not reach the tageted rmsd (Thu Jan 08 2004 - 18:15:12 CST)
  • Re: AMBER: Parameters for deuterium (Tue Jan 06 2004 - 10:32:14 CST)
  • Re: AMBER: Molecular Frame (Sat Jan 03 2004 - 09:51:13 CST)
  • Re: AMBER: Molecular Frame (Fri Jan 02 2004 - 10:22:10 CST)
• David E. Konerding
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 09:45:59 CST)
  • Re: AMBER: pmemd. (Mon Aug 16 2004 - 11:27:02 CDT)
  • Re: AMBER: Problems with CPU scaling on cluster (Fri Jul 16 2004 - 10:46:01 CDT)
  • Re: AMBER: understanding SANDER source code (Mon Mar 22 2004 - 10:15:49 CST)
  • Re: AMBER: segmentation fault in Leap (Thu Jan 22 2004 - 09:22:47 CST)
  • Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning (Wed Jan 07 2004 - 10:16:49 CST)
• David E. Konerding DSD Staff
  • Re: AMBER: MOIL-View question (Wed Jun 16 2004 - 17:30:47 CDT)
  • Re: AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH (Tue Apr 27 2004 - 17:11:33 CDT)
  • Re: AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD (Fri Apr 09 2004 - 17:41:57 CDT)
  • Re: AMBER: Intel fortran compiler and -static switch in older pmemd releases (Fri Apr 02 2004 - 15:21:11 CST)
• David LeBard
  • AMBER: Question about Xleap (Wed Oct 20 2004 - 17:28:28 CDT)
  • Re: AMBER: Question about Parallel Compilation (Wed Sep 22 2004 - 21:49:47 CDT)
  • AMBER: Question about Parallel Compilation (Tue Sep 21 2004 - 18:12:54 CDT)
• David Lomelin
  • Re: AMBER: Compiling using pgf90 (Wed Oct 06 2004 - 15:30:34 CDT)
  • AMBER: Compiling using pgf90 (Tue Oct 05 2004 - 20:33:22 CDT)
• David Smith
  • Re: AMBER: cluster analysis with ptraj in amber 8.0 (Tue Dec 21 2004 - 02:47:46 CST)
  • Re: AMBER: extracting energy from trajector? (Thu Dec 02 2004 - 15:30:59 CST)
  • Re: AMBER: ntt parameter (Thu Dec 02 2004 - 04:30:01 CST)
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 11:44:16 CST)
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 08:19:24 CST)
  • Re: AMBER: extracting energy from trajector? (Mon Nov 29 2004 - 11:39:30 CST)
  • Re: AMBER: extracting energy from trajector? (Mon Nov 29 2004 - 10:54:53 CST)
  • Re: AMBER: extracting energy from trajector? (Mon Nov 29 2004 - 07:04:52 CST)
  • Re: AMBER: extracting energy from trajector? (Mon Nov 29 2004 - 06:37:41 CST)
  • Re: AMBER: extracting energy from trajector? (Wed Nov 24 2004 - 13:29:34 CST)
  • Re: AMBER: free energy perturbation (Tue Apr 06 2004 - 10:45:06 CDT)
  • Re: AMBER: PMEMD COMPILATION REDHAT (Fri Mar 12 2004 - 07:55:13 CST)
  • Re: AMBER: pmf calculation using gibbs (Thu Feb 26 2004 - 02:57:02 CST)
  • Re: AMBER: free energy profile calculation (Thu Jan 15 2004 - 08:37:27 CST)
• david.evans_at_ulsop.ac.uk
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Tue Dec 14 2004 - 09:28:24 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Thu Dec 09 2004 - 10:15:52 CST)
  • Re: AMBER: Residue Loading Problem (Fri Dec 03 2004 - 03:41:13 CST)
  • Re: AMBER: nucgen problem (Thu Nov 25 2004 - 03:04:28 CST)
  • Re: AMBER: Problem with converting AMBER PREP to MOL2 (Tue Nov 23 2004 - 11:06:22 CST)
  • Re: AMBER: Problem with a single aminoacid as inhibitor (Wed Nov 17 2004 - 06:55:58 CST)
  • Re: AMBER: constructing a small colecule (Fri Nov 05 2004 - 03:53:07 CST)
  • Re: AMBER: about FEP (Tue Nov 02 2004 - 06:42:25 CST)
  • Re: AMBER: about FEP (Tue Nov 02 2004 - 05:28:44 CST)
  • Re: AMBER: MAXATOM failure in ANTECHAMBER (Fri Oct 08 2004 - 05:09:18 CDT)
  • AMBER: replica exchange with thermodynamic integration (Thu Sep 23 2004 - 06:18:44 CDT)
  • Re: AMBER: AMBER7 : Hybrid macromolecule (Mon Sep 13 2004 - 11:30:43 CDT)
  • Re: AMBER: Setting up thermodynamic integration (Wed Sep 01 2004 - 12:24:40 CDT)
  • AMBER: Setting up thermodynamic integration (Wed Sep 01 2004 - 09:31:10 CDT)
  • Re: AMBER: How to covalently bind a ligand to a residue? (Fri Aug 06 2004 - 03:22:17 CDT)
  • Re: AMBER: How to covalently bind a ligand to a residue? (Fri Aug 06 2004 - 03:11:39 CDT)
  • Re: AMBER: mm_pbsa problem (Fri Jul 02 2004 - 05:53:23 CDT)
  • AMBER: PARSE radius for P (Thu Jun 10 2004 - 12:59:30 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 11:32:18 CDT)
  • RE: AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 11:09:26 CDT)
  • AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 03:22:21 CDT)
  • Re: AMBER: MM_PBSA GB parameters (Thu Mar 25 2004 - 10:25:56 CST)
  • AMBER: MM_PBSA GB parameters (Thu Mar 25 2004 - 04:54:59 CST)
  • Re: AMBER: rdparm/ptraj writeparm + leap problem (Wed Mar 17 2004 - 10:50:16 CST)
  • Re: AMBER: rdparm/ptraj writeparm + leap problem (Wed Mar 17 2004 - 03:36:51 CST)
  • AMBER: rdparm/ptraj writeparm (Tue Mar 16 2004 - 02:57:16 CST)
  • Re: AMBER: Leap atom removal bug? (Thu Mar 04 2004 - 05:30:00 CST)
  • AMBER: Leap atom removal bug? (Thu Mar 04 2004 - 04:30:01 CST)
• Dawei Zhang
  • AMBER: mm-pbsa problem (Thu Oct 14 2004 - 09:36:03 CDT)
• Dawsonzhu_at_aol.com
  • AMBER: Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 17:03:46 CST)
  • AMBER: Re: AMBER: Temperature Regulation (Wed Jul 28 2004 - 19:44:56 CDT)
• Difei Wang
  • AMBER: old trajectory file (amber6) to new trajectory file ? (Mon Jun 07 2004 - 21:55:39 CDT)
  • AMBER: mm_pbsa test problem (Wed Jun 02 2004 - 10:54:40 CDT)
• ding
  • AMBER: single strand simulation (Tue Nov 09 2004 - 18:12:17 CST)
  • AMBER: Temp control (Fri Aug 13 2004 - 13:46:20 CDT)
• Do Anh Tuan
  • Re: AMBER: Amber 8 Installation - C compiler? (Thu Aug 12 2004 - 00:28:37 CDT)
  • AMBER: Program error in testing of Amber8 (Sat May 15 2004 - 23:16:44 CDT)
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 22:20:04 CST)
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 15:11:25 CST)
  • AMBER: How to remove Cl- ions (Fri Feb 06 2004 - 07:24:10 CST)
  • AMBER: How to remove Cl- ions (Fri Feb 06 2004 - 04:38:41 CST)
• Don Bashford
  • AMBER: Bug: ptraj adds spurious box information (Fri Aug 13 2004 - 15:27:54 CDT)
• Donald Thomas
  • Re: AMBER: process_mdout.perl (Tue Oct 12 2004 - 01:23:13 CDT)
• donna j
  • Re: AMBER: problem with frcmod file (Sun Feb 29 2004 - 13:43:24 CST)
  • Re: AMBER: problem with frcmod file (Thu Feb 26 2004 - 12:23:25 CST)
  • AMBER: problem with frcmod file (Mon Feb 23 2004 - 15:47:12 CST)
  • AMBER: problem with tleap in Amber (Sun Feb 15 2004 - 21:01:27 CST)
  • AMBER: problem with tleap in Amber (Sun Feb 15 2004 - 20:44:25 CST)
• Dr Gavin Seddon
  • AMBER: installing amber8 (Mon Aug 16 2004 - 04:20:20 CDT)
  • AMBER: installing amber 8 on 64 bit amd opteron (Wed Aug 11 2004 - 00:55:05 CDT)
• Dr. Noah Allen
  • AMBER: xfl90 and xlc "C" compiler (Sat Nov 27 2004 - 14:05:28 CST)
• Dr. Rainer Glaser
  • AMBER: unnatural base - RESP charges in ANTECHAMBER (Mon Jun 07 2004 - 19:12:56 CDT)
• Dr. Turgut Bastug
  • AMBER: perturb a water to a dummy water with shake (Mon Aug 09 2004 - 19:24:25 CDT)
• Dr. Yong Duan
  • Re: AMBER: all_amino03.in discrepancy (Mon Jun 21 2004 - 11:41:03 CDT)
  • Re: AMBER: energy conservation with GB !! (Sun May 16 2004 - 01:58:25 CDT)
  • Re: AMBER: why delete water molecule (Tue May 04 2004 - 09:40:57 CDT)
  • Re: Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 10:59:58 CDT)
  • Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 09:41:59 CDT)
  • Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 07:56:19 CDT)
  • Re: AMBER: Box of mixed solvant (Wed Feb 11 2004 - 00:09:28 CST)
  • Re: AMBER: adding ions to nucleic acids (Tue Feb 10 2004 - 23:54:58 CST)
  • Re: AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 11:27:41 CST)
  • Re: AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 10:48:55 CST)
  • Re: AMBER: B factors from simulation and from cryst (Mon Jan 26 2004 - 12:37:29 CST)
  • Re: AMBER: restrt (Thu Jan 22 2004 - 20:27:05 CST)
  • Re: AMBER: restrt (Thu Jan 22 2004 - 07:24:40 CST)
• echanco_at_uci.edu
  • AMBER: Weird compiling problem in Amber 8 (Mon Jul 19 2004 - 00:51:29 CDT)
• Ed Pate
  • AMBER: saving trajectory parameters (Sat Nov 27 2004 - 18:17:40 CST)
  • AMBER: Amber7 tleap problem (Sat Sep 04 2004 - 14:03:47 CDT)
• Edward Patrick Obrien
  • AMBER: Creating Parmtop files for NAMD (Tue Apr 13 2004 - 19:37:52 CDT)
• Elijah Gregory
  • Re: AMBER: RSM & ptraj (Sun Oct 31 2004 - 01:29:23 CDT)
  • Re: AMBER: Continued:No skew or curtosis when zero variance in moment (Tue Oct 26 2004 - 08:48:55 CDT)
  • Re: AMBER: Ptraj data (Tue Sep 21 2004 - 17:04:45 CDT)
  • Re: AMBER: question about covariance matrix from ptraj (Mon Aug 09 2004 - 15:00:06 CDT)
• Emmanuel Giudice
  • AMBER: AMBER8 parallel job (Mon Nov 15 2004 - 01:39:50 CST)
  • AMBER: size.h error (Thu Feb 26 2004 - 15:15:20 CST)
• Eric Hu
  • AMBER: cluster analysis with ptraj in amber 8.0 (Mon Dec 20 2004 - 20:01:26 CST)
  • Re: AMBER: build a cyclic peptide (Wed Nov 24 2004 - 14:11:18 CST)
  • Re: AMBER: build a cyclic peptide (Wed Nov 24 2004 - 12:26:44 CST)
  • Re: AMBER: cannot load frcmod file properly (Wed Nov 24 2004 - 12:28:02 CST)
  • AMBER: build a cyclic peptide (Tue Nov 23 2004 - 19:34:13 CST)
  • AMBER: cannot load frcmod file properly (Tue Nov 23 2004 - 17:10:17 CST)
  • Re: AMBER: questions on dummy atom types in FEP setup (Mon Nov 22 2004 - 20:22:45 CST)
  • AMBER: questions on dummy atom types in FEP setup (Mon Nov 22 2004 - 15:37:54 CST)
  • AMBER: crosslink a residue with a small molecule (Wed Jan 21 2004 - 15:41:08 CST)
• Fabian Boes
  • Re: AMBER: ptraj hbond memory allocation on opteron (Tue Dec 14 2004 - 08:33:42 CST)
  • AMBER: ptraj hbond memory allocation on opteron (Mon Dec 13 2004 - 06:07:11 CST)
  • AMBER: ptraj and clustering (Fri Oct 15 2004 - 03:15:51 CDT)
  • AMBER: factor used in b-factor calculation (Tue Mar 09 2004 - 02:12:11 CST)
• Fajar Rakhman Wibowo
  • AMBER: Parameter for chlorophyll (Tue Oct 12 2004 - 05:46:27 CDT)
• Fang, Jianwen
  • AMBER: mm_pbsa nmode problem (Fri Sep 17 2004 - 17:28:47 CDT)
  • RE: AMBER: questions on mm_pbsa (Fri Jun 11 2004 - 09:59:18 CDT)
  • AMBER: mm_pbsa.pl question (Thu Jun 03 2004 - 12:14:29 CDT)
  • AMBER: mm_pbsa energy decomposition error (Tue May 25 2004 - 09:40:32 CDT)
  • AMBER: why EGB = nan (Mon May 17 2004 - 09:54:44 CDT)
  • AMBER: questions on mm_pbsa (Fri May 14 2004 - 13:49:54 CDT)
  • AMBER: ions in mm_pbsa (Thu May 06 2004 - 10:30:12 CDT)
  • AMBER: mm_pbsa question: MAXAT=10000 exceeded (Wed Apr 28 2004 - 23:48:09 CDT)
  • AMBER: gibbs error (Tue Mar 23 2004 - 10:27:22 CST)
  • AMBER: how to use prep file (Mon Feb 23 2004 - 13:15:19 CST)
  • RE: AMBER: antechamber error (Mon Feb 09 2004 - 12:00:28 CST)
  • AMBER: Suse AMD64 cluster installation (Mon Jan 26 2004 - 12:49:54 CST)
• fangyu liang
  • AMBER: How is optimization done during energy minimization of the force field? (Thu Dec 30 2004 - 23:11:28 CST)
  • Re: AMBER: Amber 8 Installation - C compiler? (Wed Aug 11 2004 - 19:23:03 CDT)
  • Re: AMBER: Problem: Installing Amber8 on PC with Windows XP (Tue Aug 03 2004 - 16:47:08 CDT)
  • Re: AMBER: Weird compiling problem in Amber 8 (Mon Jul 19 2004 - 01:30:22 CDT)
  • Re: RE: AMBER: Amber 8 installation (Fri Jun 25 2004 - 02:34:45 CDT)
  • Re: AMBER: Setup for parallel computing (Sat Jul 10 2004 - 18:10:19 CDT)
  • AMBER: Setup for parallel computing (Fri Jul 09 2004 - 12:00:32 CDT)
  • Re: AMBER: best PC laptop system to run Amber 8 (Mon Jul 05 2004 - 00:04:41 CDT)
  • AMBER: best PC laptop system to run Amber 8 (Sat Jul 03 2004 - 16:05:35 CDT)
  • AMBER: tleap input file error (Thu Jul 01 2004 - 18:26:18 CDT)
  • AMBER: no 'water.lib' in /amber8/dat/leap/ (Thu Jul 01 2004 - 15:21:50 CDT)
  • Re: AMBER: Amber 8 installation error (Thu Jul 01 2004 - 02:53:21 CDT)
  • Re: AMBER: Amber 8 installation error (Tue Jun 29 2004 - 17:52:29 CDT)
  • Re: AMBER: Amber 8 installation error (Tue Jun 29 2004 - 17:31:28 CDT)
  • AMBER: Amber 8 installation error (Tue Jun 29 2004 - 02:00:32 CDT)
  • RE: AMBER: Amber 8 installation (Fri Jun 25 2004 - 13:03:06 CDT)
  • AMBER: Amber 8 installation (Thu Jun 24 2004 - 17:24:43 CDT)
  • AMBER: Config file for installing Amber 8 on PC with Windows XP (Mon Jun 14 2004 - 18:21:07 CDT)
• Feng, Hanqiao (NIH/NCI)
  • RE: AMBER: sander of AMBER 8 doesn't work (Wed Jun 02 2004 - 07:45:01 CDT)
  • AMBER: sander of AMBER 8 doesn't work (Tue Jun 01 2004 - 13:39:56 CDT)
  • AMBER: protein is out of the water box (Tue May 25 2004 - 17:35:01 CDT)
• Fernandez-Carmona Juan
  • Re: AMBER: reference with ptraj (Fri May 07 2004 - 01:27:53 CDT)
• ferranna_at_unimore.it
  • AMBER: fluorine in mmpbsa (Wed Mar 24 2004 - 03:49:27 CST)
• Filip Lankas
  • AMBER: NEC and Regatta (Mon Jun 28 2004 - 06:47:26 CDT)
• florent.barbault
  • RE: AMBER: A few questions in the protein unfolding simulations using GB model (Wed Jan 28 2004 - 06:38:13 CST)
• Florian Barth
  • AMBER: pmemd problems (Fri Aug 13 2004 - 13:52:22 CDT)
  • Re: AMBER: pka calculation (Sat Feb 28 2004 - 09:46:04 CST)
  • Re: AMBER: ambpdb in AMBER7 (Mon Jan 26 2004 - 13:23:36 CST)
• franck
  • AMBER: radial distribution (Mon Mar 29 2004 - 07:20:48 CST)
• Furse, Kristina Elisabet
  • Re: AMBER: Residue Loading Problem (Fri Dec 03 2004 - 01:23:05 CST)
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 17:32:28 CST)
  • Re: AMBER: combine crd files (Fri Nov 26 2004 - 17:42:09 CST)
  • Re: AMBER: Re: md.out & plot (Tue Nov 23 2004 - 22:37:21 CST)
  • Re: AMBER: Re: md.out & plot (Tue Nov 23 2004 - 22:29:37 CST)
  • Re: AMBER: building parameters with Amber (Wed Sep 22 2004 - 13:36:41 CDT)
  • Re: AMBER: md problem (Wed Sep 15 2004 - 14:53:23 CDT)
  • Re: AMBER: Pulling versus Distance Restraints (Wed Sep 01 2004 - 12:08:49 CDT)
  • Re: AMBER: how to deal with the initial structure? (Tue Aug 24 2004 - 14:29:39 CDT)
  • RE: AMBER: Sander : Vrand flag (Tue Aug 24 2004 - 13:47:38 CDT)
  • Re: AMBER: lib file (Fri Jul 30 2004 - 16:38:37 CDT)
  • Re: AMBER: user force (Thu Jul 22 2004 - 16:07:46 CDT)
  • Re: AMBER: torsion scan (Tue Jul 13 2004 - 12:37:35 CDT)
• FyD
  • Re: AMBER: Problem with computing Resp charges using RED (Wed Dec 29 2004 - 14:54:05 CST)
  • Re: AMBER: Why the charge is not an integer? (Sun Dec 12 2004 - 13:47:02 CST)
  • Re: AMBER: Babel (Mon Nov 15 2004 - 17:07:11 CST)
  • Re: AMBER: gaussian command line (Fri Nov 05 2004 - 14:02:45 CST)
  • Re: AMBER: ESPGEN problems to read G03 output files (Fri Nov 05 2004 - 13:56:52 CST)
  • Re: AMBER: basis set (Fri Nov 05 2004 - 13:55:06 CST)
  • Re: AMBER: solvation free energies using mmpbsa (Thu Oct 28 2004 - 12:33:34 CDT)
  • Re: AMBER: changepot & mol2 file (Fri Oct 15 2004 - 13:59:46 CDT)
  • Re: AMBER: About missing residues (Tue Oct 12 2004 - 00:27:58 CDT)
  • Re: AMBER: resp error message (Thu Sep 30 2004 - 11:54:33 CDT)
  • Re: AMBER: resp error message (Wed Sep 29 2004 - 15:54:12 CDT)
  • Re: AMBER: resp error message (Wed Sep 29 2004 - 14:55:26 CDT)
  • Re: AMBER: phosphoserine library component (Fri Sep 24 2004 - 12:10:40 CDT)
  • AMBER: RESP problem... (Mon Sep 20 2004 - 14:59:04 CDT)
  • Re: AMBER: R.E.D. II to Vlad (Wed Sep 15 2004 - 11:25:44 CDT)
  • Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases (Mon Sep 13 2004 - 16:59:11 CDT)
  • Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases (Fri Sep 10 2004 - 19:35:09 CDT)
  • Re: AMBER: Differences in RESP charges for G in RG and DG residues (Sat Sep 04 2004 - 05:12:33 CDT)
  • Re: AMBER: peoblemwith RED II (Sat Aug 28 2004 - 04:52:20 CDT)
  • Re: AMBER: peoblemwith RED II (Fri Aug 27 2004 - 05:02:37 CDT)
  • Re: AMBER: RESP charges in Fe+3 heme system (Thu Aug 26 2004 - 13:33:09 CDT)
  • Re: AMBER: RESP calculation with different multiplicities (Thu Aug 26 2004 - 13:09:18 CDT)
  • Re: AMBER: peoblemwith RED II (Thu Aug 26 2004 - 10:44:16 CDT)
  • Re: AMBER: RED fails to read g94 output (Sat Aug 14 2004 - 03:26:33 CDT)
  • Re: AMBER: RED fails to read g94 output (Sat Aug 14 2004 - 00:34:21 CDT)
  • Re: AMBER: Gaussian in RED (Sat Aug 14 2004 - 00:16:30 CDT)
  • Re: AMBER: RESP charge derivation (Wed Aug 11 2004 - 11:55:57 CDT)
  • AMBER: Re: RED II and changepot (Tue Aug 10 2004 - 13:35:05 CDT)
  • Re: AMBER: RESP partial charge calculation (Tue Aug 10 2004 - 12:46:16 CDT)
  • Re: AMBER: charge not zero (Wed Aug 04 2004 - 14:57:51 CDT)
  • Re: AMBER: charge not zero (Wed Aug 04 2004 - 13:23:13 CDT)
  • Re: AMBER: charge not zero (Tue Aug 03 2004 - 09:46:54 CDT)
  • AMBER: Re: Results from RED-II beta (Sun Jul 18 2004 - 11:11:41 CDT)
  • AMBER: X-CA-CT-X dih. FF param ? (Fri Jul 16 2004 - 12:08:26 CDT)
  • RE: AMBER: (no subject) (Wed Jul 14 2004 - 14:30:04 CDT)
  • Re: AMBER: Problems with X.R.E.D. (Fri Jun 25 2004 - 12:20:30 CDT)
  • Re: AMBER: unnatural base - RESP charges in ANTECHAMBER (Tue Jun 08 2004 - 11:23:46 CDT)
  • Re: AMBER: Amber7: (Thu Jun 03 2004 - 15:11:28 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 14:18:26 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 11:26:38 CDT)
  • Re: AMBER: Use of RED (Fri May 28 2004 - 15:20:42 CDT)
  • Re: AMBER: pdb in RED (Thu May 27 2004 - 14:16:59 CDT)
  • Re: AMBER: Bug in babel conversion (Tue May 25 2004 - 13:14:55 CDT)
  • Re: AMBER: parametrizacion partial charges (Mon May 17 2004 - 10:37:02 CDT)
  • RE: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Wed May 12 2004 - 13:01:31 CDT)
  • Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Wed May 12 2004 - 11:42:31 CDT)
  • Re: AMBER: choosing 3 atoms for reorientaion in R.E.D (Thu May 06 2004 - 17:00:44 CDT)
  • Re: AMBER: reorientation in R.E.D (Wed May 05 2004 - 12:55:51 CDT)
  • Re: AMBER: methane box (Wed May 05 2004 - 10:36:08 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:48:43 CDT)
  • Re: AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 15:16:00 CDT)
  • Re: AMBER: resp demo files (Mon May 03 2004 - 16:40:15 CDT)
  • Re: AMBER: esp or resp for all_amino94.lib (Fri Apr 30 2004 - 18:28:57 CDT)
  • AMBER: Re: About RESP Calculation (Mon Mar 22 2004 - 11:09:00 CST)
  • Re: AMBER: About RESP Calculation (Sun Mar 21 2004 - 01:30:41 CST)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 14:30:00 CST)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 14:10:19 CST)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 11:45:22 CST)
  • Re: AMBER: amber98 with amberffc+INSIGHT II (Wed Mar 17 2004 - 09:50:28 CST)
  • Re: AMBER: Some questions in building a new residue (Wed Mar 10 2004 - 14:31:25 CST)
  • Re: AMBER: R.E.D. (Tue Feb 24 2004 - 10:16:57 CST)
  • Re: AMBER: R.E.D. (Mon Feb 23 2004 - 19:42:13 CST)
  • Re: AMBER: contributed parameters (Fri Feb 20 2004 - 18:05:48 CST)
  • Re: AMBER: contributed parameters (Fri Feb 20 2004 - 11:08:34 CST)
  • Re: AMBER: compiling software(RESP) on MAC G5 (Thu Feb 19 2004 - 10:27:54 CST)
  • Re: AMBER: contributed parameters (Wed Feb 18 2004 - 11:12:04 CST)
  • AMBER: Box of mixed solvant (Tue Feb 10 2004 - 22:18:42 CST)
  • Re: AMBER: Which program to use to visualize the RESP Outputs (Tue Jan 27 2004 - 10:59:51 CST)
  • Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 (Fri Jan 23 2004 - 13:52:28 CST)
  • Re: AMBER: Parm98 Vs 02 (Wed Jan 21 2004 - 12:38:31 CST)
• Gabbar Daaku
  • AMBER: NTT=0 and TAUTP (Mon Aug 23 2004 - 17:25:26 CDT)
  • AMBER: ptraj -- velocities set to zero? (Thu Aug 12 2004 - 10:53:04 CDT)
  • AMBER: Membrane protein simulation (Tue Aug 10 2004 - 15:37:22 CDT)
  • AMBER: Amber8 compilation problems on AIX (Tue Jun 29 2004 - 21:50:13 CDT)
  • AMBER: CHARMM PSF to PRMTOP (Thu Apr 29 2004 - 16:42:33 CDT)
  • AMBER: Can anybody help me with CHARMM (Sun Feb 22 2004 - 21:13:09 CST)
• Garhan Attebury
  • AMBER: Residue Loading Problem (Fri Dec 03 2004 - 00:20:51 CST)
• Gary Waters
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 15:08:49 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 12:36:16 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 11:55:14 CDT)
  • AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 11:00:33 CDT)
  • AMBER: Opteron PMEMD (Thu May 06 2004 - 13:29:56 CDT)
• German Sciaini
  • Re: AMBER: antechamber - missing improper torsions (Tue Jul 20 2004 - 08:04:17 CDT)
  • Re: AMBER: Amber8: Vlimit problem again (Fri Jul 16 2004 - 08:12:59 CDT)
  • AMBER: combination rules (Mon Jul 05 2004 - 07:31:43 CDT)
  • Re: AMBER: Atom Labels (Wed Jun 30 2004 - 06:36:14 CDT)
  • AMBER: problems to run ptraj (Tue Jun 22 2004 - 17:29:36 CDT)
  • Re: AMBER: leap.log warnings (Tue Jun 22 2004 - 05:50:01 CDT)
  • Re: AMBER: problems with extra points (Fri Jun 18 2004 - 06:08:18 CDT)
  • AMBER: problems with extra points (Wed Jun 16 2004 - 11:29:45 CDT)
• Germán Sciaini
  • AMBER: a question (Tue Dec 21 2004 - 08:10:14 CST)
  • AMBER: Kinetics energy (Sat Dec 18 2004 - 11:54:04 CST)
  • AMBER: some questions.... (Wed Dec 08 2004 - 10:49:55 CST)
• Giulio Rastelli
  • AMBER: LCPO parameters in gbsa (Thu Feb 19 2004 - 10:53:56 CST)
  • AMBER: water as a "ligand" in GBSA and MM-PBSA? (Fri Feb 06 2004 - 11:41:50 CST)
  • AMBER: modeling GPCR in lipid environment (Thu Jan 08 2004 - 10:49:53 CST)
• Golebiowski Jerome
  • AMBER: savepdb vs ambpdb (Fri Jun 11 2004 - 10:17:40 CDT)
• Grace Li
  • AMBER: want to generate ammonium ion..where to start? (Tue Sep 14 2004 - 11:48:20 CDT)
  • AMBER: density calculation in AMBER output (Wed Aug 25 2004 - 08:51:47 CDT)
  • AMBER: error estimates in AMBER (Mon Aug 23 2004 - 15:43:14 CDT)
  • AMBER: how to read in CHARMM or AMBER binary trajectories (Thu Aug 19 2004 - 13:19:48 CDT)
  • AMBER: Minimum imaging (Mon Aug 02 2004 - 22:21:50 CDT)
  • Re: AMBER: AMBER 6 compilation problems! (Fri Jul 30 2004 - 15:42:03 CDT)
  • RE: AMBER: AMBER 6 compilation problems! (Fri Jul 30 2004 - 13:52:15 CDT)
  • AMBER: AMBER 6 compilation problems! (Fri Jul 30 2004 - 12:17:39 CDT)
  • AMBER: about RDF calculation in action.c (Fri Jul 23 2004 - 15:39:07 CDT)
  • RE: AMBER: cut offs in amber? (Wed Jul 21 2004 - 17:03:05 CDT)
  • RE: AMBER: cut offs in amber? (Wed Jul 21 2004 - 16:20:40 CDT)
  • AMBER: cut offs in amber? (Wed Jul 21 2004 - 15:47:43 CDT)
  • AMBER: ptraj-closestwaters command (Sat Jul 10 2004 - 11:14:34 CDT)
  • AMBER: "closestwater" algorithm (Mon Jul 05 2004 - 17:42:08 CDT)
  • AMBER: traj. analysis (Wed Jun 30 2004 - 14:05:07 CDT)
• Greg Jezierski
  • AMBER: Simulation of lipid bilayers (Tue Apr 20 2004 - 09:41:50 CDT)
• Greg Kellogg
  • AMBER: Leap (Tue Nov 09 2004 - 10:24:43 CST)
  • AMBER: PMEMD (Fri Sep 17 2004 - 11:20:00 CDT)
• Guanglei Cui
  • Re: AMBER: Why the charge is not an integer? (Sun Dec 12 2004 - 10:21:32 CST)
  • Re: AMBER: exclusion list (Mon Oct 11 2004 - 10:26:20 CDT)
  • AMBER: exclusion list (Sun Oct 10 2004 - 11:34:38 CDT)
  • AMBER: anal error (Thu Sep 30 2004 - 15:28:35 CDT)
  • Re: AMBER: intramolecular energies (Tue Sep 28 2004 - 12:38:16 CDT)
  • Re: AMBER: intramolecular energies (Tue Sep 28 2004 - 11:11:10 CDT)
  • Re: AMBER: intramolecular energies (Mon Sep 27 2004 - 20:55:41 CDT)
  • AMBER: intramolecular energies (Mon Sep 27 2004 - 16:17:11 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 12:49:35 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 11:20:30 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 10:52:01 CDT)
  • AMBER: sander8 compile: myrinet and mpigm (Mon Sep 20 2004 - 15:42:14 CDT)
  • Re: AMBER: F90 compiler for linux ppc64 (Wed Sep 15 2004 - 10:28:17 CDT)
  • AMBER: F90 compiler for linux ppc64 (Wed Sep 15 2004 - 09:42:12 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 14:38:44 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:27:20 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 16:11:37 CDT)
  • AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 14:38:57 CDT)
  • Re: AMBER: Increasing MAXATOM in antechamber (Sat Aug 21 2004 - 10:07:10 CDT)
  • Re: AMBER: leap: impose (Tue Aug 17 2004 - 15:15:27 CDT)
  • Re: AMBER: leap: impose (Tue Aug 17 2004 - 14:23:27 CDT)
  • AMBER: leap: impose (Tue Aug 17 2004 - 13:44:04 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Sun Aug 15 2004 - 09:08:29 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Thu Aug 12 2004 - 09:18:06 CDT)
  • Re: AMBER: parameter (Wed Aug 11 2004 - 16:07:18 CDT)
  • Re: AMBER: error while loading shared libraries: libcxa.so.5 (Mon Aug 09 2004 - 09:24:06 CDT)
  • Re: AMBER: (Fri Jul 30 2004 - 08:39:51 CDT)
  • Re: AMBER: animation? (Wed Jul 28 2004 - 08:20:12 CDT)
  • Re: AMBER: question about ptraj (Wed Jul 21 2004 - 15:32:29 CDT)
  • Re: AMBER: X-CA-CT-X dih. FF param ? (Fri Jul 16 2004 - 12:24:46 CDT)
  • Re: AMBER: torsion scan (Tue Jul 13 2004 - 16:12:50 CDT)
  • AMBER: torsion scan (Tue Jul 13 2004 - 10:18:32 CDT)
  • Re: AMBER: How to make leap recognise Zn2+? (Tue Jul 06 2004 - 08:58:27 CDT)
  • Re: AMBER: Namelist problem (Mon Jul 05 2004 - 07:56:10 CDT)
  • Re: AMBER: Questions about pert.charge and atom type change. (Wed Jun 30 2004 - 19:54:28 CDT)
  • Re: AMBER: N-terminal Arg charges in ff99 not 1.00 (Wed Jun 30 2004 - 16:13:55 CDT)
  • Re: AMBER: About TI with sander (Mon Jun 28 2004 - 14:46:52 CDT)
  • Re: AMBER: Trajectory file (Wed Jun 09 2004 - 15:27:16 CDT)
  • Re: AMBER: How to neutralize system? (Wed Jun 09 2004 - 09:58:37 CDT)
  • Re: AMBER: antechamber (Wed Jun 09 2004 - 09:05:02 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 14:45:56 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 13:30:05 CDT)
  • Re: AMBER: amber8 compile on Lemieux (Thu Jun 03 2004 - 22:56:13 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 14:20:26 CDT)
  • AMBER: amber8 compile on Lemieux (Thu Jun 03 2004 - 10:06:21 CDT)
  • Re: AMBER: Add Hydrogen bond through xLeap? (Wed Jun 02 2004 - 09:06:47 CDT)
  • Re: AMBER: question about replica exchange in amber8 (Wed Jun 02 2004 - 08:58:32 CDT)
  • Re: AMBER: about amber8, replica exchange (Fri May 28 2004 - 23:04:33 CDT)
  • Re: AMBER: Cannot read in sander-again (Thu May 27 2004 - 16:28:39 CDT)
  • Re: AMBER: parallel installation problem (Wed May 19 2004 - 20:54:21 CDT)
  • Re: AMBER: ptraj and LES (Wed May 12 2004 - 14:34:31 CDT)
  • AMBER: ptraj and LES (Tue May 11 2004 - 16:00:12 CDT)
  • AMBER: antechamber (Tue May 04 2004 - 21:49:28 CDT)
  • AMBER: partition error in shake (Fri Apr 23 2004 - 10:18:19 CDT)
  • Re: AMBER: solvateCap warning (Fri Apr 23 2004 - 08:47:49 CDT)
  • Re: AMBER: xleap console message (Mon Apr 19 2004 - 15:48:28 CDT)
  • Re: AMBER: xleap console message (Mon Apr 19 2004 - 12:11:11 CDT)
  • AMBER: xleap console message (Mon Apr 19 2004 - 10:06:05 CDT)
  • AMBER: scali amber8 (Mon Apr 12 2004 - 15:02:11 CDT)
  • Re: AMBER: mol2 vs. prepin (Tue Mar 09 2004 - 11:05:22 CST)
  • Re: AMBER: NMR restraint in sander (Tue Mar 09 2004 - 08:55:15 CST)
  • Re: AMBER: antechamber prepin (Mon Mar 08 2004 - 10:22:40 CST)
  • AMBER: antechamber prepin (Sun Mar 07 2004 - 13:03:22 CST)
  • AMBER: torsion term (Wed Mar 03 2004 - 10:48:36 CST)
• Guillaume Bollot
  • AMBER: Problem to update antechamber package. (Wed Nov 17 2004 - 07:50:49 CST)
  • AMBER: Problem with MacroMolecule to AMBER7 (Fri Sep 17 2004 - 10:56:22 CDT)
  • AMBER: AMBER7 : Hybrid macromolecule (Mon Sep 13 2004 - 10:54:28 CDT)
  • AMBER: AMBER7 : update gaff and parm99 force field (Mon Sep 13 2004 - 08:35:01 CDT)
  • AMBER: Problem to converge minimization (Mon Jul 05 2004 - 03:41:06 CDT)
  • AMBER: Restrain or freeze molecule question? (Thu Jun 24 2004 - 05:48:33 CDT)
  • AMBER: AMBER7 update force field (Thu Jun 24 2004 - 08:23:44 CDT)
  • AMBER: AMBER7 : update force field gaff.dat and parm99.dat (Thu Jun 24 2004 - 07:48:39 CDT)
• Guillermo Mulliert Carlín
  • Re: AMBER: segmentation fault in leap (Thu Jul 08 2004 - 07:02:05 CDT)
  • Re: AMBER: Amber8 on Digital UNIX (Wed Jul 07 2004 - 04:41:53 CDT)
  • AMBER: Amber8 on Digital UNIX (Mon Jul 05 2004 - 10:30:15 CDT)
• Guowen Han
  • AMBER: unknown residue: ABA (Tue Aug 10 2004 - 13:31:25 CDT)
• Gustavo Pierdominici Sottile
  • AMBER: angle bending (Thu Aug 19 2004 - 07:31:21 CDT)
  • AMBER: bending (Thu Aug 12 2004 - 15:47:16 CDT)
  • AMBER: bending (Thu Aug 12 2004 - 14:28:42 CDT)
  • AMBER: parameter (Wed Aug 11 2004 - 15:45:02 CDT)
  • AMBER: units (Wed Aug 11 2004 - 10:03:38 CDT)
  • AMBER: Heme parameters (Tue Jun 01 2004 - 10:32:06 CDT)
  • AMBER: Use of RED (Fri May 28 2004 - 13:44:26 CDT)
  • Re: AMBER: types of water atom (Fri May 28 2004 - 13:25:45 CDT)
  • Re: AMBER: types of water atom (Thu May 27 2004 - 14:28:27 CDT)
  • AMBER: pdb in RED (Thu May 27 2004 - 12:29:44 CDT)
  • AMBER: types of water atom (Wed May 26 2004 - 12:06:16 CDT)
  • AMBER: Clean in RESP (Tue May 18 2004 - 06:46:38 CDT)
  • AMBER: (Mon May 17 2004 - 13:38:53 CDT)
  • AMBER: parametrizacion partial charges (Mon May 17 2004 - 08:45:58 CDT)
  • AMBER: installing RESP (Sat May 15 2004 - 06:52:59 CDT)
  • AMBER: install RESP (Sat May 15 2004 - 06:54:41 CDT)
• Haijun Yang
  • Re: AMBER: a quick question about carnal (Mon Nov 15 2004 - 11:31:53 CST)
  • AMBER: a quick question about carnal (Fri Nov 12 2004 - 14:51:17 CST)
  • Re: AMBER: Problems in Amber MPI version (64 bits machine) (Wed Jun 23 2004 - 12:33:49 CDT)
  • AMBER: Problems in Amber MPI version (64 bits machine) (Tue Jun 22 2004 - 16:57:07 CDT)
• Hailong Lin
  • Re: AMBER: overlap between HE and OE in GLH (Tue Apr 27 2004 - 09:32:47 CDT)
  • AMBER: overlap between HE and OE in GLH (Mon Apr 26 2004 - 10:49:36 CDT)
  • Re: AMBER: minimization of GLH (Mon Apr 05 2004 - 10:51:47 CDT)
  • AMBER: minimization of GLH (Mon Apr 05 2004 - 06:57:31 CDT)
  • Re: AMBER: segmentation fault (Fri Mar 19 2004 - 06:41:50 CST)
  • AMBER: segmentation fault (Thu Mar 18 2004 - 06:48:24 CST)
• Hannes Barsch
  • AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) (Mon Nov 29 2004 - 11:02:15 CST)
  • AMBER: xLeap menus not working properly (Wed Sep 08 2004 - 03:14:38 CDT)
• Harald Lanig
  • AMBER: MD simulations on heparin and heparin sulfate (Thu Dec 30 2004 - 10:23:24 CST)
• Harianto
  • Re: AMBER: Output of sander (Thu Dec 23 2004 - 14:36:27 CST)
  • Re: AMBER: energy unit (Thu Dec 23 2004 - 10:25:32 CST)
  • AMBER: Output of sander (Wed Dec 22 2004 - 10:09:37 CST)
  • AMBER: IBELLY (Tue Nov 09 2004 - 14:40:58 CST)
  • AMBER: Minimization failure: 1cbn (Fri Nov 05 2004 - 11:16:30 CST)
• Harsh Parikh
  • AMBER: Dr. Herman Von Grafenstein (Tue Aug 17 2004 - 18:43:06 CDT)
• Harvey, David Richard
  • AMBER: PMF correction factor (Tue May 04 2004 - 08:35:13 CDT)
• Heike.Meiselbach_at_chemie.uni-erlangen.de
  • Re: AMBER: xLeap menus not working properly (Wed Sep 08 2004 - 04:19:13 CDT)
• Helios
  • AMBER: Amber:how to increase the memory allocation? (Wed Sep 08 2004 - 22:35:14 CDT)
  • AMBER: Amber: BOMB (Wed Sep 08 2004 - 07:18:11 CDT)
  • AMBER: Amber: Anal program format (Tue Aug 17 2004 - 01:15:57 CDT)
  • AMBER: Amber: xleap crash (Fri Aug 13 2004 - 07:00:30 CDT)
• Helios Chen
  • AMBER: Amber: what different? (Thu Oct 21 2004 - 20:58:42 CDT)
  • AMBER: bugfix.17 (Thu Oct 21 2004 - 11:26:23 CDT)
  • AMBER: mm_pbsa for Delphi (Tue Sep 14 2004 - 04:28:28 CDT)
  • AMBER: "Total vdw box size" information is gone (Sun Jun 27 2004 - 02:57:50 CDT)
  • AMBER: single amino acid energy (Tue May 18 2004 - 03:15:02 CDT)
  • AMBER: why delete water molecule (Mon May 03 2004 - 23:18:49 CDT)
  • AMBER: any program or tool (Mon May 03 2004 - 05:16:15 CDT)
  • AMBER: just sander not run (Fri Apr 30 2004 - 04:27:45 CDT)
  • AMBER: Redhat install (Thu Apr 29 2004 - 09:24:17 CDT)
  • AMBER: tutorial of Biotin/Streptavidin (Sat Apr 24 2004 - 08:37:43 CDT)
  • AMBER: NSNB parameter (Fri Apr 23 2004 - 22:45:42 CDT)
  • AMBER: solvateCap warning (Fri Apr 23 2004 - 04:47:25 CDT)
  • AMBER: PERT.charge problem in xleap (Fri Apr 02 2004 - 06:10:54 CST)
  • Re: AMBER: fix two groups (Sun Mar 28 2004 - 22:54:58 CST)
  • AMBER: fix two groups (Sun Mar 28 2004 - 21:07:07 CST)
• Herbert Georg
  • Re: AMBER: weird box expansion (Thu Jul 08 2004 - 12:38:01 CDT)
  • AMBER: weird box expansion (Thu Jul 08 2004 - 11:57:57 CDT)
  • AMBER: solvents reference. (Fri May 14 2004 - 14:56:38 CDT)
  • Re: AMBER: free energy perturbation (Tue Apr 06 2004 - 12:03:51 CDT)
  • AMBER: free energy perturbation (Tue Apr 06 2004 - 10:21:55 CDT)
  • AMBER: flexible water potential (Tue Feb 17 2004 - 05:22:12 CST)
  • AMBER: center of mass in CARNAL (Thu Feb 12 2004 - 10:15:17 CST)
  • AMBER: dipole moment in ptraj (Sun Feb 08 2004 - 12:42:07 CST)
  • AMBER: ptraj and dipoles.... (Fri Feb 06 2004 - 15:12:10 CST)
  • Re: AMBER: ptraj and dipoles (Fri Feb 06 2004 - 05:47:12 CST)
  • AMBER: ptraj and dipoles (Thu Feb 05 2004 - 15:40:24 CST)
  • AMBER: carnal (Wed Feb 04 2004 - 13:18:37 CST)
  • Re: AMBER: Carnal (Tue Feb 03 2004 - 13:30:33 CST)
  • AMBER: Carnal (Tue Feb 03 2004 - 10:11:28 CST)
  • Re: AMBER: Improper dihedral (Tue Jan 13 2004 - 09:36:29 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 14:21:39 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 13:39:12 CST)
  • Re: AMBER: Improper dihedral (Mon Jan 12 2004 - 12:57:39 CST)
  • AMBER: Improper dihedral (Mon Jan 12 2004 - 08:23:22 CST)
• Hernán Alonso
  • AMBER: ESPGEN problems to read G03 output files (Wed Nov 03 2004 - 01:03:12 CST)
• Herr/Señor/Monsieur/Mister Gregory
  • Re: AMBER: question about Ptraj - AND OR (Mon Jul 12 2004 - 11:15:47 CDT)
• hj zou
  • Re: Re: Re: AMBER: Why the surface calculations sometimes fail? (Wed Dec 15 2004 - 22:12:59 CST)
  • Re: Re: AMBER: Why the surface calculations sometimes fail? (Wed Dec 08 2004 - 19:58:19 CST)
  • AMBER: Why the surface calculations sometimes fail? (Wed Dec 08 2004 - 00:53:09 CST)
  • AMBER: translational and rotational entropy (Fri Nov 05 2004 - 00:48:22 CST)
  • AMBER: small molecule simulation (Sun Oct 03 2004 - 00:59:55 CDT)
  • AMBER: dihedral (Sun Sep 26 2004 - 20:08:20 CDT)
  • AMBER: minimization problem (Sat Sep 25 2004 - 04:30:11 CDT)
  • AMBER: Re: Re: Delphi PATH question (Wed Sep 22 2004 - 08:40:23 CDT)
  • AMBER: Re: Delphi PATH question (Sat Sep 18 2004 - 01:22:08 CDT)
  • AMBER: re:your message to amber... (Fri Sep 10 2004 - 08:46:58 CDT)
  • AMBER: how to deal with the initial structure? (Mon Aug 23 2004 - 20:48:22 CDT)
  • Re: Re: AMBER: xleap problem (Mon Jul 12 2004 - 09:56:55 CDT)
  • AMBER: Fe parameter (Mon Jul 12 2004 - 02:09:29 CDT)
  • AMBER: solvation free energy (Sun Jul 11 2004 - 01:16:19 CDT)
  • AMBER: (Sun Jul 11 2004 - 01:16:17 CDT)
  • Re: Re: AMBER: xleap problem (Sun Jul 11 2004 - 01:16:19 CDT)
  • AMBER: solvation free energy (Fri Jul 09 2004 - 02:38:39 CDT)
  • AMBER: program compatibility (Sun May 30 2004 - 21:07:39 CDT)
  • AMBER: tmd questions (Wed May 12 2004 - 21:07:36 CDT)
  • Re: AMBER: xleap problem (Tue May 04 2004 - 21:44:43 CDT)
  • Re: Re: AMBER: xleap problem (Mon May 03 2004 - 03:02:34 CDT)
  • AMBER: xleap problem (Sun May 02 2004 - 08:49:40 CDT)
  • AMBER: free energy perturbation questions (Sat Apr 17 2004 - 09:38:28 CDT)
  • AMBER: solvation energy (Tue Mar 30 2004 - 06:55:20 CST)
  • AMBER: solvation energy (Sun Mar 28 2004 - 11:36:31 CST)
  • AMBER: re:can i get help from you? (Tue Mar 16 2004 - 07:53:48 CST)
  • AMBER: positive binding free energy (Thu Mar 11 2004 - 07:59:09 CST)
  • AMBER: positive binding free energy (Wed Mar 10 2004 - 00:43:58 CST)
  • AMBER: pka questions (Sat Mar 06 2004 - 21:22:54 CST)
  • AMBER: positive binding free energy (Fri Mar 05 2004 - 00:53:18 CST)
  • AMBER: PKA calculation (Fri Mar 05 2004 - 00:34:21 CST)
  • AMBER: pka calculation (Fri Feb 27 2004 - 20:42:34 CST)
  • AMBER: mmpbsa qustion (Wed Feb 25 2004 - 19:23:37 CST)
  • AMBER: pka calculation (Mon Feb 23 2004 - 07:33:00 CST)
  • AMBER: mm_pbsa question (Wed Feb 18 2004 - 21:22:00 CST)
  • AMBER: tmd question (Wed Feb 18 2004 - 20:58:45 CST)
• HL Eastwood
  • Re: AMBER: Amber8: ifort 8.0.046 Woo hoo! (Fri Oct 15 2004 - 05:36:57 CDT)
  • RE: AMBER: Problem with installing Amber8: Where are the MK libraries? (Thu Oct 14 2004 - 12:42:54 CDT)
  • AMBER: Problem with installing Amber8: Where are the MK libraries? (Thu Oct 14 2004 - 11:34:54 CDT)
  • AMBER: (no subject) (Thu Oct 14 2004 - 11:33:34 CDT)
  • AMBER: Problems with Carnal coordinate average (Mon Aug 09 2004 - 06:35:37 CDT)
  • AMBER: xleap problem fixed! (Tue Aug 03 2004 - 12:20:21 CDT)
  • RE: AMBER: (no subject) (Fri Jul 30 2004 - 13:12:34 CDT)
  • AMBER: (no subject) (Fri Jul 30 2004 - 10:47:18 CDT)
• Holger Gohlke
  • Re: AMBER: mm_gbsa results for charged ligands (Fri Dec 24 2004 - 04:31:22 CST)
  • Re: AMBER: No radius found for 2412 Zn Zn (Fri Dec 10 2004 - 04:22:19 CST)
  • Re: AMBER: No radius found for 2412 Zn Zn (Fri Dec 10 2004 - 02:21:45 CST)
  • Re: AMBER: Problems using mm_pbsa.perl (Fri Nov 05 2004 - 10:41:39 CST)
  • Re: AMBER: continue for No radius for F atom in MM_PBSA (Sun Oct 24 2004 - 15:06:15 CDT)
  • Re: AMBER: error in mm_pbsa (Sat Oct 16 2004 - 08:53:36 CDT)
  • Re: AMBER: question on mm-pbsa (Wed Sep 01 2004 - 13:55:50 CDT)
  • Re: AMBER: mm_pbsa Abmer8 example (Tue Aug 03 2004 - 01:39:06 CDT)
  • Re: AMBER: found unknown atflg PB (Thu Jul 22 2004 - 09:56:38 CDT)
  • Re: AMBER: ptraj bug? (Wed May 19 2004 - 10:31:12 CDT)
  • Re: AMBER: single amino acid energy (Tue May 18 2004 - 10:23:26 CDT)
  • Re: AMBER: questions on mm_pbsa (Tue May 18 2004 - 10:18:24 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Mon May 17 2004 - 13:05:57 CDT)
  • Re: AMBER: mm-pbsa:- atom charges and radii ? (Wed May 12 2004 - 01:40:52 CDT)
  • Re: AMBER: ptraj read in matrix (Tue May 11 2004 - 09:45:11 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Fri May 07 2004 - 07:48:51 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 11:32:23 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 05:28:57 CDT)
  • Re: AMBER: problem with MM/PBSA (Wed May 05 2004 - 05:14:47 CDT)
  • Re: AMBER: VS: mmpbsa question (Fri Apr 30 2004 - 02:47:32 CDT)
  • Re: AMBER: mm_pbsa question: MAXAT=10000 exceeded (Thu Apr 29 2004 - 01:42:27 CDT)
  • Re: AMBER: mm_pbsa examples; delphi in mm_pbsa (Mon Apr 26 2004 - 08:11:28 CDT)
  • Re: AMBER: Parameters for nonpolar contribution to solvation (Sat Apr 24 2004 - 07:06:34 CDT)
  • Re: AMBER: "matrix" in ptraj (Sat Apr 24 2004 - 06:47:41 CDT)
  • Re: AMBER: Time to minimize the energy by NMODE (Wed Apr 14 2004 - 14:40:28 CDT)
  • Re: AMBER: atomicfluct in ptraj (Wed Apr 14 2004 - 14:14:47 CDT)
  • Re: AMBER: how to use mm_pbsa_statistics.pl independently (Tue Apr 13 2004 - 12:06:43 CDT)
  • Re: AMBER: (Thu Apr 08 2004 - 09:20:51 CDT)
  • Re: AMBER: positive binding free energy (Fri Mar 05 2004 - 02:30:35 CST)
  • Re: AMBER: questions about mmpbsa (Fri Mar 05 2004 - 01:35:57 CST)
  • Re: AMBER: PB in mm-pbsa (Sun Feb 29 2004 - 08:02:29 CST)
  • Re: AMBER: mmpbsa qustion (Thu Feb 26 2004 - 01:29:06 CST)
  • Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? (Tue Feb 17 2004 - 01:24:25 CST)
  • Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? (Mon Feb 16 2004 - 04:09:07 CST)
  • Re: AMBER: Normal modes of protein-ligand (Wed Jan 28 2004 - 13:38:57 CST)
  • Re: AMBER: Normal modes of protein-ligand (Wed Jan 28 2004 - 13:32:49 CST)
  • Re: AMBER: NMODE via MM-PBSA (Wed Jan 21 2004 - 06:49:48 CST)
  • Re: AMBER: Errors in MM-PBSA??? (Wed Jan 21 2004 - 06:37:39 CST)
• Holly Freedman
  • AMBER: average using ptraj (Thu Jul 08 2004 - 14:13:58 CDT)
  • Re: AMBER: ptraj (Wed May 26 2004 - 12:30:07 CDT)
  • Re: AMBER: ptraj (Tue May 25 2004 - 19:45:24 CDT)
  • AMBER: ptraj (Tue May 25 2004 - 11:16:42 CDT)
  • AMBER: average structure from traj (Tue May 18 2004 - 16:30:07 CDT)
  • Re: AMBER: water hole (Wed Apr 14 2004 - 19:32:06 CDT)
  • Re: AMBER: water hole (Mon Apr 12 2004 - 19:39:19 CDT)
  • AMBER: water hole (Mon Apr 12 2004 - 16:43:32 CDT)
• Hong Wu
  • Re: AMBER: ambpdb in AMBER7 (Mon Jan 26 2004 - 13:14:28 CST)
  • AMBER: ambpdb in AMBER7 (Mon Jan 26 2004 - 12:52:10 CST)
• Huang, Hai
  • RE: AMBER: SHAKE probelm (Tue Nov 23 2004 - 16:01:25 CST)
  • RE: AMBER: SHAKE probelm (Fri Nov 19 2004 - 16:56:54 CST)
  • AMBER: SHAKE probelm (Fri Nov 19 2004 - 10:25:24 CST)
• Hwankyu Lee
  • Re: AMBER: Installation of AMBER8 on AMD cluster using pgf90 (Wed Nov 24 2004 - 08:03:28 CST)
  • AMBER: Installation of AMBER8 on AMD cluster using pgf90 (Tue Nov 23 2004 - 20:41:13 CST)
  • Re: AMBER: A question on AMBER8 installation (Tue Oct 19 2004 - 23:12:20 CDT)
  • Re: AMBER: A question on AMBER8 installation (Tue Oct 19 2004 - 15:43:48 CDT)
  • Re: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 22:01:05 CDT)
  • RE: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 13:13:33 CDT)
  • RE: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 12:57:45 CDT)
  • RE: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 11:04:18 CDT)
  • Re: AMBER: A question on AMBER8 installation (Wed Oct 13 2004 - 12:53:30 CDT)
  • AMBER: A question on AMBER8 installation (Tue Oct 12 2004 - 23:39:33 CDT)
  • AMBER: Questions on simulating dendrimer in AMBER. (Sun Sep 19 2004 - 22:21:03 CDT)
  • AMBER: A tool for building coordinates of huge macromolecules (Wed Sep 15 2004 - 11:28:19 CDT)
• ian gould
  • Re: AMBER: Opteron-64bit work station (Mon Jun 21 2004 - 11:34:33 CDT)
• Ian Withers
  • AMBER: ptraj bug? (Wed May 19 2004 - 09:33:38 CDT)
• Ilyas Yildirim
  • AMBER: Dummy Atoms: How to create them? (Thu Dec 30 2004 - 19:23:02 CST)
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Mon Dec 20 2004 - 18:42:29 CST)
  • Re: AMBER: General Question about AMBER's Free Energy Perturbation Method (Fri Dec 17 2004 - 15:53:07 CST)
  • AMBER: General Question about AMBER's Free Energy Perturbation Method (Wed Dec 15 2004 - 22:13:07 CST)
  • AMBER: Free Energy Perturbation using Sander (TI Method) (Wed Dec 15 2004 - 20:43:09 CST)
  • RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation (Wed Dec 15 2004 - 18:47:05 CST)
  • AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation (Mon Dec 13 2004 - 22:34:34 CST)
  • AMBER: Re: INSTALLATION GUIDE FOR IFORT AND AMBER8 IN LINUX SUSE 9.1 ....Re: AMBER: SUSE 9.1 and AMBER 8 (Wed Dec 01 2004 - 15:12:49 CST)
  • AMBER: SUSE 9.1 and AMBER 8 (Tue Nov 16 2004 - 05:12:16 CST)
  • AMBER: ifort 8.0 (Mon Nov 15 2004 - 16:41:28 CST)
  • Re: AMBER: xleap problems (Fri Nov 12 2004 - 17:58:21 CST)
  • AMBER: About the parameter names (Wed Nov 10 2004 - 15:20:31 CST)
  • AMBER: Building the parallel version in AMBER 8 and GIBBS (Tue Nov 09 2004 - 21:03:54 CST)
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 16 2004 - 17:36:22 CDT)
  • AMBER: About DelPhi and GRASP (Wed Jun 02 2004 - 23:10:07 CDT)
  • AMBER: Surface E&S Potential Mapping (Tue May 25 2004 - 16:14:45 CDT)
  • AMBER: Bug in babel conversion (while following the RED manual in pp.15) (Tue May 25 2004 - 13:00:39 CDT)
  • AMBER: Nonplanar ring systems in nucleic acid (Wed May 19 2004 - 15:14:14 CDT)
  • AMBER: Optimizing a structure and the interpretation of it (Sat Apr 24 2004 - 18:08:14 CDT)
  • AMBER: What kind of informations are needed in a .pdb file in order to start using antechamber? (Wed Apr 21 2004 - 23:51:40 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Tue Apr 20 2004 - 18:42:34 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Tue Apr 20 2004 - 15:51:55 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Tue Apr 20 2004 - 15:28:13 CDT)
  • Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Tue Apr 20 2004 - 15:13:09 CDT)
  • AMBER: Do we have to optimize the structure in order to do MEP Calculations? (Mon Apr 19 2004 - 15:35:45 CDT)
  • AMBER: Gaussian 98 Installation (Thu Apr 08 2004 - 15:52:05 CDT)
  • AMBER: respgen (Wed Apr 07 2004 - 17:45:33 CDT)
  • Re: AMBER: error in antechamber (Wed Apr 07 2004 - 08:30:55 CDT)
  • Re: AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly? (Tue Apr 06 2004 - 20:25:46 CDT)
  • AMBER: MOPAC 7 - How to modift the mopac.sh file to run antechamber properly? (Tue Apr 06 2004 - 19:27:31 CDT)
  • AMBER: AMBER 7 Installation (Fri Apr 02 2004 - 17:17:09 CST)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 13:50:13 CST)
  • AMBER: About RESP Calculation (Fri Mar 19 2004 - 01:20:16 CST)
  • Re: AMBER: Some questions in building a new residue (Wed Mar 10 2004 - 12:57:11 CST)
  • Re: AMBER: Which program to use to visualize the RESP Outputs (Tue Jan 27 2004 - 12:49:01 CST)
  • AMBER: Error message in antechamber (Tue Jan 27 2004 - 12:44:26 CST)
  • AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 (Fri Jan 23 2004 - 12:18:23 CST)
• Ioana Cozmuta
  • AMBER: universal recognition of chemicals (Mon Apr 26 2004 - 17:15:55 CDT)
  • RE: AMBER: script on tutorial page (Fri Apr 09 2004 - 17:03:57 CDT)
  • AMBER: script on tutorial page (Thu Apr 08 2004 - 21:25:50 CDT)
  • AMBER: residence time (Tue Mar 23 2004 - 21:51:10 CST)
  • AMBER: diffusion coefficient with external applied electric field (Tue Mar 02 2004 - 14:36:35 CST)
  • AMBER: how to add force field parameters (Thu Feb 19 2004 - 14:27:02 CST)
  • Re: AMBER: segmentation fault in Leap (Fri Jan 23 2004 - 01:26:41 CST)
  • AMBER: oxygen positions around a DNA (Thu Jan 22 2004 - 20:19:51 CST)
  • Re: AMBER: segmentation fault in Leap (Wed Jan 21 2004 - 23:56:10 CST)
  • AMBER: segmentation fault in Leap (Tue Jan 20 2004 - 22:39:28 CST)
• ioana_at_pegasus.arc.nasa.gov
  • AMBER: question on NAB (Mon Oct 18 2004 - 16:18:19 CDT)
• Itziar Maestre Asenjo
  • AMBER: problem with MM/PBSA (Tue May 04 2004 - 11:38:32 CDT)
  • Re: AMBER: How to remove Cl- ions (Fri Feb 06 2004 - 04:58:05 CST)
  • AMBER: Problem using GLYCAM with sander (Fri Jan 23 2004 - 11:05:52 CST)
  • AMBER: remove rotational motion (Thu Jan 22 2004 - 01:39:15 CST)
  • Re: AMBER: error in minimization (Thu Jan 15 2004 - 00:58:46 CST)
  • AMBER: error in minimization (Tue Jan 13 2004 - 09:12:22 CST)
• J Pang
  • AMBER: ptraj and PCA (Wed Oct 06 2004 - 05:54:17 CDT)
• j-shimada_at_az.jp.nec.com
  • AMBER: scaling 1-4 NB interaction for rings (Wed Sep 29 2004 - 09:16:38 CDT)
• J. Zhang, Dr
  • AMBER: how to calculate E-pot from restart file? (Thu Jul 08 2004 - 22:13:44 CDT)
  • Re: Re: AMBER: why the enegy of native state of protein is high in GBSA calculation? (Sat Jun 05 2004 - 20:25:20 CDT)
  • AMBER: why the enegy of native state of protein is high in GBSA calculation? (Fri Jun 04 2004 - 04:21:20 CDT)
  • Re: AMBER: question about replica exchange in amber8 (Wed Jun 02 2004 - 21:16:19 CDT)
  • AMBER: question about replica exchange in amber8 (Wed Jun 02 2004 - 04:24:24 CDT)
  • Re: Re: AMBER: about amber8, replica exchange (Sun May 30 2004 - 19:09:24 CDT)
  • AMBER: about amber8, replica exchange (Fri May 28 2004 - 22:45:49 CDT)
  • Re: Re: AMBER: Does this warning matter? (about improper torsion parameters) (Wed May 19 2004 - 20:57:35 CDT)
  • AMBER: Does this warning matter? (about improper torsion parameters) (Tue May 18 2004 - 22:04:32 CDT)
• Jack Lei
  • Re: AMBER: No radius found for 2412 Zn Zn (Fri Dec 10 2004 - 08:49:53 CST)
  • Re: AMBER: Compiling Antechamber/Amber8 with ia64_ifort (Mon Dec 06 2004 - 09:11:05 CST)
  • AMBER: RMS of energy in Minimization using SANDER (Wed Nov 17 2004 - 12:15:31 CST)
  • Re: AMBER: AMBER8 compiling error under Itanium 2. (Tue Nov 16 2004 - 11:32:23 CST)
  • AMBER: Can xleap handle homology model altogether with X-ray structure? (Mon Nov 15 2004 - 17:08:44 CST)
  • Re: AMBER: ifort 8.0 (Mon Nov 15 2004 - 16:46:01 CST)
  • AMBER: Can xleap to handle homology model altogether X-ray structure? (Mon Nov 15 2004 - 16:39:55 CST)
  • AMBER: The question about SAS calculation in MM_PBSA (Mon Sep 20 2004 - 12:19:29 CDT)
• Jagdish Rai
  • AMBER: bond between two polypeptides (Tue Sep 14 2004 - 03:19:48 CDT)
• james tomomi macdonald
  • AMBER: question about Ptraj - AND OR (Mon Jul 12 2004 - 10:06:59 CDT)
• James W. Caldwell
  • Re: AMBER: Compiling question (Tue Dec 14 2004 - 14:10:19 CST)
  • Re: AMBER: RESP partial charge calculation (Tue Aug 10 2004 - 12:25:55 CDT)
  • Re: AMBER: resp charge calculation for Fe+3 heme (Mon Aug 09 2004 - 15:18:46 CDT)
  • Re: AMBER: xleap solvatebox problem (Wed Jun 09 2004 - 17:49:07 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 22:02:01 CDT)
  • Re: AMBER: problem with frcmod file (Thu Feb 26 2004 - 12:45:44 CST)
  • Re: AMBER: mmpbsa qustion (Thu Feb 26 2004 - 12:06:13 CST)
  • Re: AMBER: compiling software(RESP) on MAC G5 (Thu Feb 19 2004 - 12:50:28 CST)
  • AMBER: off-subject ROCKS/Qbank (Fri Feb 06 2004 - 14:03:09 CST)
  • Re: AMBER: trajectory file corruption (Tue Jan 27 2004 - 12:30:20 CST)
  • Re: AMBER: compilation under fedora core 1 (Tue Jan 27 2004 - 12:40:48 CST)
  • Re: AMBER: prep file (Mon Jan 05 2004 - 18:01:20 CST)
• james.m.woolven_at_gsk.com
  • AMBER: AMBER7 sander compiled on SGI R10000 fails to complete test suite (Fri Mar 05 2004 - 06:40:31 CST)
• javier perez
  • AMBER: About Hbond calculations using ptraj (Mon Jun 28 2004 - 12:43:37 CDT)
• Javier Perez Miron
  • AMBER: about glycam 04 (Mon Mar 29 2004 - 11:40:18 CST)
  • AMBER: About glycam2004 (Wed Mar 17 2004 - 21:02:47 CST)
  • AMBER: Problems with xleap (Thu Feb 26 2004 - 19:18:11 CST)
• Jean-Christophe Ducom
  • AMBER: Amber7 (8):FLUSH--FAILED:: Resource temporarily unavailable (Sat Jul 17 2004 - 15:01:47 CDT)
• Jeffrey Dyason
  • AMBER: mm-pbsa:- atom charges and radii ? (Tue May 11 2004 - 03:07:12 CDT)
• Jerry Grooms
  • Re: AMBER: sander and mpich (which compilers/mpich work) (Sat Jan 31 2004 - 17:08:57 CST)
  • Re: AMBER: sander and mpich (which compilers/mpich work) (Sat Jan 31 2004 - 14:44:30 CST)
  • Re: AMBER: sander and mpich (which compilers/mpich work) (Fri Jan 30 2004 - 17:00:22 CST)
• Jessica Koplin
  • AMBER: order parameter (Sun Oct 17 2004 - 05:30:44 CDT)
  • AMBER: hydrogen bonds (Fri Oct 01 2004 - 11:24:29 CDT)
  • AMBER: compressed files (Wed Sep 22 2004 - 11:56:27 CDT)
• Ji Changge
  • AMBER: about PARALLEL run on SGI. (Sat Sep 18 2004 - 01:47:38 CDT)
• jianhui wu
  • AMBER: Gigabit Ethernet Switch/Opteron 246 (Tue Dec 07 2004 - 11:09:11 CST)
• Jianwen Jiang
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Wed Dec 22 2004 - 15:59:47 CST)
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Wed Dec 22 2004 - 14:01:40 CST)
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Tue Dec 21 2004 - 20:22:00 CST)
  • Re: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Tue Dec 21 2004 - 16:30:47 CST)
  • AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Mon Dec 20 2004 - 18:18:52 CST)
  • AMBER: regular ewald sum in Amber8 (Fri Sep 24 2004 - 11:15:34 CDT)
• Jiayun
  • RE: AMBER: a question on MM-PBSA and Delphi (Tue Jun 29 2004 - 04:54:46 CDT)
  • RE: AMBER: a question on MM-PBSA and Delphi (Wed Jun 23 2004 - 13:00:17 CDT)
  • AMBER: a question on MM-PBSA and Delphi (Wed Jun 23 2004 - 08:34:31 CDT)
• Jiayun Pang
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Thu Jan 29 2004 - 04:47:52 CST)
  • Re: AMBER: A few questions in the protein unfolding simulations using GB model (Wed Jan 28 2004 - 06:20:48 CST)
  • AMBER: A few questions in the protein unfolding simulations using GB model (Tue Jan 27 2004 - 14:33:15 CST)
• Jiri Sponer
  • Re: AMBER: Parameters for Inosine (Fri Sep 24 2004 - 15:02:59 CDT)
  • Re: AMBER: metal atoms in Xleap (Fri Aug 20 2004 - 14:04:32 CDT)
  • Re: Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 09:42:27 CDT)
  • Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 09:09:46 CDT)
  • Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 07:41:12 CDT)
  • Re: AMBER: Nonplanar ring systems in nucleic acid (Thu May 20 2004 - 07:42:16 CDT)
  • Re: AMBER: Nonplanar ring systems in nucleic acid (Thu May 20 2004 - 06:46:41 CDT)
  • Re: AMBER: positive binding free energy (Thu Mar 11 2004 - 11:02:18 CST)
• Jiten
  • AMBER: mm_pbsa +fillratio (Fri Dec 31 2004 - 03:31:57 CST)
  • AMBER: MM_PBSA calculation error (Thu Dec 30 2004 - 04:57:30 CST)
  • AMBER: MM_PBSA calculations (Thu Dec 30 2004 - 01:22:25 CST)
  • Re: AMBER: ESPGEN problems to read G03 output files (Wed Nov 03 2004 - 02:33:04 CST)
  • Re: AMBER: sander error (Sat Oct 30 2004 - 02:58:33 CDT)
  • Re: AMBER: Settings about frozen atoms in sander (Fri Oct 29 2004 - 11:05:36 CDT)
  • AMBER: (Fri Oct 22 2004 - 10:17:15 CDT)
  • AMBER: Amber8 compilation in Dec-Alpha (Sun Oct 10 2004 - 11:22:01 CDT)
  • Re: AMBER: Running on MPI (Sun Oct 03 2004 - 22:08:54 CDT)
  • Re: AMBER: (no subject) (Wed Sep 29 2004 - 10:23:55 CDT)
  • Re: AMBER: phosphoserine library component (Fri Sep 24 2004 - 09:25:24 CDT)
  • Re: AMBER: Amber job submission using PBS (Fri Sep 24 2004 - 01:21:27 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 23:09:06 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 23:05:39 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 12:04:36 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 11:57:35 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 11:11:41 CDT)
  • AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 10:44:39 CDT)
  • AMBER: (Thu Sep 23 2004 - 03:44:49 CDT)
  • Re: AMBER: all_nucleic94 versus all_nucleic02 (Wed Sep 22 2004 - 10:45:36 CDT)
  • Re: AMBER: sander : constraints to conserve hydrogen bonds (Fri Jul 23 2004 - 00:58:15 CDT)
  • Re: AMBER: xleap solvatebox/oct problem (Fri Jul 16 2004 - 04:07:09 CDT)
  • Re: AMBER: xleap solvatebox/oct problem (Thu Jul 15 2004 - 10:18:59 CDT)
  • Re: AMBER: Angle restraint during MD and namelist problem in amber8 (Wed Jul 14 2004 - 11:13:38 CDT)
  • Re: AMBER: Angle restraint during MD (Wed Jul 14 2004 - 00:51:42 CDT)
  • Re: AMBER: Angle restraint during MD (Tue Jul 13 2004 - 11:21:28 CDT)
  • AMBER: Angle restraint during MD (Tue Jul 13 2004 - 04:28:14 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Tue Jul 13 2004 - 04:46:57 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Tue Jul 13 2004 - 04:52:06 CDT)
  • AMBER: (Tue Jul 13 2004 - 04:25:53 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Mon Jul 12 2004 - 04:36:36 CDT)
  • Re: AMBER: Rigid counteranion during MD !! (Sun Jul 11 2004 - 09:51:48 CDT)
  • AMBER: Rigid counteranion during MD !! (Sun Jul 11 2004 - 03:26:35 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sun Jul 11 2004 - 00:24:27 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sun Jul 11 2004 - 00:04:35 CDT)
  • AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sat Jul 10 2004 - 10:30:15 CDT)
  • Re: AMBER: Problem to converge minimization (Mon Jul 05 2004 - 07:38:26 CDT)
  • Re: AMBER: Test run error in amber8 : IBM-AIX (Tue Jun 29 2004 - 20:19:43 CDT)
  • AMBER: Test run error in amber8 : IBM-AIX (Tue Jun 29 2004 - 07:16:48 CDT)
  • Re: AMBER: Amber8 compilation in IBM-AIX (Mon Jun 28 2004 - 19:48:25 CDT)
  • Re: AMBER: Amber8 compilation in IBM-AIX (Mon Jun 28 2004 - 09:39:02 CDT)
  • Re: AMBER: "Total vdw box size" information is gone (Mon Jun 28 2004 - 09:45:39 CDT)
  • AMBER: Amber8 compilation in IBM-AIX (Mon Jun 28 2004 - 04:19:42 CDT)
  • Re: AMBER: simulated anealling (Wed Jun 02 2004 - 23:02:00 CDT)
  • Re: AMBER: Re: AMBER (Wed Jun 02 2004 - 20:48:37 CDT)
  • AMBER: Gaussian Interface ? (Wed Jun 02 2004 - 10:06:12 CDT)
  • Re: AMBER: Free energy in Amber8 (Tue Jun 01 2004 - 20:02:40 CDT)
  • Re: AMBER: Periodic boundary simulation (Tue Jun 01 2004 - 05:14:59 CDT)
  • AMBER: Free energy in Amber8 (Tue Jun 01 2004 - 05:11:54 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Mon May 24 2004 - 22:54:40 CDT)
  • AMBER: Free energies using Sander in Amber8 (Mon May 24 2004 - 21:52:52 CDT)
  • Re: AMBER: Amber8 on Tru64 UNIX on Alpha systems (Thu May 20 2004 - 19:49:42 CDT)
  • AMBER: PF6- force field parameters (Thu May 20 2004 - 19:32:29 CDT)
  • AMBER: Amber8 on Tru64 UNIX on Alpha systems (Wed May 19 2004 - 20:28:50 CDT)
  • AMBER: Atom type with/without POL (Thu May 13 2004 - 09:01:38 CDT)
  • Re: AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 05:58:20 CDT)
  • AMBER: %GIBBS-F-MISMATCH, The parm and coord files disagree on the number of atoms (Tue Apr 27 2004 - 21:29:25 CDT)
  • AMBER: AMBER Gibbs Memory problem (Tue Apr 27 2004 - 11:01:09 CDT)
  • Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 08:28:26 CDT)
  • Re: AMBER: How to solve these warnings? (Wed Apr 21 2004 - 07:06:41 CDT)
  • Re: AMBER: loading PDB problem in leap (Sun Apr 18 2004 - 22:57:16 CDT)
  • Re: AMBER: Dipole moment changes during MD (Fri Apr 09 2004 - 19:48:03 CDT)
  • Re: AMBER: Dipole moment changes during MD (Fri Apr 09 2004 - 13:05:01 CDT)
  • AMBER: Dipole moment changes during MD (Thu Apr 08 2004 - 20:31:17 CDT)
  • Re: AMBER: Amber: Equilibrated DMSO solvent box (Wed Mar 24 2004 - 07:37:30 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 20:54:52 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 08:41:15 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 08:42:01 CST)
  • Re: AMBER: MD at different pH !! (Sat Mar 06 2004 - 01:37:27 CST)
  • AMBER: MD at different pH !! (Fri Mar 05 2004 - 00:30:30 CST)
  • Re: AMBER: (Mon Mar 01 2004 - 18:14:13 CST)
  • AMBER: (Mon Mar 01 2004 - 08:04:17 CST)
  • Re: AMBER: How does LEaP place Na+ ions? (Sun Jan 25 2004 - 19:44:36 CST)
  • Re: AMBER: Cartitian Restraint Error (Sun Jan 25 2004 - 19:36:24 CST)
  • Re: AMBER: Cartitian Restraint Error (Sun Jan 25 2004 - 08:26:31 CST)
  • AMBER: Cartitian Restraint Error (Sun Jan 25 2004 - 08:17:11 CST)
  • AMBER: NTR force constant for restraint !! (Sun Jan 25 2004 - 01:37:09 CST)
  • AMBER: Amber compilation in IBM-SP4 (Sat Jan 10 2004 - 02:28:12 CST)
• Joachim Reichelt
  • Re: AMBER: Can xleap to handle homology model altogether X-ray structure? (Tue Nov 16 2004 - 11:42:02 CST)
  • AMBER: Wich CPU? (Thu Oct 21 2004 - 04:34:26 CDT)
  • Re: AMBER: A tool for building coordinates of huge macromolecules (Wed Sep 15 2004 - 11:37:05 CDT)
  • AMBER: ifort -parallel (Fri Jun 11 2004 - 04:15:58 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:27:59 CDT)
  • Re: AMBER: NTT=4 (Tue May 18 2004 - 12:01:50 CDT)
  • AMBER: NTT=4 (Tue May 18 2004 - 09:30:33 CDT)
• Joe Harriman
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Sat Jul 17 2004 - 07:44:47 CDT)
• Joe Nolan
  • AMBER: LEaP compilation error on Solaris 9 (Mon Nov 22 2004 - 15:21:41 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Thu Nov 11 2004 - 16:00:33 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Thu Nov 11 2004 - 12:50:06 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Wed Nov 10 2004 - 16:43:54 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Wed Nov 10 2004 - 15:11:44 CST)
  • Re: AMBER: Solaris f77 Machine file for Amber7? (Wed Nov 10 2004 - 10:45:50 CST)
  • AMBER: Solaris f77 Machine file for Amber7? (Tue Nov 09 2004 - 16:13:58 CST)
  • AMBER: Amber7 compilation error (Fri Nov 05 2004 - 09:17:39 CST)
  • AMBER: Amber7 installation error on Solaris 9 (Mon Nov 01 2004 - 14:03:25 CST)
• Joey Harriman
  • AMBER: MD simulations with 2 molecules (Wed Feb 18 2004 - 14:32:47 CST)
  • Re: AMBER: mopac.sh (Mon Jan 26 2004 - 08:46:31 CST)
  • Re: AMBER: Which program to use to visualize the RESP Outputs derived by AMBER 7 (Fri Jan 23 2004 - 12:43:43 CST)
• John
  • AMBER: time-averaged restraints (Mon Nov 08 2004 - 14:21:51 CST)
  • AMBER: positive VDWAALS (Sun Nov 07 2004 - 12:11:13 CST)
  • AMBER: parameters-DGnp (Wed Sep 01 2004 - 19:25:03 CDT)
  • AMBER: mm_pbsa Abmer8 example (Tue Jul 27 2004 - 05:38:50 CDT)
  • AMBER: MMPBSA problem (Thu Jun 03 2004 - 11:09:05 CDT)
  • AMBER: torsion angles (Fri May 28 2004 - 18:02:04 CDT)
  • AMBER: time-averaged restraints (Fri May 14 2004 - 12:04:49 CDT)
  • AMBER: reference with ptraj (Thu May 06 2004 - 14:50:48 CDT)
  • AMBER: NMR refinement (Tue Mar 30 2004 - 08:32:55 CST)
  • AMBER: HBOND calculation (Mon Mar 29 2004 - 11:40:26 CST)
  • AMBER: Hydrogen Bond-statistics (Mon Mar 15 2004 - 10:56:53 CST)
  • RE: AMBER: NMR restraints-Floating point exception (Wed Feb 25 2004 - 12:19:25 CST)
  • AMBER: NMR restraints-Floating point exception (Wed Feb 25 2004 - 08:44:52 CST)
  • AMBER: distance-aromatic ring (Thu Feb 19 2004 - 05:03:56 CST)
  • AMBER: (Tue Feb 17 2004 - 04:05:22 CST)
  • AMBER: bad crd file (Mon Feb 16 2004 - 09:30:26 CST)
  • AMBER: SIGSEGV (Mon Feb 16 2004 - 04:43:36 CST)
  • AMBER: dielectric constant (Wed Jan 28 2004 - 08:20:16 CST)
  • AMBER: trajectory file corruption (Tue Jan 27 2004 - 05:11:54 CST)
• John Bushnell
  • Re: AMBER: NMR constraint problem (Wed Dec 08 2004 - 14:39:32 CST)
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 16:41:14 CST)
  • Re: AMBER: xleap couldn't display any word (Mon Mar 15 2004 - 13:46:50 CST)
  • Re: AMBER: Star like (branching) molecule (Tue Feb 24 2004 - 17:33:45 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 17:39:46 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 16:19:48 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 14:44:44 CST)
• John Mongan
  • Re: AMBER: Why the charge is not an integer? (Tue Dec 14 2004 - 21:10:49 CST)
  • Re: AMBER: cpinutil.pl error (Tue Aug 03 2004 - 13:03:40 CDT)
  • AMBER: Re: constant pH calculation in Amber8 (Thu Jul 29 2004 - 16:40:36 CDT)
  • Re: AMBER: Software to visualize normal modes! (Tue Jun 01 2004 - 18:20:38 CDT)
  • Re: AMBER: Titratable amino acid termini (Tue Apr 27 2004 - 18:28:15 CDT)
• Johnson Agbo
  • AMBER: Antechamber Failure (Wed Sep 08 2004 - 16:56:58 CDT)
  • AMBER: Glycam-04 Parameters in Amber 7 (Mon Aug 30 2004 - 20:12:17 CDT)
  • Re: AMBER: Atomic charges in Lactose (Fri Aug 20 2004 - 14:35:48 CDT)
  • AMBER: Updating Amber 7 (Fri Aug 20 2004 - 13:52:23 CDT)
  • AMBER: Atomic charges in Lactose (Tue Aug 10 2004 - 19:23:53 CDT)
  • AMBER: Temperature Regulation (Mon Jul 26 2004 - 23:40:44 CDT)
  • Re: AMBER: Ewald parameter range (Fri Jul 23 2004 - 13:00:12 CDT)
  • AMBER: Ewald parameter range (Thu Jul 22 2004 - 19:16:08 CDT)
  • AMBER: Cubic Ice (Fri Jul 16 2004 - 20:08:14 CDT)
  • AMBER: Normal mode calculation with periodic boundary condition (Thu Jul 15 2004 - 00:15:09 CDT)
  • AMBER: Units of Charges on Atoms (Thu Jun 24 2004 - 14:22:49 CDT)
  • Re: AMBER: The first and second derivatives (Fri Jun 18 2004 - 16:31:15 CDT)
  • Re: AMBER: The first and second derivatives (Fri Jun 18 2004 - 14:05:25 CDT)
  • AMBER: The first and second derivatives (Fri Jun 18 2004 - 13:08:49 CDT)
  • Re: AMBER: Improper Torsional Parameters (Thu Jun 17 2004 - 15:57:08 CDT)
  • AMBER: Improper Torsional Parameters (Mon Jun 14 2004 - 15:41:12 CDT)
  • Re: AMBER: Amber Transition State Output (Fri Jun 11 2004 - 00:28:05 CDT)
  • Re: AMBER: Amber Transition State Output (Wed Jun 09 2004 - 19:33:58 CDT)
  • AMBER: Amber Transition State Output (Wed Jun 09 2004 - 14:46:03 CDT)
• Jon Gray
  • Re: AMBER: PMEMD Problems... (Mon Apr 05 2004 - 22:56:47 CDT)
  • AMBER: PMEMD Problems... (Mon Apr 05 2004 - 15:38:23 CDT)
• Jones, Garth A
  • AMBER: DEBUG and GB (Tue May 18 2004 - 07:02:32 CDT)
• Jose Ramon Blas
  • Re: AMBER: How does LEaP place Na+ ions? (Thu Jan 22 2004 - 15:38:03 CST)
• Joseph E. Maxwell
  • AMBER: Installing AMBER on SGI Octane 2-CPU - erfcfun.c compile prob. (Tue Feb 10 2004 - 17:36:26 CST)
• Joseph Fernandez
  • AMBER: Restraints in sander.QMMM (Tue Sep 14 2004 - 15:54:07 CDT)
• Joseph Nachman
  • Re: AMBER: how to neutralize the peptide (Wed Oct 27 2004 - 12:04:50 CDT)
  • Re: AMBER: Phosphoserine parameters (Wed Sep 29 2004 - 10:50:24 CDT)
  • Re: AMBER: Minimum imaging (Wed Aug 04 2004 - 00:01:54 CDT)
  • RE: AMBER: Molecular dynamic (Tue Jul 13 2004 - 10:21:09 CDT)
  • Re: AMBER: traj. analysis (Wed Jun 30 2004 - 16:44:43 CDT)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Mon Jun 21 2004 - 10:07:57 CDT)
  • Re: AMBER: MOIL-View question (Wed Jun 16 2004 - 15:22:07 CDT)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Wed Jun 16 2004 - 15:16:52 CDT)
  • Re: AMBER: MOIL-View question (Wed Jun 16 2004 - 14:35:17 CDT)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Tue Jun 15 2004 - 14:37:18 CDT)
  • AMBER: RMSD calculations in ptraj and Carnal (Tue Jun 15 2004 - 13:24:38 CDT)
  • AMBER: MOIL-View question (Tue Jun 15 2004 - 13:11:30 CDT)
  • AMBER: Trajectory file (Wed Jun 09 2004 - 14:22:45 CDT)
  • Re: AMBER: trajectory file (Mon Mar 29 2004 - 11:16:58 CST)
  • Re: AMBER: fix two groups (Mon Mar 29 2004 - 10:14:33 CST)
  • Re: AMBER: trajectory file (Tue Mar 23 2004 - 16:38:28 CST)
  • AMBER: trajectory file (Tue Mar 16 2004 - 15:11:58 CST)
  • AMBER: AMBER6 manual (Tue Mar 16 2004 - 15:09:53 CST)
  • Re: AMBER: B factors from simulation and from cryst (Mon Jan 26 2004 - 15:23:49 CST)
• Joshua Hicks
  • AMBER: back interpret (Wed Sep 15 2004 - 16:49:57 CDT)
• Juan Fernandez-Carmona
  • Re: AMBER: How to use these parameters? (Wed Mar 17 2004 - 02:41:39 CST)
  • AMBER: new wed site for amber tutorials (Mon Mar 15 2004 - 02:57:29 CST)
• Jufang Shan
  • AMBER: how to use mm_pbsa_statistics.pl independently (Mon Apr 12 2004 - 21:23:36 CDT)
• Julien Michel
  • Re: AMBER: How to compile antechamber? (Fri Mar 26 2004 - 04:35:11 CST)
  • AMBER: Antechamber license ? (Thu Mar 25 2004 - 04:24:30 CST)
  • AMBER: Assignment of parameters, missing parameters (Mon Mar 22 2004 - 09:47:15 CST)
• Julien Pecher
  • AMBER: carnal (Mon Feb 16 2004 - 07:17:33 CST)
  • AMBER: ptraj (Thu Feb 05 2004 - 02:46:09 CST)
• Junmei Wang
  • RE: AMBER: antechamber - missing improper torsions (Wed Jul 21 2004 - 11:11:04 CDT)
  • RE: AMBER: Restrain or freeze molecule question? (Thu Jun 24 2004 - 12:44:03 CDT)
  • Re: AMBER: unnatural base - RESP charges in ANTECHAMBER (Mon Jun 07 2004 - 20:22:31 CDT)
  • Re: AMBER: problem in antechamber (Wed May 19 2004 - 17:21:43 CDT)
  • Re: AMBER: Problem : antechamber produces no output (Wed May 12 2004 - 09:40:00 CDT)
  • AMBER: Possible amber8 antechamber PDB parsing bug (Thu May 06 2004 - 12:09:30 CDT)
  • Re: AMBER: some bugfixes (Tue May 04 2004 - 14:23:55 CDT)
  • Re: AMBER: antechamber + FAILED TO ACHIEVE SCF (Mon Feb 09 2004 - 13:27:02 CST)
  • Re: AMBER: (No subject) (Fri Jan 30 2004 - 15:37:46 CST)
  • Re: AMBER: (No subject) (Fri Jan 30 2004 - 09:02:50 CST)
  • RE: AMBER: atom type CM (Tue Jan 20 2004 - 10:43:23 CST)
  • Re: AMBER: atom type CM (Fri Jan 16 2004 - 15:13:19 CST)
  • Re: AMBER: "ATTN, need revision" (Wed Jan 14 2004 - 14:39:47 CST)
• justin litchfield
  • Re: AMBER: xfl90 and xlc "C" compiler (Sat Nov 27 2004 - 14:42:22 CST)
  • Re: AMBER: sander.QMMM on Mac (Sat Nov 27 2004 - 02:29:26 CST)
  • AMBER: sander.QMMM on Mac (Fri Nov 26 2004 - 17:17:35 CST)
  • Re: AMBER: ambpdb segmentation fault (Sun Nov 21 2004 - 23:09:25 CST)
  • Re: AMBER: ambpdb segmentation fault (Wed Nov 17 2004 - 16:46:01 CST)
  • AMBER: ambpdb segmentation fault (Mon Nov 15 2004 - 20:57:14 CST)
• Justin Sanders
  • AMBER: Compiling AMBER8 (Thu Sep 30 2004 - 09:54:05 CDT)
  • AMBER: Force Compiling AMBER8 for an SGI O2 (Thu Sep 16 2004 - 13:34:12 CDT)
• jwcraft_at_uh.edu
  • AMBER: phosphoserine library component (Fri Sep 24 2004 - 09:01:28 CDT)
  • AMBER: Re. HSG Convention (Wed Sep 01 2004 - 10:48:41 CDT)
  • AMBER: (Mon Aug 30 2004 - 14:54:46 CDT)
• jwfang
  • AMBER: question about J. Am. Chem. Soc. 2001, 123, 5221 paper (Thu Sep 23 2004 - 10:15:36 CDT)
  • AMBER: mm_pbsa.pl nmode entropy estimating problem (Wed Sep 22 2004 - 14:30:21 CDT)
  • AMBER: gibbs dynamic memory error (Mon Mar 22 2004 - 10:43:46 CST)
  • AMBER: antechamber error (Mon Feb 09 2004 - 09:50:17 CST)
• Jyh-Shyong Ho
  • Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler andMPICH on AMD OPTERON 64 (Tue May 25 2004 - 19:07:34 CDT)
• jz7_at_duke.edu
  • AMBER: can MM-PBSA be applied to Charmm format trajectory file? (Thu Aug 19 2004 - 13:55:06 CDT)
  • AMBER: question about covariance matrix from ptraj (Mon Aug 09 2004 - 14:25:10 CDT)
  • AMBER: trival question about format of pev file and covariance matrix (Mon Aug 09 2004 - 10:52:03 CDT)
  • AMBER: about correlation calculation in ptraj (Tue Jul 27 2004 - 16:20:53 CDT)
  • AMBER: about running ptraj in ambber8 (re-post) (Mon Jul 26 2004 - 15:47:52 CDT)
  • RE: AMBER: about running ptraj in amber8 (Mon Jul 26 2004 - 11:30:42 CDT)
  • AMBER: about running ptraj in amber8 (Mon Jul 26 2004 - 09:04:33 CDT)
  • AMBER: question about ptraj (Wed Jul 21 2004 - 15:00:01 CDT)
  • RE: AMBER: what is averaged RMS fluctuation? (Mon Jul 12 2004 - 14:59:26 CDT)
  • AMBER: what is averaged RMS fluctuation? (Mon Jul 12 2004 - 11:17:30 CDT)
  • AMBER: question about Ptraj (Thu Jul 08 2004 - 11:32:07 CDT)
  • AMBER: question about water molecule (Mon Jun 28 2004 - 12:34:19 CDT)
  • AMBER: question about building prmtop and inpcrd files in xleap (Mon Jun 28 2004 - 09:49:39 CDT)
  • RE: AMBER: question about xleap (Thu Jun 03 2004 - 14:40:10 CDT)
  • Re: AMBER: question about xleap (Thu Jun 03 2004 - 13:34:03 CDT)
  • AMBER: question about xleap (Thu Jun 03 2004 - 12:19:27 CDT)
  • AMBER: Amber force field for protein-DNA system (again) (Wed Jun 02 2004 - 12:31:56 CDT)
  • AMBER: Amber force field for protein-DNA system (again) (Tue Jun 01 2004 - 14:51:59 CDT)
  • AMBER: Amber force field for protein-DNA system (Tue Jun 01 2004 - 11:14:16 CDT)
• Kamp, Marc vander
  • AMBER: antechamber: atomtype assignment of cc/cd etc pairs in GAFF / creating atom type definition file (Thu May 27 2004 - 08:01:13 CDT)
• Kara Wald
  • AMBER: Antechamber problems (Tue Nov 23 2004 - 12:49:43 CST)
  • AMBER: Re: Amber Re: Antechamber problems (Mon Nov 15 2004 - 15:05:19 CST)
  • Re: AMBER: Re: Antechamber (Mon Nov 08 2004 - 15:49:13 CST)
  • AMBER: Re: Antechamber (Thu Nov 04 2004 - 15:13:28 CST)
  • AMBER: (Thu Nov 04 2004 - 15:05:42 CST)
• Karin Schleinkofer
  • AMBER: ptraj (Thu Feb 12 2004 - 04:57:47 CST)
  • AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 08:39:40 CST)
  • AMBER: conversion of amber trajectories to gromos /(xtc) (Thu Jan 29 2004 - 07:10:28 CST)
• Karl N. Kirschner
  • AMBER: solvation free energies using mmpbsa (Thu Oct 28 2004 - 12:15:38 CDT)
  • Re: AMBER: MM_PBSA reproduction of literature values and accuracy (Tue Oct 26 2004 - 17:35:19 CDT)
  • AMBER: MM_PBSA reproduction of literature values and accuracy (Mon Oct 25 2004 - 12:41:34 CDT)
  • RE: AMBER: MAXRING Antechamber problem (Wed Sep 22 2004 - 15:17:31 CDT)
  • AMBER: MAXRING Antechamber problem (Tue Sep 21 2004 - 14:37:44 CDT)
  • Re: AMBER: Atomic charges in Lactose (Wed Aug 11 2004 - 07:47:46 CDT)
  • Re: AMBER: how to correct the charge of oligosaccharides (Tue Aug 10 2004 - 09:53:29 CDT)
  • Re: AMBER: problems in using glycam (Wed Jun 30 2004 - 10:29:37 CDT)
  • AMBER: Atom Labels (Tue Jun 29 2004 - 15:36:22 CDT)
  • AMBER: Glycam04 (Wed Mar 24 2004 - 13:37:56 CST)
  • AMBER: Sorry about that... (Thu Mar 04 2004 - 10:22:53 CST)
  • AMBER: Glycam_04.prep (Thu Mar 04 2004 - 10:20:24 CST)
• Karol Miaskiewicz
  • AMBER: Re: parallel Sander (amber8): run-time error under Irix (Tue Jun 08 2004 - 15:30:38 CDT)
  • AMBER: Re: parallel Sander (amber8): run-time error under Irix (Tue Jun 08 2004 - 15:04:14 CDT)
  • Re: AMBER: parallel Sander (amber8): run-time error under Irix (Thu Jun 03 2004 - 14:15:05 CDT)
  • Re: AMBER: parallel Sander (amber8): run-time error under Irix (Thu Jun 03 2004 - 10:29:06 CDT)
  • AMBER: parallel Sander (amber8): run-time error under Irix (Thu Jun 03 2004 - 09:42:25 CDT)
• Karsten Suhre
  • AMBER: announcing normal mode analysis web server ElNemo (Thu Jul 15 2004 - 03:21:07 CDT)
• Kazuo Koyano
  • Re: AMBER: free energy (Mon Jun 28 2004 - 03:45:41 CDT)
  • Re: AMBER: PBCAL in mm-pbsa calculation (Mon Jun 21 2004 - 01:14:56 CDT)
  • Re: AMBER: mm_pbsa examples; delphi in mm_pbsa (Fri May 14 2004 - 04:35:36 CDT)
  • Re: AMBER: Optimizing a structure and the interpretation of it (Mon Apr 26 2004 - 00:14:25 CDT)
  • AMBER: mm_pbsa examples; delphi in mm_pbsa (Thu Apr 22 2004 - 03:34:03 CDT)
• Kei ODAI
  • AMBER: Amber 8 installation error on Xeon 2-CPU (Thu Sep 23 2004 - 18:11:15 CDT)
• Kennie Merz
  • Re: AMBER: Problem with divcon - increasing MXATTS? (Wed Jul 14 2004 - 12:03:32 CDT)
  • Re: AMBER: Problem with divcon - increasing MXATTS? (Wed Jul 14 2004 - 11:01:54 CDT)
  • Re: AMBER: Pang-model of Zn2+ (Fri Mar 26 2004 - 07:52:43 CST)
• Kepa Koldo Burusco Goñi
  • AMBER: sander, MD problems (Mon Nov 22 2004 - 06:00:37 CST)
  • FWD: RE: AMBER: xleap problems (Tue Nov 16 2004 - 04:56:40 CST)
  • AMBER: xleap problems (Fri Nov 12 2004 - 13:33:42 CST)
• Kevin Murphy
  • AMBER: install problem (Tue Dec 07 2004 - 04:23:11 CST)
• Kijeong Kwac
  • AMBER: MD simulation at pH=1 (Wed Nov 03 2004 - 22:20:01 CST)
• klamothe_at_uiuc.edu
  • AMBER: "ATTN, need revision" (Wed Jan 14 2004 - 14:07:56 CST)
• Knut Langsetmo
  • AMBER: amber 7 nmode on osx (Mon Nov 08 2004 - 17:26:26 CST)
  • AMBER: amber7 test on osx (Fri Oct 29 2004 - 13:03:25 CDT)
  • Re: AMBER: amber7, namelist, xlf and osx (Tue May 25 2004 - 08:17:26 CDT)
  • AMBER: amber7, namelist, xlf and osx (Wed May 19 2004 - 17:47:26 CDT)
  • AMBER: oxs g5 machine file (Wed Jan 21 2004 - 14:10:33 CST)
• koby levy
  • AMBER: Removal of rotation: Flying ice cube (Tue May 18 2004 - 19:23:54 CDT)
• Kristina Furse
  • RE: AMBER: MD & running time (Wed Jun 23 2004 - 14:53:13 CDT)
  • RE: AMBER: How to solve these warnings? (Wed Apr 21 2004 - 15:35:57 CDT)
  • RE: AMBER: free energy perturbation (Tue Apr 06 2004 - 11:53:39 CDT)
  • RE: AMBER: how to use prep file (Mon Feb 23 2004 - 14:14:20 CST)
  • RE: AMBER: PMEMD and nmropt=1 (Thu Feb 05 2004 - 15:19:52 CST)
  • RE: AMBER: atom type CM (Fri Jan 16 2004 - 15:56:47 CST)
  • AMBER: atom type CM (Fri Jan 16 2004 - 14:37:38 CST)
• Kristy Mardis
  • AMBER: resp demo files (Mon May 03 2004 - 14:29:45 CDT)
• Kuhn, Bernd {PRBD~Basel}
  • Re: AMBER: leap problem in AMBER7 (residue insertion) (Wed Jul 14 2004 - 06:44:00 CDT)
  • AMBER: leap problem in AMBER7 (residue insertion) (Mon Jul 05 2004 - 06:26:34 CDT)
• Kun Song
  • Re: AMBER: question about ptraj's Mask (Thu Oct 28 2004 - 16:10:34 CDT)
  • AMBER: question about ptraj's Mask (Thu Oct 28 2004 - 15:52:08 CDT)
• L Jin
  • AMBER: XLeap: head/tail and frcmod (Mon Apr 12 2004 - 06:35:47 CDT)
  • RE: AMBER: add Na+ (Wed Feb 25 2004 - 04:33:02 CST)
  • RE: AMBER: add Na+ (Tue Feb 24 2004 - 13:29:36 CST)
  • AMBER: add Na+ (Tue Feb 24 2004 - 12:23:55 CST)
  • Re: AMBER: minimization output (Fri Feb 20 2004 - 04:36:35 CST)
  • RE: AMBER: Close contact warnings (Thu Feb 19 2004 - 09:11:54 CST)
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 12:56:49 CST)
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 10:55:55 CST)
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 04:14:55 CST)
  • Re: AMBER: Close contact warnings (Tue Feb 17 2004 - 12:14:37 CST)
  • AMBER: Close contact warnings (Tue Feb 17 2004 - 08:29:57 CST)
  • AMBER: DIELC (Mon Feb 16 2004 - 07:51:35 CST)
  • Re: AMBER: minimization output (Fri Feb 13 2004 - 03:49:52 CST)
  • AMBER: minimization output (Tue Feb 10 2004 - 10:36:25 CST)
  • AMBER: xleap & antechamber (Tue Feb 03 2004 - 03:46:54 CST)
  • AMBER: XLEAP (Thu Jan 29 2004 - 08:40:28 CST)
  • Re: AMBER: restrt (Thu Jan 22 2004 - 08:05:03 CST)
  • AMBER: restrt (Thu Jan 22 2004 - 05:03:51 CST)
  • AMBER: NTF (Fri Jan 16 2004 - 05:15:16 CST)
  • Re: AMBER: strange output of MD (Wed Jan 07 2004 - 12:21:03 CST)
  • AMBER: strange output of MD (Wed Jan 07 2004 - 10:42:49 CST)
  • AMBER: Atom type (Wed Jan 07 2004 - 05:26:25 CST)
  • AMBER: rms in ptraj (Mon Jan 05 2004 - 08:49:47 CST)
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Thu Jan 01 2004 - 04:47:18 CST)
• Lao_3
  • RE: AMBER: unknown residue: ABA (Wed Aug 11 2004 - 10:45:44 CDT)
  • Re: AMBER: unknown residue: ABA (Tue Aug 10 2004 - 16:45:27 CDT)
• Lee SL
  • RE: AMBER: simulated annealing (Sat Aug 14 2004 - 05:40:54 CDT)
  • AMBER: simulated annealing (Sat Aug 14 2004 - 04:51:14 CDT)
• lei jia
  • Re: AMBER: paramitrization problem (Tue Jun 08 2004 - 12:45:02 CDT)
  • RE: AMBER: paramitrization problem (Tue Jun 08 2004 - 10:00:11 CDT)
  • AMBER: paramitrization problem (Mon Jun 07 2004 - 17:12:37 CDT)
• Lifeng Tian_at_PantherServer
  • Re: AMBER: compiling software(RESP) on MAC G5 (Thu Feb 19 2004 - 14:41:05 CST)
• Lihua Wang
  • Re: AMBER: parm94 (Tue Aug 31 2004 - 17:22:29 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 19:16:46 CDT)
  • AMBER: residue database (Sat Aug 14 2004 - 16:55:59 CDT)
  • AMBER: bugfix.all (Tue Aug 10 2004 - 15:48:51 CDT)
• Lijiang Yang
  • AMBER: rdparm problem (Mon Aug 09 2004 - 17:43:10 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Fri Aug 06 2004 - 13:42:06 CDT)
  • Re: AMBER: Using TIP4P water in free energy calculation (Fri Aug 06 2004 - 00:04:07 CDT)
  • AMBER: Using TIP4P water in free energy calculation (Thu Aug 05 2004 - 17:03:36 CDT)
• Linda Prengaman
  • Re: AMBER: MD & running time (Tue Jun 22 2004 - 14:12:00 CDT)
  • AMBER: Checking Results? (Thu Jun 10 2004 - 20:49:33 CDT)
  • Re: AMBER: LINMIN failure (Thu Jun 10 2004 - 16:41:46 CDT)
  • AMBER: Amber 7 (sander) use of PME (Thu May 27 2004 - 14:42:13 CDT)
  • AMBER: Sander klambda question (Wed May 05 2004 - 17:14:22 CDT)
  • AMBER: more vlimit exceeded problems... (Tue Apr 06 2004 - 21:22:44 CDT)
• Lishan Yao
  • AMBER: Ammonia (Thu May 20 2004 - 16:11:43 CDT)
  • AMBER: shake option in sander (Wed May 12 2004 - 08:32:48 CDT)
  • Re: AMBER: hbond analysis in ptraj(%occupied>1) (Thu Mar 25 2004 - 12:54:59 CST)
  • AMBER: hbond analysis in ptraj(%occupied>1) (Thu Mar 25 2004 - 09:19:01 CST)
  • AMBER: NMR restraint in sander (Tue Mar 09 2004 - 08:19:30 CST)
  • AMBER: image in ptraj (Mon Feb 16 2004 - 10:11:25 CST)
  • Re: AMBER: TER in amber (Thu Feb 12 2004 - 11:12:45 CST)
  • Re: AMBER: TER in amber (Thu Feb 12 2004 - 12:08:29 CST)
  • Re: AMBER: TER in amber (Thu Feb 12 2004 - 10:17:02 CST)
  • AMBER: TER in amber (Thu Feb 12 2004 - 09:04:03 CST)
  • Re: AMBER: LES question (Thu Feb 12 2004 - 07:59:02 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 13:52:09 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 13:20:54 CST)
  • Re: AMBER: LES question (Wed Feb 11 2004 - 08:16:01 CST)
  • Re: AMBER: LES question (Tue Feb 10 2004 - 15:02:18 CST)
  • AMBER: LES question (Tue Feb 10 2004 - 14:47:20 CST)
  • Re: AMBER: LES question (Thu Jan 29 2004 - 08:46:22 CST)
  • Re: AMBER: LES question (Wed Jan 28 2004 - 16:17:55 CST)
  • AMBER: LES question (Wed Jan 28 2004 - 12:52:58 CST)
  • AMBER: File format generated by respgen (Mon Jan 05 2004 - 10:50:38 CST)
• Livadaru, Lucian
  • AMBER: amber compilation (Mon Jul 26 2004 - 15:15:50 CDT)
• Lubos Vrbka
  • Re: AMBER: -p4pg problem (Sat Jun 26 2004 - 09:42:55 CDT)
  • Re: AMBER: -p4pg problem (Sat Jun 26 2004 - 05:59:53 CDT)
  • Re: AMBER: amber8 performance on linux cluster (Tue Apr 27 2004 - 12:26:14 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Tue Apr 27 2004 - 09:58:25 CDT)
  • AMBER: PMEMD scaling (Sun Apr 25 2004 - 09:07:43 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Sat Apr 24 2004 - 16:18:11 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Sat Apr 24 2004 - 05:50:02 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Fri Apr 23 2004 - 13:18:36 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Fri Apr 23 2004 - 12:33:32 CDT)
  • AMBER: pmemd and mpich - myrinet (Fri Apr 23 2004 - 10:59:31 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Wed Apr 14 2004 - 14:21:54 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Wed Apr 14 2004 - 11:18:22 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Wed Apr 14 2004 - 07:48:59 CDT)
  • Re: AMBER: amber/pmemd with mpiexec (Sun Apr 11 2004 - 09:00:36 CDT)
  • AMBER: amber/pmemd with mpiexec (Sat Apr 10 2004 - 11:50:30 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Wed Mar 31 2004 - 13:44:19 CST)
  • AMBER: pmemd speedup and interactions (Wed Mar 31 2004 - 03:55:14 CST)
  • AMBER: pmemd speedup and interactions (Wed Mar 31 2004 - 03:27:21 CST)
  • Re: AMBER: pmemd machinefiles (Mon Mar 29 2004 - 07:34:50 CST)
  • AMBER: pmemd machinefiles (Mon Mar 29 2004 - 04:38:13 CST)
  • Re: AMBER: non-isotropic pressure scaling (Wed Mar 24 2004 - 08:33:20 CST)
  • AMBER: non-isotropic pressure scaling (Wed Mar 24 2004 - 06:38:08 CST)
• lucian livadaru
  • RE: AMBER: amber8 compilation (Mon Nov 22 2004 - 16:22:43 CST)
  • AMBER: amber8 compilation (Fri Nov 19 2004 - 12:51:00 CST)
• Luis Gracia
  • Re: AMBER: md.out & plot (Tue Nov 23 2004 - 16:43:33 CST)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Tue Jun 15 2004 - 19:19:53 CDT)
  • Re: AMBER: conversion of amber trajectories to gromos /(xtc) (Thu Jan 29 2004 - 14:27:48 CST)
• luocheng
  • AMBER: a problem about alanine scan of proline (Tue Mar 09 2004 - 03:00:27 CST)
• M. L. Dodson
  • Re: AMBER: Problem with a single aminoacid as inhibitor (Wed Nov 17 2004 - 09:29:26 CST)
  • Re: AMBER: More AMBER 8 compilation problems on OSF1 4.0F (Tue Oct 19 2004 - 07:22:32 CDT)
  • Re: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 13:41:15 CDT)
  • Re: AMBER: (no subject) (Wed Sep 29 2004 - 10:39:12 CDT)
  • Re: AMBER: Neutral C and N termini. (Sun Aug 29 2004 - 21:14:10 CDT)
  • AMBER: temperature control in coupled potential runs (Mon Aug 16 2004 - 14:05:49 CDT)
  • Re: AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Thu Aug 05 2004 - 17:30:20 CDT)
  • Re: AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Wed Aug 04 2004 - 19:08:07 CDT)
  • AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Wed Aug 04 2004 - 14:23:29 CDT)
  • Re: AMBER: peptide-DNA crosslink modeling (Fri Jul 02 2004 - 13:06:39 CDT)
  • AMBER: peptide-DNA crosslink modeling (Thu Jul 01 2004 - 16:51:24 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Tue May 18 2004 - 07:33:28 CDT)
  • Re: AMBER: thermodynamic integration of ring opening (Mon May 17 2004 - 18:46:29 CDT)
  • Re: AMBER: Creating Parmtop files for NAMD (Tue Apr 13 2004 - 20:39:26 CDT)
• Madalin Giambasu
  • AMBER: impose: Illegal angle internal definition (Wed Sep 29 2004 - 11:34:18 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 09:47:55 CDT)
  • Re: AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 08:51:35 CDT)
  • AMBER: temperature scaling with ntt=3(Langevin thermostat) (Mon Aug 30 2004 - 03:01:05 CDT)
  • AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 12:47:53 CDT)
  • AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Fri Aug 13 2004 - 05:02:57 CDT)
  • Re: AMBER: different cooling schedules for simulated annealing (Wed Aug 11 2004 - 11:23:08 CDT)
  • AMBER: different cooling schedules for simulated annealing (Wed Aug 11 2004 - 06:51:09 CDT)
  • AMBER: error while loading shared libraries: libcxa.so.5 (Mon Aug 09 2004 - 08:54:00 CDT)
• Madan
  • Re: AMBER: Error while protonating a PDB file (Thu Mar 25 2004 - 23:03:56 CST)
• madeleine.richard_at_bull.net
  • AMBER: Amber on RedHat 3.0 (Tue Mar 09 2004 - 03:39:47 CST)
• Magne Olufsen
  • AMBER: strange bond energies (Mon Dec 06 2004 - 07:42:16 CST)
  • AMBER: mm_PBSA: problems calculating molecular surface for some snapshots (Mon Nov 08 2004 - 03:50:39 CST)
  • AMBER: mmpbsa: can not generate coordinates/snapshots (Mon Sep 13 2004 - 05:37:54 CDT)
• Mail System Internal Data
  • DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA (Thu May 05 2005 - 14:26:38 CDT)
• Majid moghaddam
  • AMBER: PCA prep file (Tue May 18 2004 - 03:19:26 CDT)
• Marc Baaden
  • Re: AMBER: amber8 parallel installation with mpich (Tue Nov 30 2004 - 06:27:18 CST)
  • Re: AMBER: amber8 parallel installation with mpich (Tue Nov 30 2004 - 06:00:26 CST)
  • AMBER: MMPBSA PB parameters - PARSE implementation in Amber (Wed Oct 13 2004 - 12:42:34 CDT)
  • AMBER: PBSA parameter question (Radii and Charges) (Tue Oct 12 2004 - 19:01:19 CDT)
  • Re: AMBER: WHICH LINUX (Tue Apr 13 2004 - 10:20:35 CDT)
• Marc Perea
  • AMBER: SANDER BOMB in subroutine nonbond_list (Tue Nov 02 2004 - 06:45:34 CST)
  • AMBER: Problems with amber8 and pgf90 (Thu Jul 15 2004 - 05:30:36 CDT)
  • AMBER: Problem : antechamber produces no output (Tue May 11 2004 - 05:19:52 CDT)
• Marcela Madrid
  • Re: AMBER: idecomp (Thu Jul 08 2004 - 14:35:57 CDT)
  • AMBER: idecomp (Tue Jul 06 2004 - 10:42:20 CDT)
• Marcin Krol
  • AMBER: Slowly releasing restraints (Tue Nov 30 2004 - 05:12:37 CST)
  • Re: AMBER: RMSD result from GB model (Thu Aug 05 2004 - 03:32:36 CDT)
  • AMBER: multiple heat bath GB+LES (Mon Jul 05 2004 - 11:53:31 CDT)
  • AMBER: GB+LES (Wed Jun 30 2004 - 04:43:27 CDT)
  • AMBER: Born radii (Fri Jun 25 2004 - 06:24:48 CDT)
  • Re: AMBER: How to neutralize system? (Wed Jun 09 2004 - 09:57:11 CDT)
  • AMBER: Scaling nb between groups (Tue May 25 2004 - 10:34:00 CDT)
  • AMBER: IGR1/grnam1 problem (Tue May 18 2004 - 12:40:58 CDT)
  • AMBER: ptraj read in matrix (Mon May 10 2004 - 06:57:25 CDT)
  • AMBER: ptraj analyze matrix entropy (Fri May 07 2004 - 03:01:23 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Thu May 06 2004 - 08:48:02 CDT)
  • Re: AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 10:07:05 CDT)
  • AMBER: ptraj analyze matrix entropy (Wed May 05 2004 - 04:19:32 CDT)
• Marco Aurelio Correia Preto
  • AMBER: RE: Amber: Equilibrated DMSO solvent box (Thu Mar 25 2004 - 03:26:41 CST)
  • AMBER: Amber: Equilibrated DMSO solvent box (Wed Mar 24 2004 - 05:32:31 CST)
  • AMBER: Resizing sizes.h and recompiling problem! (Sat Mar 13 2004 - 08:38:56 CST)
• Marek Dynowski
  • AMBER: POPE membrane, How to obtain prep and parm files? (Sat Jun 12 2004 - 12:07:08 CDT)
• Mark Williamson
  • Re: AMBER: xleap problems (Fri Nov 12 2004 - 17:58:05 CST)
  • Re: AMBER: error while loading shared libraries: libcxa.so.5 (Mon Aug 09 2004 - 09:42:16 CDT)
  • RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sun Jul 11 2004 - 15:52:45 CDT)
  • Re: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sat Jul 10 2004 - 12:54:56 CDT)
  • AMBER: Possible amber8 antechamber PDB parsing bug (Thu May 06 2004 - 10:16:19 CDT)
• Marsita M
  • AMBER: nrespa=2 (Tue Dec 21 2004 - 09:19:58 CST)
  • AMBER: Dielectric Constant (Sat Dec 04 2004 - 05:42:36 CST)
  • AMBER: question! (Sun Nov 28 2004 - 21:01:41 CST)
  • Re: AMBER: radius of gyration (Sun Sep 26 2004 - 01:40:24 CDT)
  • AMBER: radius of gyration (Sat Sep 25 2004 - 21:13:25 CDT)
  • AMBER: ptraj problem (Thu Sep 23 2004 - 18:53:53 CDT)
  • AMBER: general questions (Mon Sep 06 2004 - 10:58:34 CDT)
  • AMBER: minimization output file format (Thu Aug 12 2004 - 12:51:35 CDT)
• Martin Fabani
  • AMBER: MD with NTR + NMROPT (Mon May 10 2004 - 03:56:28 CDT)
• Martin Lepsik
  • Re: AMBER: XLEAP (Thu Jan 29 2004 - 09:43:18 CST)
  • Re: AMBER: references? (Thu Jan 29 2004 - 09:32:23 CST)
  • Re: AMBER: Normal modes of protein-ligand (Thu Jan 29 2004 - 03:47:22 CST)
  • Re: AMBER: dielectric constant (Wed Jan 28 2004 - 09:42:05 CST)
  • AMBER: Normal modes of protein-ligand (Wed Jan 28 2004 - 07:43:12 CST)
• Martin Mucha
  • AMBER: IOUTFM and binary/unformatted files error (Tue May 25 2004 - 02:18:44 CDT)
• Martina Roeselova
  • Re: AMBER: EWALD BOMB? (Mon Mar 22 2004 - 13:42:01 CST)
  • AMBER: rstdip (Wed Feb 04 2004 - 11:57:18 CST)
  • Re: AMBER: What does this error message mean? (Tue Feb 03 2004 - 13:55:22 CST)
  • Re: AMBER: NVE&polarizable force field (Mon Feb 02 2004 - 11:33:17 CST)
  • AMBER: Fwd: NVE & polarizable force field] (Fri Jan 23 2004 - 20:16:32 CST)
  • AMBER: free energy profile calculation (Wed Jan 14 2004 - 15:14:48 CST)
• Masataka Nagaoka
  • Re: AMBER: FEP along a reaction coordinate in sander (Wed Dec 01 2004 - 06:05:01 CST)
• Matheus Froeyen
  • AMBER: antechamber (Wed Jun 09 2004 - 02:39:26 CDT)
• mathew k varghese
  • AMBER: constructing a small colecule (Thu Nov 04 2004 - 22:41:58 CST)
  • AMBER: building a small molecule (Tue Oct 05 2004 - 04:01:09 CDT)
  • AMBER: amber8 tests (Wed Sep 22 2004 - 09:30:09 CDT)
  • AMBER: amber8 installation (Wed Sep 22 2004 - 02:07:50 CDT)
  • AMBER: ifort installation (Sun Sep 19 2004 - 03:46:57 CDT)
  • AMBER: antechamber test (Sun Aug 08 2004 - 07:31:22 CDT)
  • AMBER: sander tutorial (Thu Jul 22 2004 - 07:16:33 CDT)
• Ma³gorzata Jaroñczyk
  • AMBER: Can you write me how can I add the ACE and NMe groups in the Xleap? (Tue Feb 24 2004 - 08:59:46 CST)
  • AMBER: How to add ACE and NME groups? (Mon Feb 23 2004 - 03:47:00 CST)
  • AMBER: Re: To David Case (Fri Feb 13 2004 - 05:25:52 CST)
  • Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function (Thu Feb 12 2004 - 08:28:59 CST)
  • AMBER: Run calculations for protein in Amber (Thu Feb 12 2004 - 03:18:20 CST)
• mcpreto_at_fc.up.pt
  • Re: AMBER: How to apply OPLS force field? (Wed Jul 14 2004 - 08:26:04 CDT)
• MD Tyka, Biochemistry
  • AMBER: Amber 03 Forcefield discrepancy (Mon Aug 30 2004 - 09:36:18 CDT)
  • AMBER: Thermostat comparison ? (Mon Feb 23 2004 - 11:41:56 CST)
• Meg McCarrick
  • RE: AMBER: antechamber + mopac error (Thu Feb 05 2004 - 11:12:42 CST)
• Melinda Layten
  • Re: AMBER: trajectory file question? (Thu Oct 28 2004 - 14:35:17 CDT)
  • Re: AMBER: getting new box info (Thu Oct 28 2004 - 10:46:57 CDT)
  • Re: AMBER: REST (Wed Sep 08 2004 - 15:51:30 CDT)
  • Re: AMBER: [0] MPI Abort by user Aborting program ! (Wed Sep 01 2004 - 10:04:15 CDT)
• Mengjuei Hsieh
  • Re: AMBER: Compiling Amber8 on Mac OS X (Fri Jun 11 2004 - 17:59:14 CDT)
  • Re: AMBER: Compiling Amber8 on Mac OS X (Thu Jun 10 2004 - 16:11:24 CDT)
  • Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Mon May 24 2004 - 14:12:39 CDT)
  • Re: AMBER: NHE problem (Sat May 22 2004 - 19:30:07 CDT)
  • Re: AMBER: amber7, namelist, xlf and osx (Wed May 19 2004 - 19:56:23 CDT)
  • Re: AMBER: Redhat install (Thu Apr 29 2004 - 23:44:12 CDT)
  • Re: AMBER: Mac OSX xleap compilation (Fri Apr 02 2004 - 13:46:14 CST)
  • Re: AMBER: Mac OSX xleap compilation (Fri Apr 02 2004 - 01:19:30 CST)
• Michael Crowley
  • Re: AMBER: error message about the input file of sander (Tue Nov 09 2004 - 00:48:03 CST)
  • Re: AMBER: positive VDWAALS (Sun Nov 07 2004 - 15:51:26 CST)
  • Re: AMBER: amber7 test on osx (Fri Oct 29 2004 - 13:31:09 CDT)
  • Re: AMBER: parallel of sander_classic (Tue Oct 26 2004 - 15:03:36 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 10:56:06 CDT)
  • Re: AMBER: non-periodic simulation and box information !! (Wed Apr 21 2004 - 12:32:58 CDT)
  • Re: AMBER: sander + ewald bomb (Wed Feb 18 2004 - 15:13:42 CST)
• Michael Dolan
  • Re: AMBER: N-terminal Arg charges in ff99 not 1.00 (Thu Jul 01 2004 - 14:57:37 CDT)
  • Re: AMBER: N-terminal Arg charges in ff99 not 1.00 (Thu Jul 01 2004 - 14:04:37 CDT)
  • Re: AMBER: N-terminal Arg charges in ff99 not 1.00 (Thu Jul 01 2004 - 14:00:45 CDT)
  • AMBER: N-terminal Arg charges in ff99 not 1.00 (Wed Jun 30 2004 - 16:08:15 CDT)
• Michael George Lerner
  • Re: AMBER: Close contact warnings (Wed Feb 18 2004 - 07:58:50 CST)
  • Re: AMBER: (Tue Jan 13 2004 - 13:18:57 CST)
• Michael Trieb
  • Re: AMBER: ptraj & LES (Mon Feb 02 2004 - 11:11:08 CST)
• Michele Porro
  • AMBER: simulated anealing ...vlimit exceed (Tue May 11 2004 - 02:24:56 CDT)
• Miguel
  • Re: AMBER: Periodic boundary simulation (Tue Jun 01 2004 - 06:14:34 CDT)
  • Re: AMBER: Free energy in Amber8 (Tue Jun 01 2004 - 06:11:39 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 04:54:55 CDT)
  • AMBER: Problem compiling amber7 (Fri May 21 2004 - 04:15:10 CDT)
• Miguel de Federico
  • Re: AMBER: Gibbs and solvent caps (Mon May 03 2004 - 05:28:47 CDT)
  • AMBER: GIBBS: FEP and TI (Mon Mar 29 2004 - 11:03:53 CST)
  • AMBER: GIBBS + vlimit exceeded (Mon Mar 01 2004 - 11:17:44 CST)
  • AMBER: LEaP- Error reading frcmod parameters. (Mon Feb 02 2004 - 12:03:00 CST)
  • AMBER: SANDER - Abnormal high velocities (Wed Jan 28 2004 - 05:16:45 CST)
  • AMBER: LEAP - Error loading units (Wed Jan 14 2004 - 11:12:29 CST)
• Mike
  • RE: AMBER: Problem with sander - Error on Open (Thu Jul 08 2004 - 20:57:43 CDT)
  • AMBER: Problem with sander - Error on Open (Thu Jul 08 2004 - 16:38:37 CDT)
  • Re: AMBER: Problem in loading a PDB file in Leap - Please help me (Sat Apr 17 2004 - 12:35:22 CDT)
  • Re: AMBER: Problem in loading a PDB file in Leap - Please help me (Sat Apr 17 2004 - 00:19:02 CDT)
  • AMBER: Problem in loading a PDB file in Leap - Please help me (Thu Apr 15 2004 - 01:25:07 CDT)
  • AMBER: tleap error and warnings (Fri Mar 26 2004 - 01:06:38 CST)
  • AMBER: Error while protonating a PDB file (Thu Mar 25 2004 - 17:47:54 CST)
• Mikyung Seo
  • AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Tue May 11 2004 - 17:51:01 CDT)
  • AMBER: choosing 3 atoms for reorientaion in R.E.D (Thu May 06 2004 - 16:38:19 CDT)
  • AMBER: reorientation in R.E.D (Wed May 05 2004 - 11:38:01 CDT)
  • AMBER: reproduction of RESP charges for Gly (Tue May 04 2004 - 12:51:01 CDT)
  • AMBER: esp or resp for all_amino94.lib (Fri Apr 30 2004 - 18:06:54 CDT)
  • AMBER: neutral residues (Mon Apr 26 2004 - 11:33:04 CDT)
  • AMBER: parameters for neutral Arg (Fri Apr 23 2004 - 15:51:14 CDT)
  • AMBER: protein-carbohydrate complex (Thu Apr 22 2004 - 17:27:31 CDT)
  • AMBER: MD for protein-carbohydrate complex (Thu Apr 22 2004 - 15:03:33 CDT)
• Ming Lei
  • AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 (Tue May 25 2004 - 10:27:49 CDT)
  • AMBER: "No radius found for F" error and vdw radii for F in MMPBSA (Tue Apr 20 2004 - 10:47:40 CDT)
• Ming-Hsun Ho
  • Re: AMBER: A Question about RESP (Sun Mar 07 2004 - 00:15:16 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 09:58:38 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 09:28:25 CST)
  • Re: AMBER: A Question about RESP (Sat Mar 06 2004 - 07:58:44 CST)
• Mingfeng Yang
  • AMBER: PBC in sander (Tue Aug 31 2004 - 15:27:26 CDT)
  • AMBER: Amber on Redhat Enterprise (Tue Feb 03 2004 - 12:23:44 CST)
• Mizuguchi Mineyuki
  • Re: AMBER: LINMIN failure (Thu Jun 10 2004 - 21:58:24 CDT)
  • AMBER: LINMIN failure (Wed Jun 09 2004 - 21:40:16 CDT)
• ML
  • Re: AMBER: factor used in b-factor calculation (Tue Mar 09 2004 - 04:36:57 CST)
  • Re: AMBER: (Mon Mar 01 2004 - 08:49:18 CST)
  • Re: AMBER: MM-PBSA:??Decomposition of receptor energies?? (Mon Feb 16 2004 - 09:59:04 CST)
  • AMBER: MM-PBSA:??Decomposition of receptor energies?? (Mon Feb 16 2004 - 03:18:17 CST)
  • Re: AMBER: MM-PBSA: molecular charges and active site water (Fri Feb 13 2004 - 01:30:23 CST)
  • Re: AMBER: Nmode convergence (Wed Feb 11 2004 - 02:14:31 CST)
  • Re: AMBER: Temperature in Nmode (Tue Feb 10 2004 - 14:46:19 CST)
  • AMBER: Temperature in Nmode (Tue Feb 10 2004 - 09:25:12 CST)
  • Re: AMBER: Nmode convergence (Tue Feb 10 2004 - 09:26:12 CST)
  • AMBER: Nmode convergence (Tue Feb 10 2004 - 01:36:27 CST)
  • Re: AMBER: NMODE for protein via MM-PBSA-cntd (Wed Feb 04 2004 - 11:18:12 CST)
  • AMBER: NMODE for protein via MM-PBSA-cntd (Wed Feb 04 2004 - 10:09:57 CST)
  • Re: AMBER: NMODE via MM-PBSA (Wed Jan 21 2004 - 07:42:29 CST)
  • AMBER: NMODE via MM-PBSA (Wed Jan 21 2004 - 06:03:31 CST)
  • AMBER: Errors in MM-PBSA??? (Wed Jan 21 2004 - 05:46:35 CST)
• mmv
  • AMBER: Why the charge is not an integer? (Sun Dec 12 2004 - 03:44:36 CST)
• Mu Yuguang \(Dr\)
  • AMBER: Curves 5.3 (Thu Oct 14 2004 - 21:57:57 CDT)
• MURAT CETINKAYA
  • AMBER: nanotube parameters (Fri Dec 17 2004 - 14:28:24 CST)
  • AMBER: sander imin=5 (Thu Dec 16 2004 - 02:01:45 CST)
  • AMBER: imin=5 in sander (Tue Dec 07 2004 - 13:07:34 CST)
  • Re: AMBER: extracting energy from trajector? (Thu Dec 02 2004 - 14:56:47 CST)
  • Re: AMBER: extracting energy from trajector? (Mon Nov 29 2004 - 11:20:12 CST)
  • Re: AMBER: extracting energy from trajector? (Mon Nov 29 2004 - 09:31:14 CST)
  • Re: AMBER: extracting energy from trajector? (Sun Nov 28 2004 - 18:59:27 CST)
  • AMBER: extracting energy from trajector? (Wed Nov 24 2004 - 12:33:04 CST)
  • AMBER: ptraj (Thu Nov 11 2004 - 15:19:45 CST)
  • RE: AMBER: sander gets stuck (Fri Oct 29 2004 - 10:11:15 CDT)
  • AMBER: sander gets stuck (Fri Oct 29 2004 - 09:32:22 CDT)
  • Re: AMBER: long minimization in sander (Mon Oct 25 2004 - 10:32:10 CDT)
  • AMBER: long minimization in sander (Mon Oct 25 2004 - 09:53:14 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 13:13:07 CDT)
  • Re: AMBER: const-P MD at high T (Mon Oct 18 2004 - 11:52:11 CDT)
  • AMBER: const-P MD at high T (Mon Oct 18 2004 - 10:27:49 CDT)
  • AMBER: about antechamber (Sat Oct 09 2004 - 20:48:52 CDT)
• myang
  • Re: AMBER: How is optimization done during energy minimization of the force field? (Fri Dec 31 2004 - 10:49:58 CST)
  • AMBER: fit a 3D line to points (Thu May 27 2004 - 16:11:08 CDT)
  • AMBER: Normal Mode Analysis possibility (Tue May 04 2004 - 10:52:05 CDT)
  • AMBER: understanding SANDER source code (Sat Mar 20 2004 - 09:33:33 CST)
• myang_at_vitamin.uni.cc
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 12:48:43 CST)
  • Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! (Mon Nov 15 2004 - 19:26:17 CST)
  • Re: AMBER: nmode:Number of atoms in -p and -c files do not agree! (Mon Nov 15 2004 - 13:58:58 CST)
  • AMBER: nmode:Number of atoms in -p and -c files do not agree! (Sun Nov 14 2004 - 20:20:25 CST)
  • Re: AMBER: MD problem (very long parhabs endless runtime) (Sat Oct 23 2004 - 13:35:59 CDT)
  • Re: AMBER: Question about restart MD (Mon Oct 11 2004 - 14:05:04 CDT)
  • Re: AMBER: solute leaving PBC box (Thu Oct 07 2004 - 17:00:09 CDT)
  • Re: AMBER: problem with protonate (Tue Oct 05 2004 - 15:36:36 CDT)
  • Re: AMBER: Is AME equal to NME? (Mon Oct 04 2004 - 15:07:12 CDT)
  • AMBER: Is AME equal to NME? (Mon Oct 04 2004 - 14:15:46 CDT)
• Myunggi Yi
  • AMBER: user force (Thu Jul 22 2004 - 12:00:16 CDT)
  • AMBER: pmf calculation using gibbs (Wed Feb 25 2004 - 10:47:25 CST)
  • Re: AMBER: pmf calculation using gibbs. (Thu Feb 19 2004 - 09:13:30 CST)
  • AMBER: pmf calculation using gibbs. (Wed Feb 18 2004 - 23:22:46 CST)
• myunggi_at_csit.fsu.edu
  • RE: AMBER: user force (Thu Jul 22 2004 - 18:26:14 CDT)
  • RE: AMBER: user force (Thu Jul 22 2004 - 17:25:50 CDT)
  • Re: AMBER: user force (Thu Jul 22 2004 - 16:48:28 CDT)
  • AMBER: (no subject) (Thu Jul 22 2004 - 12:10:09 CDT)
• Nadine Homeyer
  • Re: AMBER: Parameters for phosphorylated aminoacids (Wed Oct 06 2004 - 05:57:14 CDT)
  • AMBER: Parameters for phosphorylated aminoacids (Tue Oct 05 2004 - 10:21:31 CDT)
  • AMBER: Amber7 - mm_pbsa/molsurf (Fri Sep 10 2004 - 07:25:20 CDT)
  • AMBER: phosphorylated serin / histidin (Thu Mar 25 2004 - 07:04:38 CST)
• Nan Lin
  • AMBER: nmode with mm/pbsa (Wed Jun 09 2004 - 20:18:15 CDT)
  • AMBER: antechamber/parmchk ATTN: needs revision (Wed Jun 09 2004 - 13:48:55 CDT)
  • AMBER: Partial Charge on ligand for MD & MM/PBSA (Mon Jun 07 2004 - 21:11:25 CDT)
  • AMBER: Constant Pressure Problem of MD (Mon Jun 07 2004 - 21:04:23 CDT)
  • AMBER: Add Hydrogen bond through xLeap? (Wed Jun 02 2004 - 01:25:18 CDT)
• Narang Manpreet Kaur
  • Re: AMBER: Simulated annealing ...vlimit problem (Tue May 18 2004 - 09:09:31 CDT)
• Natasja Brooijmans
  • Re: AMBER: about AM1-BCC charge method (Mon Oct 18 2004 - 08:38:11 CDT)
  • Re: AMBER: positive binding free energy (Thu Mar 11 2004 - 10:10:41 CST)
• Nelson Fonseca
  • AMBER: Implicit Solvent Models (Thu Dec 09 2004 - 06:02:10 CST)
  • AMBER: TI with electrostatic decoupling (Tue Nov 23 2004 - 03:56:44 CST)
  • AMBER: <dV/dL> fluctuations in TI (Wed Nov 17 2004 - 05:39:01 CST)
  • AMBER: gibbs compilation error (Mon Nov 15 2004 - 11:41:27 CST)
  • AMBER: klambdas and Weights for Gaussian Quadrature (Tue Oct 12 2004 - 12:01:33 CDT)
  • AMBER: Distance Restraints (Mon Oct 11 2004 - 07:56:23 CDT)
  • AMBER: ptraj and hbond (Thu Aug 26 2004 - 04:50:39 CDT)
  • AMBER: mutation of atoms (Thu Jul 22 2004 - 07:41:22 CDT)
• Nhat-hang Duong
  • AMBER: Ideal bonds and angles (Tue Dec 21 2004 - 11:49:38 CST)
  • AMBER: Amber8 - Energy Calculations (Thu Oct 14 2004 - 10:53:29 CDT)
  • Re: AMBER: ifort installation (Sun Sep 19 2004 - 14:03:32 CDT)
  • Re: AMBER: restrain on the distance between two molecules. (Tue Sep 14 2004 - 16:34:49 CDT)
  • AMBER: Pulling versus Distance Restraints (Tue Aug 31 2004 - 16:16:15 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 11:51:28 CDT)
  • Re: AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 09:15:00 CDT)
  • AMBER: Amber8 - Floating point (Thu Aug 26 2004 - 08:28:24 CDT)
  • RE: AMBER: Amber 8 - Energy Minimization Parameters (Wed Aug 25 2004 - 15:26:56 CDT)
  • AMBER: Amber 8 - Energy Minimization Parameters (Wed Aug 25 2004 - 10:34:28 CDT)
  • AMBER: Amber 8 Installation - C compiler? (Wed Aug 11 2004 - 16:51:51 CDT)
  • AMBER: Problem: Installing Amber8 on PC with Windows XP (Tue Aug 03 2004 - 15:38:55 CDT)
• NI AI
  • Re: AMBER: average structure using ptraj (Fri Jul 02 2004 - 10:15:53 CDT)
  • AMBER: average structure using ptraj (Thu Jul 01 2004 - 11:18:34 CDT)
• Nicolas Grima
  • Re: AMBER: Amber8 compilation problems on AIX (Wed Jun 30 2004 - 02:12:19 CDT)
  • Re: AMBER: Amber8 compilation in IBM-AIX (Mon Jun 28 2004 - 10:13:32 CDT)
  • Re: AMBER: Amber8 compilation in IBM-AIX (Mon Jun 28 2004 - 05:55:59 CDT)
• nie beining
  • AMBER: Parameters for ions? (Fri Apr 02 2004 - 12:15:51 CST)
  • AMBER: What does this error message mean? (Tue Feb 03 2004 - 09:58:41 CST)
• Niko Jukarainen
  • AMBER: pmemd and ifort 8.1 (Fri Oct 15 2004 - 08:14:03 CDT)
  • Re: AMBER: Increasing MAXATOM in antechamber (Sat Aug 21 2004 - 11:13:56 CDT)
  • AMBER: Increasing MAXATOM in antechamber (Sat Aug 21 2004 - 04:45:08 CDT)
  • RE: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Fri Aug 13 2004 - 05:09:10 CDT)
• Nikolai Smolin
  • AMBER: TIP4P extended (Mon Feb 16 2004 - 11:10:19 CST)
  • AMBER: TIP4P extended (Mon Feb 16 2004 - 11:06:30 CST)
  • AMBER: TIP4P (Mon Feb 16 2004 - 04:58:56 CST)
  • AMBER: protonation (Tue Feb 03 2004 - 03:50:23 CST)
  • AMBER: CYS, CYX and CYM (Thu Jan 29 2004 - 03:56:09 CST)
• Nitin Bhardwaj
  • AMBER: missing XaLeap_wcl file (Wed Nov 24 2004 - 12:22:04 CST)
  • RE: AMBER: generating parmfile containing topology and parameter information (Mon Nov 22 2004 - 17:53:07 CST)
  • AMBER: generating parmfile containing topology and parameter information (Mon Nov 22 2004 - 15:29:00 CST)
• nlxc
  • Re: AMBER: About MM/PBSA, PB Calculation (Thu Dec 16 2004 - 16:31:13 CST)
  • AMBER: About MM/PBSA, PB Calculation (Wed Dec 15 2004 - 17:11:29 CST)
  • AMBER: Energy change for isomerization reaction of cyclic peptide (Fri Nov 12 2004 - 12:03:00 CST)
  • Re: AMBER: PBCAL in mmpbsa (Tue Jun 29 2004 - 19:29:51 CDT)
  • AMBER: PBCAL in mmpbsa (Tue Jun 29 2004 - 13:17:25 CDT)
  • AMBER: PBCAL in MM/PBSA (Fri Jun 25 2004 - 14:09:19 CDT)
  • AMBER: Deeper problem with the energetics of the system (Fri Jun 18 2004 - 12:56:52 CDT)
  • AMBER: DENSITY in constant pressure MD (Tue Jun 15 2004 - 13:17:41 CDT)
  • AMBER: Suface area parameter for fluorine in MM/PBSA (Fri Jun 11 2004 - 18:38:30 CDT)
  • AMBER: PBCAL in mm-pbsa calculation (Fri Jun 11 2004 - 12:26:21 CDT)
• northrop_at_chem.ucla.edu
  • Re: AMBER: running on Itanium machines (Fri Jan 09 2004 - 13:28:56 CST)
  • AMBER: running on Itanium machines (Thu Jan 08 2004 - 13:14:52 CST)
• nurul bahiyah
  • Re: AMBER: simulated annealing (Sun Aug 15 2004 - 07:42:53 CDT)
• O. Hucke
  • AMBER: antechamber - missing improper torsions (Mon Jul 19 2004 - 13:58:39 CDT)
• Obdulia Rabal
  • AMBER: CG maxitn exceeded (Tue May 18 2004 - 11:29:53 CDT)
  • AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 04:32:29 CDT)
  • AMBER: NMODE COMPILATION (Mon Mar 15 2004 - 04:58:11 CST)
  • AMBER: PMEMD COMPILATION REDHAT (Thu Mar 11 2004 - 12:36:45 CST)
  • RE: AMBER: A question about RMSD calculation (Thu Mar 11 2004 - 12:09:25 CST)
  • AMBER: IFC COMPILER (Mon Feb 16 2004 - 06:54:00 CST)
• Okimoto Noriaki
  • AMBER: Question on tleap of amber8 (Mon Dec 20 2004 - 03:00:38 CST)
• Olayiwola Adekoya
  • AMBER: VS: mmpbsa question (Thu Apr 29 2004 - 04:32:32 CDT)
• Oliver Hucke
  • Re: AMBER: where is the VDW radius? (Sat Nov 06 2004 - 13:16:00 CST)
  • Re: AMBER: Fluctuation in temperature (Thu Nov 04 2004 - 12:14:36 CST)
  • Re: AMBER: ptraj questions (Wed Dec 01 2004 - 11:59:06 CST)
  • Re: AMBER: Settings about frozen atoms in sander (Mon Nov 29 2004 - 10:54:10 CST)
  • Re: AMBER: AM1-BCC charges (Tue Oct 26 2004 - 20:29:02 CDT)
  • Re: AMBER: building a small molecule (Tue Oct 05 2004 - 12:15:00 CDT)
  • Re: AMBER: Phosphoserine parameters (Tue Sep 28 2004 - 18:53:27 CDT)
  • Re: AMBER: about mm_pbsa parameter (Fri Sep 24 2004 - 10:49:22 CDT)
  • Re: AMBER: About binding energy (Sat Sep 18 2004 - 23:53:36 CDT)
  • AMBER: TI with sander (Tue Sep 14 2004 - 13:58:01 CDT)
  • Re: AMBER: Amber7 - mm_pbsa/molsurf (Fri Sep 10 2004 - 13:03:57 CDT)
  • AMBER: charge perturbation - xleap question (Thu Aug 26 2004 - 13:57:43 CDT)
  • AMBER: mutation of Tyr to Leu with TI (Tue Aug 24 2004 - 18:56:47 CDT)
  • AMBER: born radius and screening parameter for Br (Thu Aug 19 2004 - 17:58:44 CDT)
  • AMBER: intrinsic born radius of Br (Tue Aug 17 2004 - 20:33:18 CDT)
  • AMBER: mm-gbsa (Tue Aug 17 2004 - 18:59:21 CDT)
  • Re: AMBER: Antechamber and dummy atoms (Fri Aug 13 2004 - 12:55:57 CDT)
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 23 2004 - 12:41:05 CDT)
  • AMBER: antechamber - improper torsions (Tue Jul 20 2004 - 11:23:02 CDT)
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 16 2004 - 17:49:00 CDT)
  • AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 16 2004 - 16:00:57 CDT)
  • Re: AMBER: free energy (Fri Jun 04 2004 - 14:19:25 CDT)
  • Re: AMBER: sander8 performance (Tue Jun 01 2004 - 14:46:06 CDT)
  • AMBER: sander8 performance (Tue Jun 01 2004 - 12:53:46 CDT)
  • Re: AMBER: parallel installation problem (Mon May 24 2004 - 18:57:01 CDT)
  • AMBER: parallel installation problem (Sat May 22 2004 - 19:40:17 CDT)
  • AMBER: parallel installation problem (Wed May 19 2004 - 17:17:08 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Tue May 18 2004 - 16:07:45 CDT)
  • AMBER: sander_classic for cap simulations? (Thu May 13 2004 - 17:43:36 CDT)
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Thu May 13 2004 - 11:14:08 CDT)
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Wed May 12 2004 - 15:42:50 CDT)
  • AMBER: performance of periodic vs. non-periodic simulation (Wed May 12 2004 - 14:08:18 CDT)
  • AMBER: solvent cap and eedmeth (Thu May 06 2004 - 18:31:42 CDT)
  • AMBER: cap waters always flexible? (Thu May 06 2004 - 15:41:19 CDT)
  • Re: AMBER: antechamber gives GDP 0 charge (Wed May 05 2004 - 15:46:06 CDT)
  • Re: AMBER: some bugfixes (Tue May 04 2004 - 13:12:53 CDT)
  • Re: AMBER: why delete water molecule (Tue May 04 2004 - 11:23:01 CDT)
  • Re: AMBER: xleap problem (Sun May 02 2004 - 17:53:42 CDT)
  • AMBER: Antechamber: problems with bcc correction (Fri Apr 23 2004 - 17:08:47 CDT)
  • AMBER: restraintmask and ambmask (Wed Apr 21 2004 - 19:17:24 CDT)
  • AMBER: gaff "ha" atom type (Wed Apr 21 2004 - 15:38:20 CDT)
  • Re: AMBER: how to check metal ion bonding ? (Tue Apr 13 2004 - 15:28:09 CDT)
  • AMBER: equilibration does not start with SHAKE (Fri Apr 09 2004 - 17:30:55 CDT)
  • AMBER: which atoms are H's for SHAKE? (Tue Apr 06 2004 - 12:32:12 CDT)
  • AMBER: test output of amber8 (Wed Mar 31 2004 - 17:54:38 CST)
  • Re: Fwd: Re: AMBER: Pang-model of Zn2+ (Fri Mar 26 2004 - 15:29:24 CST)
  • AMBER: Pang Zn2+ model - correction (Thu Mar 25 2004 - 19:32:30 CST)
  • AMBER: Pang-model of Zn2+ (Thu Mar 25 2004 - 19:04:48 CST)
  • AMBER: description of toplogy file format? (Tue Mar 16 2004 - 19:44:10 CST)
• opitz_at_che.udel.edu
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 16:56:47 CST)
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 16:50:14 CST)
  • AMBER: Restrained minimization problem (Mon Nov 29 2004 - 16:11:56 CST)
  • AMBER: nucgen problem (Wed Nov 24 2004 - 16:08:52 CST)
  • AMBER: trajectory file question? (Thu Oct 28 2004 - 13:15:12 CDT)
  • AMBER: Carnal & Radius of gyration (Tue Oct 12 2004 - 16:29:26 CDT)
  • Re: AMBER: solute leaving PBC box (Fri Oct 08 2004 - 08:43:06 CDT)
  • Re: AMBER: solute leaving PBC box (Thu Oct 07 2004 - 17:01:19 CDT)
  • AMBER: solute leaving PBC box (Thu Oct 07 2004 - 16:24:47 CDT)
  • Re: AMBER: Antechamber on cluster with queue? (Wed Oct 06 2004 - 11:06:43 CDT)
  • AMBER: Antechamber on cluster with queue? (Wed Oct 06 2004 - 10:08:25 CDT)
  • AMBER: antechamber, mopac RESTART (Sun Oct 03 2004 - 13:41:24 CDT)
  • Re: AMBER: Moil-view & Amber trajectory (Mon Sep 20 2004 - 16:59:39 CDT)
  • AMBER: Moil-view & Amber trajectory (Fri Sep 17 2004 - 15:41:42 CDT)
  • Re: AMBER: Nucgen and PNA? (Thu Sep 09 2004 - 08:36:25 CDT)
  • AMBER: Nucgen and PNA? (Wed Sep 08 2004 - 16:14:42 CDT)
  • Re: AMBER: Minimization error (Fri Aug 27 2004 - 15:56:46 CDT)
  • Re: AMBER: Minimization error (Wed Aug 25 2004 - 15:55:24 CDT)
  • Re: AMBER: Minimization error (Tue Aug 24 2004 - 16:09:15 CDT)
  • AMBER: Minimization error (Fri Aug 20 2004 - 14:43:31 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 14:51:30 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 14:18:50 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 13:17:35 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 16:08:27 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:28:26 CDT)
  • AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:08:33 CDT)
  • Re: AMBER: Xleap crash, problem with residue bonding (Mon Jul 26 2004 - 10:39:51 CDT)
  • AMBER: Xleap crash, problem with residue bonding (Thu Jul 22 2004 - 09:24:35 CDT)
  • AMBER: question about production runs (Fri Jul 16 2004 - 14:42:06 CDT)
  • AMBER: Carnal question (Mon May 10 2004 - 10:08:18 CDT)
  • AMBER: Residue Charges (Tue Mar 23 2004 - 09:17:38 CST)
  • AMBER: literature question/residue charges (Tue Mar 16 2004 - 14:09:43 CST)
  • AMBER: antechamber/mopac question (Mon Mar 15 2004 - 14:20:24 CST)
  • AMBER: Atomic Charge in Residue (Thu Mar 11 2004 - 13:29:21 CST)
  • AMBER: mol2 vs. prepin (Tue Mar 09 2004 - 10:53:46 CST)
  • AMBER: Residue question (Tue Mar 09 2004 - 10:29:22 CST)
  • AMBER: Star like (branching) molecule (Tue Feb 24 2004 - 16:54:45 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 15:47:51 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 15:35:44 CST)
  • Re: AMBER: Defining residues (Mon Feb 23 2004 - 13:02:58 CST)
  • AMBER: Defining residues (Sat Feb 21 2004 - 22:34:56 CST)
  • AMBER: saveamberparm warning in leap? (Mon Feb 16 2004 - 15:24:45 CST)
  • Re: AMBER: (No subject) (Fri Jan 30 2004 - 15:32:01 CST)
  • Re: AMBER: (No subject) (Fri Jan 30 2004 - 10:21:30 CST)
  • AMBER: (No subject) (Thu Jan 29 2004 - 16:09:47 CST)
  • AMBER: how to correctly change frcmod? (Fri Jan 23 2004 - 17:05:38 CST)
• Oscar Rey i Puiggròs
  • AMBER: protein-protein interaction (Wed Mar 17 2004 - 08:50:06 CST)
• Osman Gani
  • AMBER: Molecular modelling. (Thu Dec 23 2004 - 08:44:05 CST)
  • RE: AMBER: Increase lastrst in the &cntrl namelist (Wed Sep 01 2004 - 01:51:32 CDT)
  • AMBER: Biotin/streptavidin tutorial. (Fri Aug 27 2004 - 04:57:51 CDT)
  • RE: AMBER: ANAL memory problem. (Tue Aug 17 2004 - 05:38:42 CDT)
  • AMBER: ANAL memory problem. (Mon Aug 16 2004 - 08:16:15 CDT)
  • RE: AMBER: pmemd. (Mon Aug 16 2004 - 08:03:15 CDT)
  • AMBER: pmemd. (Fri Jul 23 2004 - 12:09:55 CDT)
  • AMBER: FAD cofactor. (Fri May 14 2004 - 04:34:28 CDT)
  • AMBER: Ligand from CCDC. (Thu May 06 2004 - 10:38:16 CDT)
  • AMBER: FW: Problems with antechamber innstallation (Thu Mar 25 2004 - 09:12:20 CST)
  • AMBER: SANDER general questions. (Mon Mar 22 2004 - 11:37:18 CST)
  • AMBER: MD problem. (Wed Mar 17 2004 - 05:07:47 CST)
• Ozlem Demir
  • AMBER: How to covalently bind a ligand to a residue? (Thu Aug 05 2004 - 10:54:19 CDT)
  • AMBER: about GLYCAM prep files in AMBER (Tue Jul 20 2004 - 12:34:07 CDT)
• pande.vineet_at_fc.up.pt
  • Fwd: Re: AMBER: Protein with maximum hydrogen bonds (Sat Nov 27 2004 - 08:19:31 CST)
  • Re: AMBER: Protein with maximum hydrogen bonds (Sat Nov 27 2004 - 08:13:58 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 12:59:19 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 10:35:43 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 10:45:47 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Fri Nov 26 2004 - 02:45:50 CST)
  • Re: AMBER: Regarding Dielectric Constant in AMBER8 (Thu Nov 25 2004 - 10:03:27 CST)
  • AMBER: Regarding Dielectric Constant in AMBER8 (Thu Nov 25 2004 - 09:22:41 CST)
• Patil, Sachin
  • AMBER: amber8 tutorial (Sun Apr 04 2004 - 19:03:20 CDT)
• pengyo_at_UMDNJ.EDU
  • Re: AMBER: ptraj (Mon Apr 12 2004 - 16:22:26 CDT)
  • AMBER: ptraj (Mon Apr 12 2004 - 15:09:22 CDT)
  • Re: AMBER: question about image (Fri Apr 02 2004 - 21:35:06 CST)
• Perdita Barran
  • AMBER: Antechamber and dummy atoms (Fri Aug 13 2004 - 08:03:44 CDT)
• Peter Gannett
  • AMBER: cobalt parameters (Mon Dec 13 2004 - 19:21:50 CST)
  • AMBER: MAC Based Beowulf Cluster (Thu Sep 09 2004 - 18:17:14 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:43:33 CDT)
  • Re: AMBER: Amber7: pdb format file (Tue Jun 01 2004 - 13:22:32 CDT)
  • AMBER: Re: CCL:Helical parameters extraction from trajectory (Fri May 28 2004 - 06:47:08 CDT)
• Peter Oelschlaeger
  • Re: AMBER: Pang-model of Zn2+ (Thu Mar 25 2004 - 19:44:01 CST)
  • Re: AMBER: conversion of Amber 7 .pdb file to .bgf file (Fri Mar 05 2004 - 14:47:59 CST)
  • Re: AMBER: conversion of Amber 7 .pdb file to .bgf file (Thu Mar 04 2004 - 20:00:34 CST)
  • AMBER: conversion of Amber 7 .pdb file to .bgf file (Thu Mar 04 2004 - 16:31:43 CST)
  • Re: AMBER: histidine and its various forms (Wed Feb 18 2004 - 12:10:49 CST)
  • Re: AMBER: trajectory file corruption (Tue Jan 27 2004 - 12:27:44 CST)
• Peter Trodler
  • AMBER: calculation of pKa values (Mon Nov 22 2004 - 02:32:25 CST)
  • AMBER: neutral Arg, charged Tyr ?? (Mon Oct 04 2004 - 02:25:49 CDT)
• Peter Varnai
  • AMBER: generalized Born parameters (Fri Oct 08 2004 - 09:16:08 CDT)
• Petr Jeøábek
  • Re: AMBER: LES (Thu Feb 19 2004 - 16:10:00 CST)
  • Re: AMBER: LES (Thu Feb 19 2004 - 15:08:38 CST)
  • AMBER: LES (Thu Feb 19 2004 - 12:10:50 CST)
• Petr Kulhanek
  • Re: AMBER: problems with dihedrals - extended information (Sun Oct 17 2004 - 10:39:31 CDT)
  • AMBER: problems with dihedrals (Fri Oct 08 2004 - 07:53:03 CDT)
• Phineus Markwick
  • AMBER: problem in quasih.f diagonalising matrix (Mon Nov 29 2004 - 07:14:35 CST)
• Piotr Cieplak
  • Re: AMBER: calcium van der Waals parameters (Mon Nov 22 2004 - 13:03:57 CST)
  • Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases (Fri Sep 10 2004 - 12:28:25 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 17:31:37 CDT)
  • Re: AMBER: amber 8 under windows XP (Wed May 26 2004 - 17:08:38 CDT)
  • Re: AMBER: types of water atom (Wed May 26 2004 - 12:28:17 CDT)
  • Re: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D (Wed May 12 2004 - 13:57:20 CDT)
  • Re: AMBER: About RESP Calculation (Fri Mar 19 2004 - 14:20:42 CST)
  • Re: AMBER: literature question/residue charges (Tue Mar 16 2004 - 16:07:21 CST)
  • Re: AMBER: (Mon Mar 01 2004 - 11:38:49 CST)
  • Re: AMBER: Can anybody help me with CHARMM (Sun Feb 22 2004 - 21:49:21 CST)
• pl
  • Re: AMBER: H-bonded waters selection (Fri Nov 05 2004 - 04:42:01 CST)
  • AMBER: H-bonded waters selection (Thu Nov 04 2004 - 06:41:32 CST)
• Pmartin
  • Re: AMBER: Question on Amber7... (Tue Apr 06 2004 - 16:44:34 CDT)
  • AMBER: Question on Amber7... (Thu Apr 01 2004 - 17:31:49 CST)
• Poh-Guan Khoo
  • AMBER: Amber 8 - OS support. (Fri Oct 15 2004 - 00:54:27 CDT)
• Pooja Narang
  • AMBER: Angle Restraining (Fri Apr 30 2004 - 02:17:30 CDT)
• Pradipta Bandyopadhyay
  • AMBER: Electrostatic potential from the trajectory ! (Tue Sep 07 2004 - 06:40:09 CDT)
  • AMBER: High B-factor!! (Tue Jun 22 2004 - 07:13:09 CDT)
  • AMBER: Software to visualize normal modes! (Mon May 31 2004 - 23:42:39 CDT)
  • AMBER: Low frequency in quasi-harmonic analysis!! (Sun May 30 2004 - 04:23:50 CDT)
  • AMBER: Reproducing the energy during restart in MD! (Wed May 19 2004 - 01:33:27 CDT)
  • AMBER: energy conservation with GB !! (Sun May 16 2004 - 01:27:01 CDT)
  • AMBER: non-periodic simulation and box information !! (Wed Apr 21 2004 - 10:56:31 CDT)
  • AMBER: warning about improper dihedral in leap!! (Thu Apr 08 2004 - 06:50:18 CDT)
  • AMBER: Compilation problem in SUN OS 5.7! (Mon Mar 22 2004 - 02:48:59 CST)
• Prashansa Agrawal
  • AMBER: name error (Wed Jul 07 2004 - 17:57:53 CDT)
• Priti Hansia
  • Re: AMBER: Box information from Amber (Sat Oct 09 2004 - 12:51:16 CDT)
  • AMBER: Box information from Amber (Sat Oct 09 2004 - 06:19:46 CDT)
• Qiang Lu
  • Re: AMBER: MAXMASK problem (Tue Oct 19 2004 - 17:25:03 CDT)
  • AMBER: MAXMASK problem (Tue Oct 19 2004 - 12:19:54 CDT)
  • AMBER: restrain on the distance between two molecules. (Tue Sep 14 2004 - 16:18:00 CDT)
  • Re[4]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 14:19:33 CDT)
  • Re[2]: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 12:19:38 CDT)
  • AMBER: rmsd over residues using ptraj (Tue May 18 2004 - 19:41:16 CDT)
  • AMBER: A parm file suit for half beta and half alpha structure (Mon May 10 2004 - 13:51:57 CDT)
  • AMBER: hbond in ptraj (Fri May 07 2004 - 13:43:33 CDT)
  • Re[2]: AMBER: atomicfluct in ptraj (Wed Apr 14 2004 - 17:06:32 CDT)
  • AMBER: atomicfluct in ptraj (Wed Apr 14 2004 - 13:12:06 CDT)
• Qing Zhang
  • Re: AMBER: About RESP Calculation (Sat Mar 20 2004 - 00:43:03 CST)
  • RE: AMBER: temperature in DelPhi for MM-PBSA calculation (Mon Feb 02 2004 - 18:58:54 CST)
  • AMBER: temperature in DelPhi for MM-PBSA calculation (Mon Feb 02 2004 - 16:54:05 CST)
• Qizhi Cui
  • Re: AMBER: solvation free energy (Mon Jul 19 2004 - 12:32:17 CDT)
• qlu_at_notes.cc.sunysb.edu
  • RE: AMBER: question about parallel simulation (Thu Dec 02 2004 - 15:28:43 CST)
  • RE: AMBER: question about parallel simulation (Thu Dec 02 2004 - 14:30:28 CST)
  • RE: AMBER: question about parallel simulation (Wed Dec 01 2004 - 17:38:01 CST)
  • AMBER: question about parallel simulation (Wed Dec 01 2004 - 13:17:43 CST)
  • AMBER: AMBER8 compiling error under Itanium 2. (Mon Nov 15 2004 - 18:39:36 CST)
  • AMBER: Can parallel simulation have a nonperiodic boundary condition? (Wed Nov 10 2004 - 16:11:46 CST)
• quch quch
  • AMBER: amber8 performance on linux cluster (Tue Apr 27 2004 - 12:05:45 CDT)
  • RE: AMBER: compile amber8 in linux with ifort (Fri Apr 23 2004 - 16:50:52 CDT)
  • AMBER: compile amber8 in linux with ifort (Fri Apr 23 2004 - 16:08:05 CDT)
• Raik Grünberg
  • Re: AMBER: entropy implementation in ptraj (Fri Dec 17 2004 - 08:44:13 CST)
  • AMBER: entropy implementation in ptraj (Tue Dec 14 2004 - 11:37:18 CST)
  • Re: AMBER: ptraj: load crd without hydrogen (i.e. missing parm file) (Mon Aug 02 2004 - 04:30:56 CDT)
  • Re: AMBER: tleap: automatically identify and connect disulfide bonds? (Mon Aug 02 2004 - 04:15:34 CDT)
  • AMBER: ptraj: load crd without hydrogen (i.e. missing parm file) (Thu Jul 29 2004 - 05:34:44 CDT)
  • AMBER: tleap: automatically identify and connect disulfide bonds? (Wed Jul 28 2004 - 12:27:31 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Mon May 17 2004 - 10:38:17 CDT)
  • Re: AMBER: antechamber/Mopac: strange GTP charges (Fri May 14 2004 - 05:35:13 CDT)
  • AMBER: antechamber/Mopac: strange GTP charges (Thu May 13 2004 - 12:57:06 CDT)
  • AMBER: antechamber gives GDP 0 charge (Wed May 05 2004 - 15:17:53 CDT)
• Raj Badhan
  • Re: Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 09:17:18 CDT)
  • Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 07:54:54 CDT)
  • Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 06:59:34 CDT)
  • AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 06:26:36 CDT)
  • AMBER: WHICH LINUX (Tue Apr 13 2004 - 09:50:52 CDT)
• RAJA SWAMINATHAN
  • AMBER: thermal ellipsoid-DNA (Thu Aug 19 2004 - 04:29:34 CDT)
  • AMBER: atomic positional fluctuation (Sat Aug 07 2004 - 02:18:32 CDT)
• Rasha Radwan
  • AMBER: (no subject) (Fri Oct 01 2004 - 09:30:53 CDT)
  • AMBER: (no subject) (Wed Sep 29 2004 - 09:24:25 CDT)
• Ray Luo
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Thu Dec 16 2004 - 17:58:29 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Wed Dec 15 2004 - 00:17:01 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Fri Dec 10 2004 - 15:36:53 CST)
  • Re: AMBER: pbsa error in mm_pbsa amber 8 (Fri Dec 10 2004 - 12:17:07 CST)
  • Re: AMBER: about FEP (Tue Nov 02 2004 - 08:05:41 CST)
  • Re: AMBER: solvation free energies using mmpbsa (Wed Oct 27 2004 - 23:06:07 CDT)
  • Re: AMBER: PBSA parameter question (Radii and Charges) (Wed Oct 13 2004 - 11:38:38 CDT)
  • Re: AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 17:19:59 CDT)
  • Re: AMBER: (Tue Sep 28 2004 - 13:30:10 CDT)
  • Re: AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 12:58:11 CDT)
  • Re: AMBER: about MM-PBSA (Mon Sep 20 2004 - 21:26:52 CDT)
  • Re: AMBER: pb_bomb in setgrd() (Tue Aug 10 2004 - 11:29:13 CDT)
  • Re: AMBER: mm_pbsa problem (Tue Aug 03 2004 - 18:18:48 CDT)
  • Re: AMBER: PB Bomb in pb_reslist(): maxnbr too small (Mon Jul 19 2004 - 07:22:26 CDT)
  • Re: AMBER: Weird compiling problem in Amber 8 (Mon Jul 19 2004 - 00:34:03 CDT)
  • Re: AMBER: solvation free energy (Sun Jul 11 2004 - 21:25:44 CDT)
  • Re: AMBER: pbsa calculation on part of the molecule (Wed May 19 2004 - 15:31:50 CDT)
  • Re: AMBER: PB bomb in pb_saarc (Tue May 18 2004 - 19:54:21 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Mon May 17 2004 - 18:07:17 CDT)
  • Re: AMBER: PB bomb in pb_saarc (Mon May 17 2004 - 17:58:21 CDT)
  • Re: AMBER: CAP PROTOCOL SIMULATION (Mon May 17 2004 - 16:43:55 CDT)
  • Re: AMBER: CG maxitn exceeded (Mon May 17 2004 - 14:10:29 CDT)
  • Re: AMBER: mm-pbsa:- atom charges and radii ? (Tue May 11 2004 - 01:21:06 CDT)
• Rhonda Torres
  • Re: AMBER: Nucgen and PNA? (Wed Sep 08 2004 - 16:22:30 CDT)
  • Re: AMBER: metal atoms in Xleap (Thu Aug 19 2004 - 11:57:04 CDT)
  • Re: AMBER: Adding residues (Mon Aug 09 2004 - 14:00:50 CDT)
  • Re: AMBER: AMBER7 plastocyanin tutorial problem. (Fri Aug 06 2004 - 12:57:42 CDT)
  • Re: AMBER: Bondi radii for BR and F in mm_pbsa calculation (Tue Jul 20 2004 - 19:23:10 CDT)
  • Re: AMBER: RESP vs. AM1-BCC charges for isoprene (Fri Jul 16 2004 - 16:20:42 CDT)
  • Re: AMBER: no 'water.lib' in /amber8/dat/leap/ (Thu Jul 01 2004 - 15:25:15 CDT)
  • Re: AMBER: nmode with mm/pbsa (Thu Jun 10 2004 - 13:33:40 CDT)
  • Re: AMBER: simulated anealling (Thu Jun 03 2004 - 13:05:58 CDT)
  • Re: AMBER: Amber force field for protein-DNA system (Tue Jun 01 2004 - 12:24:57 CDT)
  • Re: AMBER: Sander went through (Fri May 28 2004 - 19:49:44 CDT)
  • Re: AMBER: Bad atom symbol, K+ and IB in vacuum (Tue Mar 30 2004 - 12:30:23 CST)
  • Re: AMBER: HBOND calculation (Mon Mar 29 2004 - 12:28:19 CST)
  • Re: AMBER: trajectory file (Mon Mar 29 2004 - 12:03:03 CST)
  • Re: AMBER: vlimit and vmax problem (Wed Mar 24 2004 - 15:05:20 CST)
  • Re: AMBER: make sure of the Magnesium parameters (Wed Mar 24 2004 - 12:53:55 CST)
  • Re: AMBER: How to make leap recognise inosine? (Tue Mar 23 2004 - 11:54:49 CST)
  • Re: AMBER: Residue Charges (Tue Mar 23 2004 - 11:51:55 CST)
  • RE: AMBER: xleap don't recognize my residue/atom (Tue Mar 02 2004 - 12:11:07 CST)
  • Re: AMBER: Problems with xleap (Mon Mar 01 2004 - 18:02:23 CST)
  • Re: AMBER: xleap don't recognize my residue/atom (Sun Feb 22 2004 - 16:23:59 CST)
  • Re: AMBER: Atom type (Wed Jan 07 2004 - 12:55:40 CST)
  • Re: AMBER: Atom type (Wed Jan 07 2004 - 12:09:17 CST)
  • Re: AMBER: strange output of MD (Wed Jan 07 2004 - 11:48:54 CST)
• riccardo nifosi
  • AMBER: distance between images (Thu Oct 14 2004 - 09:56:40 CDT)
• riccardodesantis_at_fastwebnet.it
  • AMBER: ANAL: how can i buld the anal.in file? (Wed Apr 07 2004 - 01:14:49 CDT)
  • AMBER: (Wed Apr 07 2004 - 01:02:57 CDT)
• richard dimelow
  • AMBER: unformatted md problem (Mon Sep 27 2004 - 08:13:40 CDT)
  • AMBER: extra points (Thu Sep 16 2004 - 11:21:05 CDT)
  • AMBER: bond constraints in nmode (Wed Sep 15 2004 - 10:15:05 CDT)
  • AMBER: binary files (Wed Jun 16 2004 - 08:29:48 CDT)
• Richard Stefl
  • AMBER: problem with protonate (Tue Oct 05 2004 - 12:44:05 CDT)
• rluo_at_uci.edu
  • Re: AMBER: pbsa (Thu Apr 15 2004 - 13:14:34 CDT)
  • Re: AMBER: temperature in DelPhi for MM-PBSA calculation (Mon Feb 02 2004 - 20:45:52 CST)
• Robert Duke
  • Re: AMBER: Compiling question (Tue Dec 14 2004 - 13:51:20 CST)
  • Re: AMBER: Wich CPU? (Thu Oct 21 2004 - 08:23:48 CDT)
  • Re: AMBER: A question on AMBER8 installation (Wed Oct 20 2004 - 07:35:00 CDT)
  • Re: AMBER: pmemd and ifort 8.1 (Fri Oct 15 2004 - 12:10:08 CDT)
  • Re: AMBER: PMEMD (Fri Sep 17 2004 - 11:56:01 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 11:12:46 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 10:38:03 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 10:30:11 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 09:52:50 CDT)
  • Re: AMBER: make install error (Sun Sep 12 2004 - 07:46:30 CDT)
  • Re: AMBER: make install error (Sun Sep 12 2004 - 06:52:48 CDT)
  • AMBER: Improving PMEMD Performance on gigabit ethernet - CORRECTION (Tue Aug 17 2004 - 07:42:33 CDT)
  • AMBER: Improving PMEMD performance on gigabit ethernet Linux clusters (Mon Aug 16 2004 - 16:17:45 CDT)
  • Re: AMBER: pmemd. - OOPS!!! (Mon Aug 16 2004 - 09:45:03 CDT)
  • Re: AMBER: pmemd. (Mon Aug 16 2004 - 09:33:21 CDT)
  • Re: AMBER: pmemd problems (Fri Aug 13 2004 - 14:14:39 CDT)
  • Re: AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 13:42:42 CDT)
  • Re: AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 13:40:05 CDT)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 11:30:41 CDT)
  • Re: AMBER: recompiling amber8 (Mon Aug 02 2004 - 20:12:52 CDT)
  • Re: AMBER: pmemd. (Fri Jul 23 2004 - 12:46:48 CDT)
  • Re: AMBER: NEC and Regatta (Mon Jun 28 2004 - 07:38:27 CDT)
  • Re: AMBER: NEC and Regatta (Mon Jun 28 2004 - 07:18:24 CDT)
  • Re: AMBER: MD & running time (Wed Jun 23 2004 - 17:25:27 CDT)
  • Re: AMBER: Opteron PMEMD (Thu May 06 2004 - 15:31:46 CDT)
  • Re: AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH (Tue Apr 27 2004 - 17:36:51 CDT)
  • AMBER: Additional note on ld.so.conf vs. LD_LIBRARY_PATH (Tue Apr 27 2004 - 13:29:35 CDT)
  • AMBER: PMEMD and ifort 8 update (Tue Apr 27 2004 - 13:08:05 CDT)
  • Re: AMBER: PMEMD scaling (Sun Apr 25 2004 - 10:24:11 CDT)
  • Re: AMBER: NSNB parameter (Sat Apr 24 2004 - 22:05:51 CDT)
  • Re: AMBER: NSNB parameter (Sat Apr 24 2004 - 09:05:05 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Sat Apr 24 2004 - 07:31:59 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Fri Apr 23 2004 - 12:57:48 CDT)
  • Re: AMBER: pmemd and mpich - myrinet (Fri Apr 23 2004 - 11:23:37 CDT)
  • Re: AMBER: Question about compiling PMEMD (Thu Apr 22 2004 - 07:10:47 CDT)
  • Re: AMBER: Question about compiling PMEMD (Thu Apr 22 2004 - 06:35:45 CDT)
  • Re: AMBER: Turning off non-bond interactions (Wed Apr 21 2004 - 11:12:11 CDT)
  • Re: AMBER: non-periodic simulation and box information !! (Wed Apr 21 2004 - 11:04:54 CDT)
  • Re: AMBER: Question about compiling PMEMD (Wed Apr 21 2004 - 07:27:02 CDT)
  • AMBER: Intel Fortran Compiler, 7.1 status (Mon Apr 19 2004 - 10:32:49 CDT)
  • Re: AMBER: non-isotropic pressure scaling (Sun Apr 18 2004 - 08:44:09 CDT)
  • Re: AMBER: amber/pmemd with mpiexec (Mon Apr 12 2004 - 09:41:22 CDT)
  • Re: AMBER: Compiling Amber 8 (Mon Apr 12 2004 - 09:22:27 CDT)
  • Re: AMBER: amber/pmemd with mpiexec (Sat Apr 10 2004 - 12:21:15 CDT)
  • AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD (Fri Apr 09 2004 - 16:13:59 CDT)
  • Re: AMBER: PMEMD Problems... (Mon Apr 05 2004 - 23:38:58 CDT)
  • Re: AMBER: PMEMD Problems... (Mon Apr 05 2004 - 16:13:24 CDT)
  • Re: AMBER: Intel fortran compiler and -static switch in older pmemd releases (Fri Apr 02 2004 - 15:35:45 CST)
  • AMBER: Intel fortran compiler and -static switch in older pmemd releases (Fri Apr 02 2004 - 15:10:49 CST)
  • Re: AMBER: installing amber8 on a dual processor single box (Fri Apr 02 2004 - 12:58:35 CST)
  • Re: AMBER: non-isotropic pressure scaling (Wed Mar 31 2004 - 14:35:14 CST)
  • Re: AMBER: pmemd speedup and interactions (Wed Mar 31 2004 - 14:03:39 CST)
  • Re: AMBER: PMEMD and myrinet trouble (Mon Mar 29 2004 - 13:16:36 CST)
  • Re: AMBER: pmemd machinefiles (Mon Mar 29 2004 - 08:27:17 CST)
  • Re: AMBER: pmemd machinefiles (Mon Mar 29 2004 - 06:51:56 CST)
  • Re: AMBER: INtel Fortran 90 compiler (Wed Mar 24 2004 - 16:54:01 CST)
  • Re: AMBER: INtel Fortran 90 compiler (Wed Mar 24 2004 - 16:01:54 CST)
  • Re: AMBER: PMEMD and myrinet trouble (Wed Mar 24 2004 - 15:56:10 CST)
  • Re: AMBER: INtel Fortran 90 compiler (Wed Mar 24 2004 - 14:36:35 CST)
  • Re: AMBER: non-isotropic pressure scaling (Wed Mar 24 2004 - 07:44:35 CST)
  • Re: AMBER: PMEMD COMPILATION REDHAT (Thu Mar 11 2004 - 12:57:45 CST)
  • Re: AMBER: Sander problem with different CPU (Fri Mar 05 2004 - 07:39:37 CST)
  • Re: AMBER: IFC COMPILER (Mon Feb 16 2004 - 07:18:03 CST)
  • AMBER: Aldo's PMEMD bug (Mon Feb 09 2004 - 07:53:43 CST)
  • Re: AMBER: PMEMD and nmropt=1 (Thu Feb 05 2004 - 15:45:07 CST)
  • Re: AMBER: PMEMD and nmropt=1 (Thu Feb 05 2004 - 06:39:58 CST)
  • Re: AMBER: Do I need to repeat MD simulation? (Wed Jan 21 2004 - 07:44:22 CST)
  • AMBER: Question for PMEMD users (Tue Jan 20 2004 - 10:05:38 CST)
  • Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning (Wed Jan 07 2004 - 08:31:19 CST)
  • Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning (Wed Jan 07 2004 - 08:17:27 CST)
  • AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning (Tue Jan 06 2004 - 14:20:44 CST)
• Robyn Ayscue
  • Re: AMBER: from gaussian to antechamber (Fri Oct 15 2004 - 13:41:56 CDT)
  • AMBER: MAXRMSPT error in MOIL-view (Thu Jul 01 2004 - 17:19:23 CDT)
  • RE: AMBER: Changing MAXPR in Amber 8? (Fri Jun 18 2004 - 15:03:06 CDT)
  • AMBER: Changing MAXPR in Amber 8? (Fri Jun 18 2004 - 14:08:13 CDT)
  • Re: AMBER: Trouble running molecular dynamics with an increase in temp in Sander (Thu Jun 17 2004 - 10:35:34 CDT)
  • AMBER: Trouble running molecular dynamics with an increase in temp in Sander (Wed Jun 16 2004 - 08:43:05 CDT)
  • Re: AMBER: Compiling Amber8 on Mac OS X (Mon Jun 14 2004 - 13:41:15 CDT)
  • Re: AMBER: Compiling Amber8 on Mac OS X (Mon Jun 14 2004 - 13:39:27 CDT)
  • AMBER: Compiling Amber8 on Mac OS X (Thu Jun 10 2004 - 07:25:40 CDT)
  • Re: AMBER: LINMIN failure (Thu Jun 10 2004 - 06:52:07 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Fri Jun 04 2004 - 13:24:05 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 13:39:37 CDT)
  • AMBER: Loading mol2 files in XLEaP (Thu Jun 03 2004 - 11:17:54 CDT)
  • AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 11:14:00 CDT)
• Rohn Wood
  • Re: AMBER: Amber 7 on SGI: Sander MPI problem (Wed Apr 14 2004 - 18:48:58 CDT)
  • Re: AMBER: Amber 7 on SGI: Sander MPI problem (Wed Apr 14 2004 - 12:28:17 CDT)
  • AMBER: Amber 7 on SGI: Sander MPI problem (Tue Apr 13 2004 - 17:34:12 CDT)
• Ross Walker
  • RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Tue Dec 21 2004 - 23:26:48 CST)
  • RE: AMBER: use leap to build top & crd files for a pdb file with crytalline water molecules (Mon Dec 20 2004 - 18:55:17 CST)
  • RE: AMBER: Compiling question (Tue Dec 14 2004 - 13:44:27 CST)
  • RE: AMBER: Workshop 2004, Tutorial #6, QMMM MD Simulation (Tue Dec 14 2004 - 11:53:58 CST)
  • RE: AMBER: Why the charge is not an integer? (Mon Dec 13 2004 - 12:15:13 CST)
  • RE: AMBER: how to prepare Zn.lib (Fri Dec 10 2004 - 12:29:24 CST)
  • RE: AMBER: calculate ligand's rmsd (Thu Dec 09 2004 - 00:00:30 CST)
  • RE: AMBER: Gigabit Ethernet Switch/Opteron 246 (Tue Dec 07 2004 - 12:11:24 CST)
  • RE: AMBER: FW: two processor amd 64 bit pc (Mon Dec 06 2004 - 21:17:41 CST)
  • RE: AMBER: cut-off & MD (Mon Dec 06 2004 - 15:17:30 CST)
  • Re: AMBER: ntt parameter (Fri Dec 03 2004 - 01:11:31 CST)
  • RE: AMBER: question about parallel simulation (Thu Dec 02 2004 - 16:37:12 CST)
  • RE: AMBER: question about parallel simulation (Wed Dec 01 2004 - 19:00:33 CST)
  • RE: AMBER: question about parallel simulation (Wed Dec 01 2004 - 14:40:19 CST)
  • RE: AMBER: MD run: frozen (Sun Nov 28 2004 - 01:00:37 CST)
  • RE: AMBER: saving trajectory parameters (Sat Nov 27 2004 - 18:52:03 CST)
  • RE: AMBER: Protein with maximum hydrogen bonds (Sat Nov 27 2004 - 01:15:34 CST)
  • RE: AMBER: sander.QMMM on Mac (Fri Nov 26 2004 - 19:56:56 CST)
  • RE: AMBER: md.out & plot (Tue Nov 23 2004 - 16:59:58 CST)
  • RE: AMBER: Problem with minimisation of an protein-inhibitor complex (Tue Nov 23 2004 - 12:16:04 CST)
  • RE: AMBER: restart calculation (Tue Nov 23 2004 - 12:02:12 CST)
  • RE: AMBER: amber8 compilation (Mon Nov 22 2004 - 16:48:03 CST)
  • RE: AMBER: generating parmfile containing topology and parameter information (Mon Nov 22 2004 - 15:46:30 CST)
  • RE: AMBER: New problem on our 64bit box: xleap Segmentation fault (Mon Nov 22 2004 - 15:29:13 CST)
  • RE: AMBER: SHAKE probelm (Fri Nov 19 2004 - 17:09:05 CST)
  • RE: AMBER: leap compiling problem on a 64-bit machine (Fri Nov 19 2004 - 13:32:01 CST)
  • RE: AMBER: amber8 compilation (Fri Nov 19 2004 - 13:20:00 CST)
  • RE: AMBER: SHAKE probelm (Fri Nov 19 2004 - 11:35:18 CST)
  • RE: AMBER: Problem with carnal on linux (Fri Nov 19 2004 - 11:36:08 CST)
  • RE: AMBER: ambpdb segmentation fault (Wed Nov 17 2004 - 15:35:40 CST)
  • RE: AMBER: ifort 8.0 (Wed Nov 17 2004 - 12:39:49 CST)
  • RE: AMBER: RMS of energy in Minimization using SANDER (Wed Nov 17 2004 - 12:36:25 CST)
  • RE: AMBER: Can parallel simulation have a nonperiodic boundary condition? (Wed Nov 10 2004 - 18:26:27 CST)
  • RE: AMBER: error message about the input file of sander (Tue Nov 09 2004 - 11:44:31 CST)
  • RE: AMBER: Re: Antechamber (Thu Nov 04 2004 - 15:31:48 CST)
  • RE: AMBER: Fluctuation in temperature (Thu Nov 04 2004 - 14:05:57 CST)
  • RE: AMBER: amber7 test on osx (Fri Oct 29 2004 - 13:38:31 CDT)
  • RE: AMBER: sander gets stuck (Fri Oct 29 2004 - 09:52:43 CDT)
  • RE: AMBER: long minimization in sander (Mon Oct 25 2004 - 19:03:19 CDT)
  • RE: AMBER: long minimization in sander (Mon Oct 25 2004 - 10:11:29 CDT)
  • RE: AMBER: parallel of sander_classic (Mon Oct 25 2004 - 08:15:58 CDT)
  • RE: AMBER: MD problem (very long parhabs endless runtime) (Sat Oct 23 2004 - 13:53:22 CDT)
  • RE: AMBER: MD problem (very long parhabs endless runtime) (Sat Oct 23 2004 - 11:57:39 CDT)
  • RE: AMBER: Question about Xleap (Fri Oct 22 2004 - 08:31:58 CDT)
  • RE: AMBER: amber 8 parallel problem (Sun Oct 17 2004 - 13:05:33 CDT)
  • RE: AMBER: amber 8 parallel problem (Sun Oct 17 2004 - 00:28:51 CDT)
  • RE: AMBER: amber 8 error (Sun Oct 17 2004 - 00:20:34 CDT)
  • RE: AMBER: Problem with installing Amber8: Where are the MK libraries? (Fri Oct 15 2004 - 02:29:47 CDT)
  • RE: AMBER: Problem with installing Amber8: Where are the MK libraries? (Fri Oct 15 2004 - 02:26:32 CDT)
  • AMBER: Use of intel compilers v8.1 for Amber 8. (Thu Oct 14 2004 - 13:13:15 CDT)
  • RE: AMBER: Problem with installing Amber8: Where are the MK libraries? (Thu Oct 14 2004 - 13:06:52 CDT)
  • RE: AMBER: Problem with installing Amber8: Where are the MK libraries? (Thu Oct 14 2004 - 12:00:02 CDT)
  • RE: AMBER: A question on AMBER8 installation (Thu Oct 14 2004 - 11:50:25 CDT)
  • RE: Re: AMBER: errors in SGI (Thu Oct 14 2004 - 11:34:46 CDT)
  • RE: AMBER: A question on AMBER8 installation (Wed Oct 13 2004 - 15:21:27 CDT)
  • RE: Re: AMBER: Running on MPI (Wed Oct 13 2004 - 11:51:23 CDT)
  • RE: AMBER: A question on AMBER8 installation (Wed Oct 13 2004 - 00:43:49 CDT)
  • RE: AMBER: Questions about MD sampling (Tue Oct 12 2004 - 12:31:12 CDT)
  • RE: AMBER: Questions about MD sampling (Tue Oct 12 2004 - 12:25:30 CDT)
  • RE: AMBER: Question about restart MD (Mon Oct 11 2004 - 14:06:09 CDT)
  • RE: AMBER: AMBER 8 installation - continued (Mon Oct 11 2004 - 12:17:50 CDT)
  • RE: AMBER: Amber8 compilation in Dec-Alpha (Mon Oct 11 2004 - 12:09:40 CDT)
  • RE: AMBER: frcmod_dmso (Tue Oct 05 2004 - 15:10:41 CDT)
  • AMBER: Note to all concerning filtering of messages posted to the amber list. (Tue Oct 05 2004 - 14:51:34 CDT)
  • RE: AMBER: frcmod_dmso (Fri Oct 01 2004 - 17:05:05 CDT)
  • RE: AMBER: Amber-7:Bugfix.47 (Mon Sep 27 2004 - 15:34:36 CDT)
  • RE: AMBER: Amber 8 installation error on Xeon 2-CPU (Thu Sep 23 2004 - 18:32:49 CDT)
  • RE: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 12:44:04 CDT)
  • RE: AMBER: (Thu Sep 23 2004 - 12:36:45 CDT)
  • RE: AMBER: compressed files (Wed Sep 22 2004 - 12:20:18 CDT)
  • RE: AMBER: all_nucleic94 versus all_nucleic02 (Wed Sep 22 2004 - 12:11:21 CDT)
  • RE: AMBER: all_nucleic94 versus all_nucleic02 (Wed Sep 22 2004 - 10:53:49 CDT)
  • RE: AMBER: MAXRING Antechamber problem (Tue Sep 21 2004 - 14:49:51 CDT)
  • RE: AMBER: Intel Fortran Compiler Problem (Thu Sep 16 2004 - 23:00:30 CDT)
  • RE: AMBER: VDWAALS error during minimisation (Thu Sep 16 2004 - 10:20:34 CDT)
  • RE: AMBER: md problem (Thu Sep 16 2004 - 09:43:19 CDT)
  • RE: AMBER: amber 8 (Tue Sep 14 2004 - 10:40:26 CDT)
  • RE: AMBER: amber 8 (Tue Sep 14 2004 - 10:09:31 CDT)
  • RE: AMBER: Compilation Problem in Amber 7 (Mon Sep 13 2004 - 23:05:35 CDT)
  • RE: AMBER: make install error (Sun Sep 12 2004 - 05:15:03 CDT)
  • RE: AMBER: MPICH problem (Sun Sep 12 2004 - 05:12:05 CDT)
  • RE: AMBER: make install error (Fri Sep 10 2004 - 17:41:02 CDT)
  • RE: AMBER: Amber: BOMB (Wed Sep 08 2004 - 09:42:53 CDT)
  • RE: AMBER: Spike in energy and RMS (Wed Sep 08 2004 - 09:37:26 CDT)
  • RE: AMBER: Electrostatic potential from the trajectory ! (Wed Sep 08 2004 - 06:32:58 CDT)
  • RE: AMBER: Minimization error (Sat Aug 28 2004 - 14:34:31 CDT)
  • RE: AMBER: Minimization error (Wed Aug 25 2004 - 17:35:18 CDT)
  • RE: AMBER: restart a MD after replacing molecules (Wed Aug 25 2004 - 12:29:13 CDT)
  • RE: AMBER: Minimization error (Wed Aug 25 2004 - 12:23:13 CDT)
  • RE: AMBER: density calculation in AMBER output (Wed Aug 25 2004 - 12:11:02 CDT)
  • RE: AMBER: Amber 8 - Energy Minimization Parameters (Wed Aug 25 2004 - 11:02:31 CDT)
  • RE: AMBER: Trajectory file conversion between Amber & Charmm (Tue Aug 24 2004 - 18:51:17 CDT)
  • RE: AMBER: problem loading pdb in leap. (Tue Aug 24 2004 - 12:35:08 CDT)
  • RE: AMBER: problem loading pdb in leap. (Mon Aug 23 2004 - 23:53:49 CDT)
  • RE: AMBER: how to deal with the initial structure? (Mon Aug 23 2004 - 21:19:23 CDT)
  • RE: AMBER: NTT=0 and TAUTP (Mon Aug 23 2004 - 18:03:30 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 15:58:15 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 14:29:06 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 13:20:15 CDT)
  • RE: AMBER: Minimization error (Fri Aug 20 2004 - 17:48:27 CDT)
  • RE: AMBER: can MM-PBSA be applied to Charmm format trajectory file? (Thu Aug 19 2004 - 14:02:50 CDT)
  • RE: AMBER: how to read in CHARMM or AMBER binary trajectories (Thu Aug 19 2004 - 13:30:59 CDT)
  • RE: AMBER: angle bending (Thu Aug 19 2004 - 12:09:52 CDT)
  • RE: AMBER: metal atoms in Xleap (Thu Aug 19 2004 - 11:59:28 CDT)
  • RE: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Mon Aug 16 2004 - 13:13:09 CDT)
  • RE: AMBER: pmemd config.h request for athlon (Fri Aug 13 2004 - 13:09:15 CDT)
  • RE: AMBER: Amber: xleap crash (Fri Aug 13 2004 - 11:23:50 CDT)
  • RE: AMBER: minimization output file format (Thu Aug 12 2004 - 14:43:02 CDT)
  • RE: AMBER: Amber 8 Installation - C compiler? (Wed Aug 11 2004 - 19:37:45 CDT)
  • RE: AMBER: How to test the used parameters. (Wed Aug 11 2004 - 12:33:56 CDT)
  • RE: AMBER: bugfix.all (Tue Aug 10 2004 - 19:54:25 CDT)
  • RE: AMBER: unknown residue: ABA (Tue Aug 10 2004 - 13:46:14 CDT)
  • RE: AMBER: Amber8 - LAM MPI Compilation problems (Tue Aug 10 2004 - 11:59:33 CDT)
  • RE: AMBER: Adding residues (Mon Aug 09 2004 - 13:50:59 CDT)
  • AMBER: RE: about PME in Amber6 (Fri Aug 06 2004 - 13:37:06 CDT)
  • RE: AMBER: sander error (Thu Aug 05 2004 - 23:50:09 CDT)
  • RE: AMBER: sander.QMMM: CHARGE keyword in divcon.in file (Wed Aug 04 2004 - 15:48:08 CDT)
  • AMBER: RE: Hello Sir, (Wed Aug 04 2004 - 13:32:28 CDT)
  • RE: AMBER: atoms not in residue templates (Wed Aug 04 2004 - 13:26:55 CDT)
  • RE: AMBER: RMSD result from GB model (Wed Aug 04 2004 - 13:06:50 CDT)
  • RE: AMBER: (no subject) (Fri Jul 30 2004 - 16:09:25 CDT)
  • RE: AMBER: AMBER 6 compilation problems! (Fri Jul 30 2004 - 12:30:54 CDT)
  • RE: AMBER: (no subject) (Fri Jul 30 2004 - 11:21:33 CDT)
  • RE: AMBER: (Fri Jul 30 2004 - 10:46:52 CDT)
  • RE: AMBER: about running ptraj in amber8 (Mon Jul 26 2004 - 11:22:36 CDT)
  • RE: AMBER: atoms not in residue templates (Sat Jul 24 2004 - 10:05:36 CDT)
  • RE: AMBER: parametrization problem (Fri Jul 23 2004 - 14:32:15 CDT)
  • RE: AMBER: user force (Thu Jul 22 2004 - 17:40:16 CDT)
  • RE: AMBER: user force (Thu Jul 22 2004 - 17:08:04 CDT)
  • RE: AMBER: Xleap crash, problem with residue bonding (Thu Jul 22 2004 - 16:31:22 CDT)
  • RE: AMBER: atom out of bounds (fwd) (Thu Jul 22 2004 - 15:54:52 CDT)
  • RE: AMBER: Problem with sander tutorial. (Thu Jul 22 2004 - 15:57:20 CDT)
  • RE: AMBER: Amber8: Vlimit problem again (Wed Jul 21 2004 - 18:55:59 CDT)
  • RE: AMBER: cut offs in amber? (Wed Jul 21 2004 - 17:10:09 CDT)
  • RE: AMBER: cut offs in amber? (Wed Jul 21 2004 - 16:39:47 CDT)
  • RE: AMBER: amparm (Wed Jul 21 2004 - 16:11:29 CDT)
  • RE: AMBER: cut offs in amber? (Wed Jul 21 2004 - 16:05:02 CDT)
  • RE: AMBER: What happen when sander reads charge increments from cpin file? (Wed Jul 21 2004 - 15:41:45 CDT)
  • RE: AMBER: Problem with sander tutorial. (Tue Jul 20 2004 - 15:16:28 CDT)
  • RE: AMBER: Problems with CPU scaling on cluster (Thu Jul 15 2004 - 13:48:15 CDT)
  • RE: AMBER: antechamber (Thu Jul 15 2004 - 13:21:44 CDT)
  • RE: AMBER: How to apply OPLS force field? (Wed Jul 14 2004 - 23:20:58 CDT)
  • RE: AMBER: (no subject) (Wed Jul 14 2004 - 13:33:38 CDT)
  • RE: AMBER: Problem with divcon - increasing MXATTS? (Wed Jul 14 2004 - 13:13:19 CDT)
  • RE: AMBER: anisotropic scaling (Tue Jul 13 2004 - 14:39:05 CDT)
  • RE: AMBER: (no subject) (Tue Jul 13 2004 - 12:32:22 CDT)
  • RE: AMBER: what is averaged RMS fluctuation? (Mon Jul 12 2004 - 15:40:23 CDT)
  • RE: AMBER: what is averaged RMS fluctuation? (Mon Jul 12 2004 - 13:51:47 CDT)
  • RE: AMBER: Problems with CPU scaling on cluster (Mon Jul 12 2004 - 13:38:27 CDT)
  • RE: AMBER: Fe parameter (Mon Jul 12 2004 - 13:19:23 CDT)
  • RE: AMBER: Molecular dynamic (Mon Jul 12 2004 - 13:12:53 CDT)
  • RE: AMBER: MD simulation : problem (Mon Jul 12 2004 - 12:55:33 CDT)
  • RE: AMBER: MD simulation : problem (Sun Jul 11 2004 - 19:41:11 CDT)
  • RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Sun Jul 11 2004 - 13:38:49 CDT)
  • RE: AMBER: MD simulation : problem (Sat Jul 10 2004 - 00:35:14 CDT)
  • RE: AMBER: execution time (Fri Jul 09 2004 - 13:52:08 CDT)
  • RE: AMBER: Disulfide bond command (Fri Jul 09 2004 - 13:27:13 CDT)
  • RE: AMBER: Problem with sander - Error on Open (Thu Jul 08 2004 - 17:15:04 CDT)
  • RE: AMBER: average using ptraj (Thu Jul 08 2004 - 15:18:58 CDT)
  • RE: AMBER: problems with mdcrd (Thu Jul 08 2004 - 14:54:08 CDT)
  • RE: AMBER: parameter development for nucleotide analogues (Thu Jul 08 2004 - 12:49:33 CDT)
  • RE: AMBER: charge problem in minimization (Thu Jul 08 2004 - 12:40:56 CDT)
  • RE: AMBER: name error (Thu Jul 08 2004 - 12:35:46 CDT)
  • RE: AMBER: problems with mdcrd (Thu Jul 08 2004 - 12:32:04 CDT)
  • RE: AMBER: Molecular dynamic (Thu Jul 08 2004 - 12:24:21 CDT)
  • RE: AMBER: segmentation fault in leap (Thu Jul 08 2004 - 12:07:28 CDT)
  • RE: AMBER: ptraj (Thu Jul 08 2004 - 12:01:43 CDT)
  • RE: AMBER: question about Ptraj (Thu Jul 08 2004 - 11:47:28 CDT)
  • RE: AMBER: Amber7 bugfix1 (Tue Jul 06 2004 - 13:17:49 CDT)
  • RE: AMBER: no 'water.lib' in /amber8/dat/leap/ (Thu Jul 01 2004 - 15:30:25 CDT)
  • RE: AMBER: N-terminal Arg charges in ff99 not 1.00 (Thu Jul 01 2004 - 15:13:00 CDT)
  • RE: AMBER: N-terminal Arg charges in ff99 not 1.00 (Thu Jul 01 2004 - 14:17:02 CDT)
  • RE: AMBER: N-terminal Arg charges in ff99 not 1.00 (Wed Jun 30 2004 - 16:26:22 CDT)
  • RE: AMBER: Amber 8 installation error (Tue Jun 29 2004 - 18:08:21 CDT)
  • RE: AMBER: Problem with menu bar in LEAP (Fri Jun 25 2004 - 17:12:13 CDT)
  • RE: RE: AMBER: Amber 8 installation (Fri Jun 25 2004 - 12:27:23 CDT)
  • RE: AMBER: Amber 8 installation (Thu Jun 24 2004 - 17:38:57 CDT)
  • RE: AMBER: MD & running time (Tue Jun 22 2004 - 22:51:28 CDT)
  • RE: AMBER: Changing MAXPR in Amber 8? (Fri Jun 18 2004 - 14:23:33 CDT)
  • RE: AMBER: LINMIN failure (Fri Jun 11 2004 - 01:10:23 CDT)
  • RE: AMBER: LINMIN failure (Thu Jun 10 2004 - 12:10:08 CDT)
  • RE: AMBER: xleap solvatebox problem (Wed Jun 09 2004 - 17:48:12 CDT)
  • RE: AMBER: paramitrization problem (Tue Jun 08 2004 - 12:31:10 CDT)
  • RE: AMBER: bug in leap? (Mon Jun 07 2004 - 18:50:10 CDT)
  • RE: AMBER: paramitrization problem (Mon Jun 07 2004 - 17:24:15 CDT)
  • RE: AMBER: question about xleap (Thu Jun 03 2004 - 14:19:55 CDT)
  • RE: AMBER: question about xleap (Thu Jun 03 2004 - 13:03:04 CDT)
  • RE: AMBER: sander of AMBER 8 doesn't work (Tue Jun 01 2004 - 13:56:29 CDT)
  • RE: AMBER: Amber7: pdb format file (Tue Jun 01 2004 - 13:49:31 CDT)
  • RE: AMBER: Amber force field for protein-DNA system (Tue Jun 01 2004 - 13:09:37 CDT)
  • RE: AMBER: Cannot read in sander (Thu May 27 2004 - 17:36:10 CDT)
  • RE: AMBER: Cannot read in sander (Wed May 26 2004 - 20:08:48 CDT)
  • RE: AMBER: amber 8 under windows XP (Wed May 26 2004 - 14:03:54 CDT)
  • RE: AMBER: ptraj (Tue May 25 2004 - 12:35:39 CDT)
  • RE: AMBER: universal recognition of chemicals (Mon Apr 26 2004 - 17:35:41 CDT)
  • RE: AMBER: compile amber8 in linux with ifort (Fri Apr 23 2004 - 16:42:39 CDT)
  • RE: AMBER: compile amber8 in linux with ifort (Fri Apr 23 2004 - 16:23:21 CDT)
  • RE: AMBER: compiling Amber 8 (Fri Apr 16 2004 - 13:47:36 CDT)
  • RE: AMBER: xleap bug? (Wed Apr 14 2004 - 17:48:18 CDT)
  • RE: AMBER: Dipole moment changes during MD (Fri Apr 09 2004 - 16:56:48 CDT)
  • RE: AMBER: Suggestions for newer pentium chips and hyperthreading with PMEMD (Fri Apr 09 2004 - 16:38:18 CDT)
  • RE: AMBER: Dipole moment changes during MD (Fri Apr 09 2004 - 11:48:29 CDT)
  • RE: AMBER: script on tutorial page (Thu Apr 08 2004 - 23:21:44 CDT)
  • RE: AMBER: amber8 tutorial (Sun Apr 04 2004 - 21:45:52 CDT)
  • RE: AMBER: pmemd speedup and interactions (Wed Mar 31 2004 - 11:42:32 CST)
  • RE: AMBER: About glycam2004 (Tue Mar 23 2004 - 12:11:01 CST)
  • RE: AMBER: MD simulation of a DNA decamer (Tue Mar 09 2004 - 12:07:35 CST)
  • RE: AMBER: xleap don't recognize my residue/atom (Tue Mar 02 2004 - 11:44:13 CST)
  • RE: AMBER: Problems with xleap (Mon Mar 01 2004 - 17:25:23 CST)
  • RE: AMBER: ptraj (Mon Mar 01 2004 - 17:25:41 CST)
  • RE: AMBER: add Na+ (Tue Feb 24 2004 - 12:42:28 CST)
  • RE: AMBER: algorithm used in AMBER (Fri Jan 02 2004 - 07:05:13 CST)
  • RE: AMBER: force field (Fri Jan 02 2004 - 06:55:24 CST)
• Ru-Zhen Li
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 17:17:08 CST)
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 11:05:57 CST)
  • AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 06:59:40 CST)
  • AMBER: AMBER 4 Manual? (Fri Nov 12 2004 - 11:02:16 CST)
  • Re: AMBER: error message about the input file of sander (Tue Nov 09 2004 - 14:33:57 CST)
  • Re: AMBER: error message about the input file of sander (Tue Nov 09 2004 - 06:49:26 CST)
  • Re: AMBER: error message about the input file of sander (Tue Nov 09 2004 - 06:20:40 CST)
  • AMBER: error message about the input file of sander (Mon Nov 08 2004 - 20:23:23 CST)
• Rukman Hertadi
  • AMBER: another cpinutil.pl error (Fri Aug 06 2004 - 00:35:09 CDT)
  • AMBER: sander error (Thu Aug 05 2004 - 23:33:41 CDT)
  • AMBER: cpinutil.pl error (Tue Aug 03 2004 - 06:22:59 CDT)
  • AMBER: pH effect on protein folding (Thu Jul 15 2004 - 21:00:54 CDT)
• Ryan Ye
  • Re: AMBER: NHE problem (Sun May 23 2004 - 10:19:56 CDT)
  • AMBER: NHE problem (Sat May 22 2004 - 00:36:44 CDT)
  • AMBER: EWALD BOMB? (Sat Mar 20 2004 - 13:28:01 CST)
  • AMBER: production input file (Mon Mar 01 2004 - 12:58:48 CST)
• S. Frank Yan
  • RE: AMBER: about MM-PBSA (Tue Sep 21 2004 - 00:59:02 CDT)
  • AMBER: animation? (Wed Jul 28 2004 - 01:29:51 CDT)
  • AMBER: Bondi radii for BR and F in mm_pbsa calculation (Tue Jul 20 2004 - 18:01:03 CDT)
  • AMBER: FW: missing bondi radii of Br and F for surface area calculation (Tue Jul 20 2004 - 12:30:13 CDT)
  • RE: AMBER: pbsa calculation on part of the molecule & nmode analysis (Thu May 20 2004 - 20:06:11 CDT)
  • AMBER: pbsa calculation on part of the molecule (Thu May 20 2004 - 15:25:46 CDT)
  • RE: AMBER: PB bomb in pb_saarc (Tue May 18 2004 - 18:14:36 CDT)
  • AMBER: PB bomb in pb_saarc (Tue May 18 2004 - 15:41:41 CDT)
  • FW: AMBER: ions in mm_pbsa (Thu May 06 2004 - 12:23:55 CDT)
  • re: AMBER: check unit + saveamberparm (Fri Feb 20 2004 - 18:17:41 CST)
  • RE: AMBER: contributed parameters (modified base - PSU) (Tue Feb 17 2004 - 20:32:56 CST)
  • AMBER: moil-view question (Mon Feb 16 2004 - 20:43:57 CST)
  • RE: AMBER: temperature in DelPhi for MM-PBSA calculation (Mon Feb 02 2004 - 17:18:22 CST)
  • FW: AMBER: Segmentation fault (core dumped) error of antechamber program (Mon Jan 26 2004 - 12:12:39 CST)
  • AMBER: Segmentation fault (core dumped) error of antechamber program (Thu Jan 22 2004 - 13:36:54 CST)
  • AMBER: antechamber and mopac5010mn (Wed Jan 21 2004 - 09:37:25 CST)
• sachin patil
  • AMBER: Question about Amino acid mutations (Wed Oct 13 2004 - 18:03:22 CDT)
  • AMBER: GIbbs : failure to start (Wed Oct 06 2004 - 13:01:23 CDT)
  • AMBER: Amber-7:Bugfix.47 (Mon Sep 27 2004 - 14:32:21 CDT)
  • RE: AMBER: Sander : Vrand flag (Tue Aug 31 2004 - 09:15:37 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 14:54:52 CDT)
  • RE: AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 14:07:32 CDT)
  • AMBER: Sander : Vrand flag (Mon Aug 23 2004 - 12:59:30 CDT)
  • AMBER: opteron 64 bit workstation (Wed Aug 11 2004 - 13:59:33 CDT)
  • Re: AMBER: Sander (Mon Aug 09 2004 - 13:26:20 CDT)
  • AMBER: Sander (Mon Aug 09 2004 - 11:24:59 CDT)
  • AMBER: sander : constraints to conserve hydrogen bonds (Thu Jul 22 2004 - 23:15:04 CDT)
  • RE: AMBER: MD simulation : problem :THANK YOU (Tue Jul 13 2004 - 09:51:28 CDT)
  • RE: AMBER: MD simulation : problem (Sun Jul 11 2004 - 23:53:51 CDT)
  • RE: AMBER: MD simulation : problem (Sun Jul 11 2004 - 10:08:13 CDT)
  • AMBER: MD simulation : problem (Sat Jul 10 2004 - 00:08:15 CDT)
  • AMBER: Amber7 bugfix1 (Tue Jul 06 2004 - 12:47:38 CDT)
  • AMBER: running MD simulatons (Tue Jul 06 2004 - 11:52:58 CDT)
  • Re: AMBER: Problem with menu bar in LEAP (Sun Jun 27 2004 - 12:01:30 CDT)
  • AMBER: Opteron-64bit work station (Mon Jun 21 2004 - 11:18:16 CDT)
• Sandro Fornili
  • AMBER: ptraj radial (Fri Nov 05 2004 - 10:28:57 CST)
• Sanjeev B.S.
  • AMBER: MD: Water network analysis + visualization (Fri Dec 17 2004 - 12:23:22 CST)
  • Re: AMBER: Protein with maximum hydrogen bonds (Sat Nov 27 2004 - 09:14:01 CST)
  • Re: AMBER: radius of gyration (Sun Sep 26 2004 - 02:04:51 CDT)
  • Re: AMBER: radius of gyration (Sat Sep 25 2004 - 22:28:32 CDT)
  • Re: AMBER: H Bonds (Fri May 07 2004 - 03:38:24 CDT)
  • Re: AMBER: H Bonds (Thu May 06 2004 - 00:09:06 CDT)
  • RE: AMBER: Anal module on PDBs (Sat Mar 13 2004 - 13:25:07 CST)
  • AMBER: Anal module on PDBs (Sat Mar 13 2004 - 09:35:31 CST)
• Sarah Harris
  • AMBER: Titratable amino acid termini (Tue Apr 27 2004 - 04:43:16 CDT)
• Sarah Rankin
  • Re: AMBER: mm_pbsa.pl in Amber8 (Mon Aug 23 2004 - 05:00:21 CDT)
  • Re: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Tue Aug 17 2004 - 03:18:30 CDT)
  • Re: AMBER: question about compilation of AMBER8 on MANDRAKE9.2 (Mon Aug 16 2004 - 12:14:38 CDT)
• Sarah Wittkopp
  • AMBER: Treating atom type LP the same as EP (Mon May 17 2004 - 14:16:20 CDT)
  • Re: AMBER: TIP4P extended (Mon Feb 16 2004 - 11:21:15 CST)
  • AMBER: leap - orientation of sequenced residues (Mon Feb 02 2004 - 19:58:33 CST)
• Satpal Virdee
  • Re: AMBER: How to compile the downloadable RESP in UNIX (Thu Nov 18 2004 - 06:36:07 CST)
  • Re: AMBER: How to compile the downloadable RESP in UNIX (Tue Nov 16 2004 - 09:58:41 CST)
  • AMBER: Parameters for new residue? (Sat Nov 13 2004 - 13:34:27 CST)
• scopio
  • AMBER: a question on ntwx and ntwr (Thu Oct 28 2004 - 09:42:14 CDT)
  • Re: AMBER: xleap problem (Mon Jul 12 2004 - 09:09:47 CDT)
  • Re: AMBER: Fe parameter (Mon Jul 12 2004 - 09:18:52 CDT)
  • AMBER: Box range in vacuum when restart MD (Wed Jun 23 2004 - 08:22:31 CDT)
  • Re: AMBER: leap.log warnings (Tue Jun 22 2004 - 19:54:37 CDT)
  • AMBER: leap.log warnings (Sun Jun 20 2004 - 20:18:40 CDT)
  • AMBER: question about force field (Mon Jun 14 2004 - 10:05:57 CDT)
  • Re: AMBER: parmcal problem (Thu Jun 10 2004 - 19:21:30 CDT)
  • AMBER: parmcal problem (Thu Jun 10 2004 - 09:46:11 CDT)
  • AMBER: How to neutralize system? (Wed Jun 09 2004 - 09:47:44 CDT)
  • Re: AMBER: ptraj (Tue May 25 2004 - 18:49:47 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:15:28 CDT)
  • AMBER: Converting ORAC's topology file to AMBER's prepi file (Fri May 14 2004 - 07:30:32 CDT)
  • AMBER: what does EAMBER stand for? (Mon May 10 2004 - 20:08:35 CDT)
  • Re: AMBER: HIS protonation (Mon May 10 2004 - 06:00:19 CDT)
  • AMBER: what is its file format ? (Sat May 08 2004 - 09:13:21 CDT)
  • Re: AMBER: xleap problem (Mon May 03 2004 - 03:51:03 CDT)
  • Re: AMBER: problem for compiling amber7 by ifc8 (Sun May 02 2004 - 23:18:31 CDT)
  • Re: AMBER: problem for compiling amber7 by ifc8 (Sun May 02 2004 - 19:15:58 CDT)
  • AMBER: problem for compiling amber7 by ifc8 (Sat May 01 2004 - 07:26:57 CDT)
  • Re: AMBER: Redhat install (Thu Apr 29 2004 - 19:32:26 CDT)
  • AMBER: xleap don't recognize formaldehyde? (Tue Apr 27 2004 - 09:53:00 CDT)
  • AMBER: segmentation fault of minimization (Mon Mar 29 2004 - 20:57:39 CST)
  • AMBER: How to compile antechamber? (Fri Mar 26 2004 - 01:17:54 CST)
  • Re: AMBER: How to use these parameters? (Wed Mar 17 2004 - 03:31:28 CST)
  • AMBER: How to use these parameters? (Tue Mar 16 2004 - 19:15:15 CST)
  • Re: AMBER: xleap couldn't display any word (Mon Mar 15 2004 - 19:44:47 CST)
  • AMBER: How to convert charmm parameters to amber (Mon Mar 15 2004 - 03:55:11 CST)
  • Re: AMBER: new wed site for amber tutorials (Mon Mar 15 2004 - 02:17:19 CST)
  • AMBER: xleap couldn't display any word (Sun Mar 14 2004 - 20:45:42 CST)
  • Re: AMBER: what's the meaning of parameter NRUN (Tue Mar 09 2004 - 19:25:07 CST)
  • AMBER: what's the meaning of parameter NRUN (Tue Mar 09 2004 - 07:40:51 CST)
  • Re: AMBER: xleap don't recognize my residue/atom (Tue Mar 02 2004 - 02:00:31 CST)
  • AMBER: xleap don't recognize my residue/atom (Sun Feb 22 2004 - 05:18:42 CST)
• Scott
  • Re: AMBER: using ptraj (Thu Jul 29 2004 - 17:48:19 CDT)
  • Re: AMBER: using ptraj (Thu Jul 29 2004 - 16:15:17 CDT)
  • RE: AMBER: Problem with sander tutorial. (Thu Jul 22 2004 - 21:08:19 CDT)
  • AMBER: found unknown atflg PB (Thu Jul 22 2004 - 08:38:33 CDT)
  • AMBER: Enthalpy of solvent-solute vanderWaals (Wed Jul 14 2004 - 14:56:45 CDT)
  • AMBER: Problems with X.R.E.D. (Fri Jun 25 2004 - 10:49:24 CDT)
• Scott Brozell
  • AMBER: icc 8.0 built antechamber (Thu Oct 28 2004 - 12:24:02 CDT)
  • Re: AMBER: A question on AMBER8 installation (Wed Oct 13 2004 - 12:24:51 CDT)
  • Re: AMBER: error in installing amber8 (Thu Sep 02 2004 - 10:56:50 CDT)
  • Re: AMBER: tleap: automatically identify and connect disulfide bonds? (Wed Jul 28 2004 - 15:22:52 CDT)
  • Re: AMBER: erroe in installing amber8 (Sun Jul 25 2004 - 19:58:58 CDT)
  • Re: AMBER: Weird compiling problem in Amber 8 (Mon Jul 19 2004 - 12:08:54 CDT)
  • Re: AMBER: Problems with amber8 and pgf90 (Thu Jul 15 2004 - 11:23:44 CDT)
  • Re: AMBER: tleap - FATAL error (Wed Jul 14 2004 - 16:44:41 CDT)
  • RE: AMBER: Problem amber8 compilation in Opteron(Linux) with PGI-workstation compiler (Mon Jul 12 2004 - 13:30:39 CDT)
  • Re: AMBER: Suface area parameter for fluorine in MM/PBSA (Sun Jun 13 2004 - 03:05:02 CDT)
  • Re: AMBER: ifort -parallel (Fri Jun 11 2004 - 10:36:36 CDT)
  • Re: AMBER: bug in leap? (Thu Jun 10 2004 - 23:32:24 CDT)
  • Re: AMBER: Xleap (Thu Jun 10 2004 - 15:36:25 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 13:11:15 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 12:53:34 CDT)
  • Re: AMBER: Loading mol2 Files in XLEaP (Thu Jun 03 2004 - 16:49:13 CDT)
  • Re: AMBER: Install Amber8 under cygwin (Tue Jun 01 2004 - 02:22:14 CDT)
  • Re: AMBER: Compiling AMBER MPI program using GCC/G77 compiler and MPICH on AMD OPTERON 64 (Tue May 25 2004 - 14:24:23 CDT)
  • Re: AMBER: Program error in testing of Amber8 (Sun May 16 2004 - 18:17:44 CDT)
  • Re: AMBER: PMEMD Built ? Wont run.. (Tue May 11 2004 - 14:41:15 CDT)
  • Re: AMBER: what does EAMBER stand for? (Tue May 11 2004 - 12:45:09 CDT)
  • Re: AMBER: antechamber (Wed May 05 2004 - 16:30:17 CDT)
  • Re: AMBER: ptraj: radius of gyration (Sun May 02 2004 - 03:09:12 CDT)
  • Re: AMBER: partition error in shake (Tue Apr 27 2004 - 17:26:44 CDT)
  • Re: AMBER: Error message while testing (Mon Apr 12 2004 - 20:10:30 CDT)
  • Re: AMBER: scali amber8 (Mon Apr 12 2004 - 17:54:42 CDT)
  • Re: AMBER: segmentation fault (Thu Mar 25 2004 - 16:33:32 CST)
  • Re: AMBER: INtel Fortran 90 compiler (Wed Mar 24 2004 - 15:37:37 CST)
  • Re: AMBER: segmentation fault (Mon Mar 22 2004 - 20:10:27 CST)
  • Re: AMBER: Compilation problem in SUN OS 5.7! (Mon Mar 22 2004 - 15:57:03 CST)
  • Re: AMBER: SANDER general questions. (Mon Mar 22 2004 - 15:26:55 CST)
  • Re: AMBER: EWALD BOMB? (Mon Mar 22 2004 - 14:44:51 CST)
  • Re: AMBER: understanding SANDER source code (Sun Mar 21 2004 - 13:47:40 CST)
  • Re: AMBER: residue insertion (Fri Mar 19 2004 - 17:01:02 CST)
  • Re: AMBER: compiling on SGI (Thu Mar 11 2004 - 16:24:36 CST)
  • Re: AMBER: Leap atom removal bug? (Fri Mar 05 2004 - 20:34:16 CST)
  • Re: AMBER: compiling software(RESP) on MAC G5 (Wed Feb 18 2004 - 23:36:06 CST)
  • AMBER: GLYCAM web site (Wed Feb 18 2004 - 14:00:39 CST)
  • Re: AMBER: rstdip (Wed Feb 04 2004 - 12:19:45 CST)
  • Re: AMBER: Ibelly and Ewald error message when ewald should be off (Wed Jan 28 2004 - 23:57:06 CST)
  • AMBER: crystal lattice determination (Wed Jan 21 2004 - 10:51:37 CST)
• Scott E. Boesch
  • AMBER: A torsion parameter in AMBER2003 force field (Fri Oct 08 2004 - 11:23:41 CDT)
• Scott Pendley
  • AMBER: Testing Delphi for mm_pbsa (Thu Sep 30 2004 - 12:20:15 CDT)
• scott.brown_at_abbott.com
  • Re: AMBER: EWALD BOMB? (Mon Mar 22 2004 - 14:21:21 CST)
• Sebastian Fernandez Alberti
  • AMBER: parameter development (Mon Dec 20 2004 - 13:34:42 CST)
  • AMBER: RESP charges in Fe+3 heme system (Thu Aug 26 2004 - 12:43:08 CDT)
  • AMBER: RESP calculation with different multiplicities (Tue Aug 17 2004 - 15:44:54 CDT)
  • AMBER: RESP partial charge calculation (Tue Aug 10 2004 - 11:21:06 CDT)
  • AMBER: resp charge calculation for Fe+3 heme (Mon Aug 09 2004 - 14:45:18 CDT)
• sebnem
  • Re: AMBER: Nmode (Thu Jun 17 2004 - 00:30:54 CDT)
  • AMBER: Nmode (Wed Jun 16 2004 - 18:47:18 CDT)
  • AMBER: nmode analysis (Sun May 02 2004 - 19:52:12 CDT)
• sebnem_at_mercury.chem.pitt.edu
  • Re: AMBER: nmode analysis (Mon May 03 2004 - 11:31:18 CDT)
• SEKIJIMA Masakazu
  • AMBER: amber8 compilation on AIX (regatta) (Thu Oct 14 2004 - 08:41:40 CDT)
• Sekwan Oh
  • AMBER: General Questions (Tue Mar 02 2004 - 18:07:08 CST)
• Seonah Kim
  • AMBER: Octahedron Box (Mon Jun 28 2004 - 10:30:34 CDT)
  • AMBER: Install Amber8 under cygwin (Mon May 31 2004 - 20:35:16 CDT)
• Seongeun Yang
  • Re: AMBER: Angle parameters in phosphate groups (Mon Aug 16 2004 - 01:04:16 CDT)
  • Re: AMBER: Angle parameters in phosphate groups (Sat Aug 14 2004 - 04:58:07 CDT)
  • AMBER: Angle parameters in phosphate groups (Thu Aug 12 2004 - 08:29:02 CDT)
  • AMBER: Angle parameters in phosphate groups (Thu Aug 05 2004 - 07:17:44 CDT)
• Sergey
  • AMBER: Memory for AMBER 6 simulation (Sat Jan 24 2004 - 03:22:56 CST)
• Sergio E. Wong
  • AMBER: constant pH simulations reference (Mon Nov 15 2004 - 19:50:16 CST)
  • Re: AMBER: Comparison of simulation results on amber7 and amber 8 (Wed Oct 06 2004 - 11:54:44 CDT)
  • Re: AMBER: amber8 performance problem on Itanium II's (Fri Sep 17 2004 - 13:23:18 CDT)
  • AMBER: amber8 performance problem on Itanium II's (Thu Sep 16 2004 - 23:18:47 CDT)
  • Re: AMBER: GB and langevin dynamics (Wed Sep 15 2004 - 14:38:43 CDT)
  • AMBER: GB and langevin dynamics (Fri Sep 10 2004 - 00:41:18 CDT)
  • Re: AMBER: REM make test (Thu Sep 09 2004 - 19:55:49 CDT)
  • AMBER: REM make test (Thu Sep 09 2004 - 17:50:50 CDT)
  • AMBER: freezing atoms in impliciti solvent (Tue Aug 24 2004 - 12:27:32 CDT)
  • AMBER: GBSA frequency update (Wed Feb 11 2004 - 17:29:10 CST)
• Sergio Emanuel Galembeck
  • AMBER: PARMSCAN (Mon Apr 26 2004 - 13:29:05 CDT)
• Sergio Pantano
  • AMBER: Mac OSX xleap compilation (Fri Apr 02 2004 - 00:32:07 CST)
• Shan, Jufang
  • AMBER: is it a bug in mmpbsa (Tue Sep 07 2004 - 09:29:27 CDT)
  • AMBER: mm_pbsa.pl in Amber8 (Fri Aug 20 2004 - 14:13:54 CDT)
  • AMBER: xleap solvatebox problem (Thu Jun 10 2004 - 09:49:25 CDT)
  • AMBER: xleap solvatebox problem (Wed Jun 09 2004 - 17:17:59 CDT)
• Shau Grossman
  • Re: AMBER: R.E.D. (Mon Feb 23 2004 - 20:13:43 CST)
  • AMBER: R.E.D. (Mon Feb 23 2004 - 19:20:44 CST)
  • Re: AMBER: contributed parameters (Fri Feb 20 2004 - 15:46:04 CST)
  • Re: AMBER: contributed parameters (Thu Feb 19 2004 - 20:55:46 CST)
  • AMBER: contributed parameters (modified base - PSU) (Tue Feb 17 2004 - 20:14:16 CST)
• Shekter, Lee
  • AMBER: nmode & mm-pbsa (Thu Dec 02 2004 - 20:50:45 CST)
• Sichun Yang
  • RE: AMBER: Increase lastrst in the &cntrl namelist (Wed Sep 01 2004 - 12:19:18 CDT)
  • Re: AMBER: Increase lastrst in the &cntrl namelist (Wed Sep 01 2004 - 01:29:27 CDT)
  • AMBER: Increase lastrst in the &cntrl namelist (Tue Aug 31 2004 - 11:06:46 CDT)
  • AMBER: NSPSOL in parm file (Wed Jul 28 2004 - 23:14:01 CDT)
  • Re: AMBER: How to apply OPLS force field? (Wed Jul 14 2004 - 11:21:41 CDT)
  • AMBER: newer OPLS/AA? (Mon Jun 21 2004 - 18:23:03 CDT)
  • AMBER: ptraj: radius of gyration (Sat May 01 2004 - 21:50:37 CDT)
  • Re: AMBER: "matrix" in ptraj (Sat Apr 24 2004 - 18:20:50 CDT)
  • AMBER: "matrix" in ptraj (Fri Apr 23 2004 - 20:19:28 CDT)
  • AMBER: Carnal in Amber7 (Wed Apr 07 2004 - 23:03:35 CDT)
  • Re: AMBER: hbond analysis in ptraj(%occupied>1) (Thu Mar 25 2004 - 12:46:01 CST)
  • AMBER: neutrality of charge in AMBER 7 (Thu Feb 12 2004 - 14:51:51 CST)
• SIVA
  • Re: AMBER: Constant Pressure Problem of MD (Mon Jun 07 2004 - 22:53:39 CDT)
• Sivakolundu, Sivashankar
  • AMBER: Amber 8 ptraj segmentation fault (Wed Apr 07 2004 - 00:49:08 CDT)
  • AMBER: nmanal - segmentation fault (Fri Mar 26 2004 - 00:11:16 CST)
• Sivanesan Dakshanamurthy
  • Re: AMBER: parameter error for a ligand (Tue Oct 05 2004 - 16:45:51 CDT)
  • AMBER: parameter error for a ligand (Tue Oct 05 2004 - 11:59:54 CDT)
  • AMBER: tleap - FATAL error (Wed Jul 14 2004 - 16:28:41 CDT)
  • AMBER: question about antechamber program (Fri Jul 02 2004 - 13:42:07 CDT)
  • Re: AMBER: Could not assign parameters (Fri Jun 18 2004 - 14:35:32 CDT)
  • AMBER: Could not assign parameters (Fri Jun 18 2004 - 13:52:18 CDT)
• Skauge Tormod
  • Re: AMBER: nucgen generated RNA duplex: leap problems (Tue Apr 20 2004 - 10:03:09 CDT)
  • Re: AMBER: Bad atom symbol, K+ and IB in vacuum (Wed Mar 31 2004 - 06:20:30 CST)
  • AMBER: Bad atom symbol, K+ and IB in vacuum (Tue Mar 30 2004 - 06:50:42 CST)
• Soon
  • AMBER: Periodic boundary simulation (Tue Jun 01 2004 - 04:08:31 CDT)
• Spero Manolatos
  • AMBER: FW: two processor amd 64 bit pc (Mon Dec 06 2004 - 19:36:33 CST)
• spookie
  • AMBER: problem not with sander, but with mpich (Mon Jun 28 2004 - 04:08:37 CDT)
  • Re: AMBER: -p4pg problem (Sun Jun 27 2004 - 00:19:33 CDT)
  • Re: AMBER: -p4pg problem (Sat Jun 26 2004 - 09:00:48 CDT)
  • AMBER: -p4pg problem (Sat Jun 26 2004 - 03:34:40 CDT)
  • Re: AMBER: sander in parallel, amber8 (Fri Jun 25 2004 - 13:26:58 CDT)
  • Re: AMBER: amber8 parallel jobs (Fri Jun 25 2004 - 13:05:23 CDT)
  • RE: AMBER: Amber 8 installation (Fri Jun 25 2004 - 13:08:21 CDT)
  • AMBER: sander in parallel, amber8 (Fri Jun 25 2004 - 03:49:30 CDT)
  • Re: AMBER: amber8 parallel jobs (Fri Jun 25 2004 - 08:42:09 CDT)
  • Re: AMBER: Amber 8 installation (Thu Jun 24 2004 - 17:42:40 CDT)
  • AMBER: amber8 parallel jobs (Wed Jun 23 2004 - 23:50:48 CDT)
• Stef
  • Re: AMBER: BOND energy during minimisation (Tue Oct 19 2004 - 03:35:05 CDT)
  • Re: AMBER: Hot solvent/cold solute reference (Mon Oct 11 2004 - 11:41:10 CDT)
  • AMBER: Hot solvent/cold solute reference (Mon Oct 11 2004 - 05:56:30 CDT)
  • Re: AMBER: Note to all concerning filtering of messages posted to the amber list. (Wed Oct 06 2004 - 03:33:17 CDT)
  • Re: AMBER: An question about PTRAJ (Sat Sep 11 2004 - 03:01:52 CDT)
  • Re: AMBER: Setup for parallel computing (Sat Jul 10 2004 - 16:14:56 CDT)
  • Re: AMBER: sander on multiprocessors (Tue Jul 06 2004 - 03:42:36 CDT)
  • Re: AMBER: sander in parallel, amber8 (Fri Jun 25 2004 - 13:11:09 CDT)
• Stefano.Pieraccini_at_unimi.it
  • Re: AMBER: Implicit 4r md (Wed Dec 01 2004 - 02:52:27 CST)
  • Re: AMBER: problem loading mdcrd to VMD (Tue Nov 30 2004 - 08:04:07 CST)
  • AMBER: langevin dynamic in sander (Tue Nov 23 2004 - 03:33:08 CST)
  • AMBER: amber with MPI (Mon Oct 04 2004 - 09:40:16 CDT)
  • Re: AMBER: general questions (Tue Sep 07 2004 - 06:11:01 CDT)
  • AMBER: cys protecting groups parameters (Fri Jul 09 2004 - 07:41:20 CDT)
  • AMBER: cys protecting group parameters (Fri Jul 09 2004 - 08:48:36 CDT)
  • AMBER: cluster analysis (Wed Jun 09 2004 - 06:19:40 CDT)
  • AMBER: gaussian03 output in antechamber (Wed May 12 2004 - 03:46:17 CDT)
  • AMBER: gaussian03 output in antechamber (Tue May 11 2004 - 04:27:46 CDT)
  • AMBER: HIS protonation (Mon May 10 2004 - 04:50:40 CDT)
  • Re: AMBER: Resizing sizes.h and recompiling problem! (Sat Mar 13 2004 - 12:03:07 CST)
  • AMBER: DMF box (Wed Jan 14 2004 - 10:42:02 CST)
• Stephen P. Molnar, Ph.D.
  • Re: AMBER: Amber 7 Compiling Problem (Fri Sep 17 2004 - 13:32:02 CDT)
  • Re: AMBER: Amber 7 Compiling Problem (Fri Sep 17 2004 - 13:24:52 CDT)
  • Re: AMBER: Amber 7 Compiling Problem (Fri Sep 17 2004 - 12:33:47 CDT)
  • AMBER: Amber 7 Compiling Problem (Fri Sep 17 2004 - 10:33:15 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 11:23:30 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 10:38:11 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 10:13:49 CDT)
  • AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 09:52:55 CDT)
  • AMBER: Compilation Problem in Amber 7 (Mon Sep 13 2004 - 10:54:27 CDT)
• Stephen.Titmuss_at_csiro.au
  • AMBER: Clustering in PTRAJ (Tue Nov 02 2004 - 19:38:31 CST)
• Stern, Julie
  • AMBER: converting from NAMD trajectory format (Mon Dec 06 2004 - 17:02:49 CST)
  • AMBER: undefined loops and protonate (Thu Mar 25 2004 - 11:52:41 CST)
  • AMBER: histidine and its various forms (Wed Feb 18 2004 - 08:38:31 CST)
• Steve Seibold
  • AMBER: file corruption with ptraj (Mon Oct 18 2004 - 10:10:51 CDT)
  • AMBER: Trajectory corruption (Fri Oct 15 2004 - 08:48:50 CDT)
  • AMBER: Ptraj data (Tue Sep 21 2004 - 13:13:49 CDT)
  • AMBER: FW: Imaging problem (Mon Aug 02 2004 - 15:32:37 CDT)
  • AMBER: Imaging problem (Fri Jul 30 2004 - 14:05:12 CDT)
  • AMBER: image and restart problems (Tue Jun 29 2004 - 07:56:52 CDT)
  • AMBER: GB and Atom Type (Tue Jan 20 2004 - 09:34:45 CST)
• steven.j.enoch_at_gsk.com
  • AMBER: pb_bomb in setgrd() (Tue Aug 10 2004 - 05:34:42 CDT)
  • Re: AMBER: PB bomb in pb_saarc (Wed Jul 28 2004 - 03:49:20 CDT)
  • AMBER: PB bomb in pb_saarc (Wed Jul 28 2004 - 03:26:38 CDT)
  • AMBER: PB Bomb in pb_reslist(): maxnbr too small (Tue Jul 20 2004 - 08:00:59 CDT)
  • Re: AMBER: Problem with divcon - increasing MXATTS? (Wed Jul 14 2004 - 11:45:54 CDT)
  • AMBER: Problem with divcon - increasing MXATTS? (Wed Jul 14 2004 - 10:33:38 CDT)
  • AMBER: Use of ibelly with nmode analysis (Tue Jul 13 2004 - 08:30:30 CDT)
  • AMBER: mm_pbsa problem (Fri Jul 02 2004 - 05:29:57 CDT)
• Sue Heavner
  • Re: AMBER: cluster analysis (Thu Jun 10 2004 - 05:40:56 CDT)
  • AMBER: PB in mm-pbsa (Sat Feb 28 2004 - 10:30:05 CST)
• Sunil_Koovakkat_at_berlex.com
  • AMBER: Solvent accessible surface area(LCPO) computation (Wed May 05 2004 - 16:51:59 CDT)
• Surjit Dixit
  • Re: AMBER: size.h error (Thu Feb 26 2004 - 15:53:20 CST)
• susan.costantini_at_unina2.it
  • AMBER: minimizating complex-protein with AMBER (Sun Feb 15 2004 - 03:27:00 CST)
• Suwipa saen-oon
  • AMBER: problem in antechamber (Wed May 19 2004 - 03:27:24 CDT)
  • AMBER: loading PDB problem in leap (Sun Apr 18 2004 - 04:35:35 CDT)
  • AMBER: questions for PNA parameters (Fri Mar 26 2004 - 21:36:56 CST)
• sychen
  • AMBER: make sure of the Magnesium parameters (Wed Mar 24 2004 - 12:15:25 CST)
  • Re: AMBER: Sander problem with different CPU (Sat Mar 06 2004 - 19:40:25 CST)
• Sébastien Fiorucci
  • AMBER: Problem with carnal on linux (Fri Nov 19 2004 - 08:13:26 CST)
• Sébastien Osborne
  • Re: AMBER: Problem with MacroMolecule to AMBER7 (Fri Sep 17 2004 - 11:04:48 CDT)
  • AMBER: mmpbsa question (Thu Aug 19 2004 - 14:58:42 CDT)
  • Re: AMBER: .lib file error in tleap (Mon Jul 19 2004 - 13:15:11 CDT)
  • AMBER: Question about dummy atoms (Tue Jun 29 2004 - 12:16:30 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 13:12:54 CDT)
  • Re: AMBER: FEP error/early termination - why? (Mon May 31 2004 - 12:51:15 CDT)
  • Re: AMBER: some bugfixes (Mon May 03 2004 - 13:14:33 CDT)
  • AMBER: Gibbs and solvent caps (Sat May 01 2004 - 13:59:07 CDT)
• Takanori TANAKA
  • AMBER: restraintmask problem in ptraj (Mon Nov 15 2004 - 05:06:23 CST)
• Taner E. Dirama
  • AMBER: restraining internal coordinates (Thu Sep 16 2004 - 11:53:51 CDT)
  • AMBER: turning off HB interactions (Tue Aug 17 2004 - 15:12:34 CDT)
• tang kwa
  • AMBER: Ewald (Wed Dec 15 2004 - 10:31:41 CST)
  • AMBER: 1-4 EEL (Tue Dec 07 2004 - 11:12:54 CST)
  • AMBER: restrainted torsion (Thu Dec 02 2004 - 07:18:43 CST)
  • AMBER: ntt parameter (Wed Dec 01 2004 - 15:32:22 CST)
  • AMBER: add dummy atoms (Tue Nov 23 2004 - 08:27:05 CST)
  • Re: AMBER: restart calculation (Tue Nov 23 2004 - 05:44:45 CST)
  • AMBER: restart calculation (Tue Nov 23 2004 - 04:31:22 CST)
  • AMBER: PMF (Mon Oct 25 2004 - 06:59:22 CDT)
  • AMBER: Monte Carlo simulation (Fri Sep 10 2004 - 07:15:35 CDT)
  • AMBER: [0] MPI Abort by user Aborting program ! (Wed Sep 01 2004 - 07:07:51 CDT)
  • AMBER: error of performing simulation (Fri Aug 27 2004 - 12:07:21 CDT)
  • AMBER: error for performing MD (Fri Aug 27 2004 - 06:51:00 CDT)
  • AMBER: WHAM program (Fri Jul 30 2004 - 11:09:02 CDT)
  • AMBER: umbrella sampling (Thu Jul 29 2004 - 12:25:00 CDT)
  • AMBER: How does LEaP place Na+ ions? (Thu Jan 22 2004 - 04:10:16 CST)
  • AMBER: restraint (Tue Jan 20 2004 - 10:10:39 CST)
• tarek mahfouz
  • AMBER: Neutral C and N termini. (Sun Aug 29 2004 - 18:37:19 CDT)
  • AMBER: Neutral C and N termini. (Fri Aug 27 2004 - 17:58:18 CDT)
  • AMBER: How to test the used parameters. (Wed Aug 11 2004 - 11:56:08 CDT)
  • Re: AMBER: Adding residues (Mon Aug 09 2004 - 13:51:26 CDT)
  • AMBER: AMBER7 plastocyanin tutorial problem. (Fri Aug 06 2004 - 12:40:33 CDT)
  • RE: AMBER: Problem with sander tutorial. (Thu Jul 22 2004 - 11:59:42 CDT)
  • AMBER: Problem with sander tutorial. (Tue Jul 20 2004 - 14:09:44 CDT)
• Teletchéa Stéphane
  • Re: Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 10:08:29 CDT)
  • Re: AMBER: moil-view question (Tue Feb 17 2004 - 07:49:31 CST)
  • Re: AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 10:17:30 CST)
• Terry Downing
  • AMBER: Nitrogen vdw type (Tue Feb 10 2004 - 16:56:37 CST)
• Thomas C. Bishop
  • AMBER: ptraj projections help (Mon Apr 19 2004 - 12:41:08 CDT)
  • Re: AMBER: Creating Parmtop files for NAMD (Wed Apr 14 2004 - 08:49:23 CDT)
  • AMBER: ptraj parser (Wed Apr 07 2004 - 10:01:15 CDT)
• Thomas E. Cheatham, III
  • Re: AMBER: converting from NAMD trajectory format (Wed Dec 08 2004 - 18:53:50 CST)
  • Re: AMBER: Restrained minimization problem (Mon Nov 29 2004 - 17:02:44 CST)
  • Re: AMBER: single strand simulation (Tue Nov 09 2004 - 18:32:58 CST)
  • Re: AMBER: H-bonded waters selection (Thu Nov 04 2004 - 23:05:24 CST)
  • Re: AMBER: ptraj problem (Thu Nov 04 2004 - 20:13:51 CST)
  • Re: AMBER: H bond calculation of CHARMM trajactory using PTRAJ (Wed Oct 20 2004 - 09:16:50 CDT)
  • Re: AMBER: file corruption with ptraj (Mon Oct 18 2004 - 10:42:02 CDT)
  • Re: AMBER: distance between images (Thu Oct 14 2004 - 10:51:33 CDT)
  • Re: AMBER: Questions about MD sampling (Tue Oct 12 2004 - 11:12:18 CDT)
  • Re: AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 14:34:59 CDT)
  • Re: AMBER: Amber (Tue Sep 28 2004 - 14:37:25 CDT)
  • Re: AMBER: Atom distance (Mon Sep 27 2004 - 15:48:11 CDT)
  • Re: AMBER: dihedral (Sun Sep 26 2004 - 21:13:42 CDT)
  • Re: AMBER: Amber job submission using PBS (Thu Sep 23 2004 - 12:59:00 CDT)
  • Re: AMBER: Ptraj data (Tue Sep 21 2004 - 13:59:58 CDT)
  • RE: AMBER: Trajectory file conversion between Amber & Charmm (Mon Sep 20 2004 - 13:18:46 CDT)
  • Re: AMBER: Moil-view & Amber trajectory (Fri Sep 17 2004 - 16:23:14 CDT)
  • Re: AMBER: principal axis (Wed Sep 15 2004 - 10:41:37 CDT)
  • Re: AMBER: An question about PTRAJ (Sat Sep 11 2004 - 14:06:05 CDT)
  • Re: AMBER: Lennard-Jones particle simulation (Wed Aug 25 2004 - 15:05:58 CDT)
  • Re: AMBER: Imaging problem (Fri Jul 30 2004 - 15:41:45 CDT)
  • Re: AMBER: about the parameter of the cystein pair in MD simulation (Sun Jul 25 2004 - 22:07:44 CDT)
  • Re: AMBER: Angle restraint during MD and namelist problem in amber8 (Wed Jul 14 2004 - 11:22:26 CDT)
  • Re: AMBER: ptraj-closestwaters command (Mon Jul 12 2004 - 15:38:41 CDT)
  • RE: AMBER: what is averaged RMS fluctuation? (Mon Jul 12 2004 - 15:28:21 CDT)
  • Re: AMBER: question about Ptraj - AND OR (Mon Jul 12 2004 - 10:15:13 CDT)
  • RE: AMBER: Problem with sander - Error on Open (Thu Jul 08 2004 - 21:18:10 CDT)
  • Re: AMBER: weird box expansion (Thu Jul 08 2004 - 12:06:57 CDT)
  • Re: AMBER: question about Ptraj (Thu Jul 08 2004 - 11:56:04 CDT)
  • Re: AMBER: average structure using ptraj (Thu Jul 01 2004 - 12:40:25 CDT)
  • Re: AMBER: About Hbond calculations using ptraj (Wed Jun 30 2004 - 13:11:05 CDT)
  • Re: AMBER: RMSD calculations in ptraj and Carnal (Tue Jun 15 2004 - 15:06:38 CDT)
  • Re: AMBER: performance of periodic vs. non-periodic simulation (Wed May 12 2004 - 15:17:33 CDT)
  • Re: AMBER: mm-pbsa:- atom charges and radii ? (Tue May 11 2004 - 09:24:17 CDT)
  • Re: AMBER: hbond in ptraj (Fri May 07 2004 - 14:15:15 CDT)
  • Re: AMBER: reference with ptraj (Thu May 06 2004 - 17:12:18 CDT)
  • Re: AMBER: reference with ptraj (Thu May 06 2004 - 15:11:58 CDT)
  • Re: AMBER: ions in mm_pbsa (Thu May 06 2004 - 14:07:42 CDT)
  • Re: AMBER: "matrix" in ptraj (Sat Apr 24 2004 - 19:30:34 CDT)
  • Re: AMBER: ptraj (Mon Apr 12 2004 - 15:23:12 CDT)
  • Re: AMBER: Group in sander (Mon Apr 12 2004 - 14:30:46 CDT)
  • RE: AMBER: script on tutorial page (Sat Apr 10 2004 - 15:31:51 CDT)
  • Re: AMBER: question about image - truncated octahedron (Mon Apr 05 2004 - 16:21:36 CDT)
  • Re: AMBER: question about image (Mon Apr 05 2004 - 11:37:00 CDT)
  • Re: AMBER: question about image (Fri Apr 02 2004 - 17:51:01 CST)
  • Re: AMBER: segmentation fault of minimization (Mon Mar 29 2004 - 21:42:01 CST)
  • Re: AMBER: hbond analysis in ptraj(%occupied>1) (Thu Mar 25 2004 - 12:26:50 CST)
  • Re: AMBER: rdparm/ptraj writeparm (Tue Mar 16 2004 - 11:04:47 CST)
  • Re: AMBER: ptraj (Thu Feb 12 2004 - 12:03:36 CST)
  • Re: AMBER: dipole moment in ptraj (Sun Feb 08 2004 - 17:00:55 CST)
  • Re: AMBER: question about the average structure from ptraj (Sun Feb 08 2004 - 13:49:23 CST)
  • Re: AMBER: Vlimit problem (Fri Jan 09 2004 - 15:53:10 CST)
  • Re: AMBER: rms in ptraj (Mon Jan 05 2004 - 10:04:20 CST)
• Thomas Exner
  • AMBER: sander and mpich (Thu Jan 29 2004 - 02:26:55 CST)
• Thomas Steinbrecher
  • AMBER: Dummy torsion paramters for thermodynamic integration (Tue Dec 21 2004 - 02:25:31 CST)
  • Re: AMBER: <dV/dL> fluctuations in TI (Wed Nov 17 2004 - 07:06:40 CST)
  • Re: Re: AMBER: about FEP (Wed Nov 03 2004 - 02:07:51 CST)
  • Re: AMBER: MM_PBSA reproduction of literature values and accuracy (Tue Oct 26 2004 - 02:05:51 CDT)
  • AMBER: Calculating H-Bond networks using ptraj (Mon Oct 18 2004 - 09:12:05 CDT)
  • Re: AMBER: charge perturbation - xleap question (Fri Aug 27 2004 - 02:19:25 CDT)
  • Re: AMBER: mutation of Tyr to Leu with TI (Wed Aug 25 2004 - 02:17:34 CDT)
  • Re: AMBER: questions on mm_pbsa (Sat Aug 21 2004 - 06:59:46 CDT)
  • AMBER: Amber8 - LAM MPI Compilation problems (Tue Aug 10 2004 - 11:16:38 CDT)
  • Re: AMBER: PBCAL in mmpbsa (Tue Jun 29 2004 - 15:50:43 CDT)
  • Re: AMBER: PBCAL in MM/PBSA (Fri Jun 25 2004 - 14:37:07 CDT)
  • RE: AMBER: a question on MM-PBSA and Delphi (Wed Jun 23 2004 - 13:09:16 CDT)
  • Re: AMBER: a question on MM-PBSA and Delphi (Wed Jun 23 2004 - 10:13:48 CDT)
  • Re: AMBER: PBCAL in mm-pbsa calculation (Fri Jun 11 2004 - 14:53:21 CDT)
  • Re: AMBER: PBCAL in mm-pbsa calculation (Fri Jun 11 2004 - 13:00:17 CDT)
  • AMBER: Decomposition in MMPBSA (Thu May 13 2004 - 19:15:03 CDT)
  • Re: AMBER: question about mm-pbsa (Mon May 10 2004 - 20:10:09 CDT)
  • AMBER: Parameters for nonpolar contribution to solvation (Fri Apr 23 2004 - 12:48:42 CDT)
  • AMBER: Using pbsa (Tue Apr 20 2004 - 18:16:37 CDT)
  • AMBER: MD simulation of a DNA decamer (Tue Mar 09 2004 - 04:10:15 CST)
• ThuZar Lwin
  • Re: AMBER: (no subject) (Tue Feb 17 2004 - 15:33:30 CST)
  • AMBER: (no subject) (Tue Feb 17 2004 - 14:52:40 CST)
• tim
  • Re: AMBER: neutral residues (Mon Apr 26 2004 - 09:26:09 CDT)
  • Re: AMBER: overlap between HE and OE in GLH (Mon Apr 26 2004 - 09:11:08 CDT)
  • Re: AMBER: Problem in loading a PDB file in Leap - Please help me (Thu Apr 15 2004 - 00:53:41 CDT)
  • Re: AMBER: salt concentration (Wed Apr 14 2004 - 06:56:52 CDT)
  • AMBER: Alignment tensor for Sander RDCs (Fri Apr 02 2004 - 08:47:47 CST)
• Tim Meyer
  • Re: AMBER: hydrogen bonds (Tue Oct 05 2004 - 06:11:09 CDT)
  • Re: AMBER: Amber & mutation (Thu Jun 10 2004 - 00:14:11 CDT)
  • Re: AMBER: cluster analysis (Wed Jun 09 2004 - 08:28:15 CDT)
• Ting Wang
  • Re: AMBER: solvate proteins in xleap/amber8 (Tue Jul 13 2004 - 07:23:51 CDT)
  • AMBER: TOP file in AMBER7/8 (Mon Jun 21 2004 - 08:32:25 CDT)
  • AMBER: solvate proteins in xleap/amber8 (Mon Jun 21 2004 - 08:20:03 CDT)
• Tod Pascal
  • RE: AMBER: Question about compiling PMEMD (Thu Apr 22 2004 - 01:29:55 CDT)
  • AMBER: Question about compiling PMEMD (Wed Apr 21 2004 - 02:21:40 CDT)
• Tom Turner
  • AMBER: using LJ 10-12 non bonded potential for glycoproteins in Amber8 (Wed Mar 17 2004 - 12:49:18 CST)
  • AMBER: RESP charges for protein fragment (Tue Feb 17 2004 - 10:20:15 CST)
• Tomas Hrobarik
  • AMBER: new atom and increase the number of bonds (Fri Apr 16 2004 - 09:01:56 CDT)
• Tomas Kubar
  • Re: AMBER: Units of Charges on Atoms (Thu Jun 24 2004 - 14:48:36 CDT)
  • Re: AMBER: solvate proteins in xleap/amber8 (Tue Jun 22 2004 - 02:44:54 CDT)
  • Re: AMBER: xleap solvatebox problem (Thu Jun 10 2004 - 03:58:51 CDT)
  • Re: AMBER: bug in leap? (Tue Jun 08 2004 - 02:27:30 CDT)
  • AMBER: xleap solvatebox problem (Thu May 27 2004 - 07:33:44 CDT)
• Tomas Linhart
  • Re: AMBER: restart calculation (Tue Nov 23 2004 - 04:53:29 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Sun Nov 21 2004 - 17:22:25 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Sat Nov 20 2004 - 16:15:44 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Fri Nov 19 2004 - 19:14:51 CST)
  • Re: AMBER: process_mdout.perl (Tue Oct 12 2004 - 02:43:28 CDT)
  • Re: AMBER: mdinfo on amber6 (Mon Oct 04 2004 - 02:49:29 CDT)
  • Re: AMBER: amber 8 error (Sat Oct 02 2004 - 03:04:43 CDT)
  • Re: AMBER: Amber (Tue Sep 28 2004 - 14:50:28 CDT)
  • Re: AMBER: Atom distance (Mon Sep 27 2004 - 02:12:59 CDT)
• Tomasz Borowski
  • AMBER: FEP along a reaction coordinate in sander (Wed Dec 01 2004 - 02:46:54 CST)
• tomjas_at_poczta.onet.pl
  • AMBER: How to choose force constant? (Tue May 04 2004 - 08:48:44 CDT)
• Toru Yagi
  • AMBER: Compiling Antechamber/Amber8 with ia64_ifort (Mon Dec 06 2004 - 00:25:02 CST)
• Toshifumi Yui
  • AMBER: restrained options (Tue Nov 16 2004 - 10:42:22 CST)
• Tru Huynh
  • (long) Re: AMBER: Leap & x86_64 / PGI (was: xleap solvatebox/oct problem) (Thu Dec 02 2004 - 14:00:17 CST)
  • AMBER: sander7 on quad opteron (Thu Jun 03 2004 - 13:13:39 CDT)
  • Re: AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Tue May 25 2004 - 09:31:34 CDT)
  • AMBER: performance of amber7/xlf/macosX 10.3 with JAC on xserve g5@2.0GHz (Mon May 24 2004 - 02:45:39 CDT)
  • Re: AMBER: Amber 7 on SGI: Sander MPI problem (Wed Apr 14 2004 - 07:45:08 CDT)
  • Re: AMBER: Can anybody help me with CHARMM (Wed Feb 25 2004 - 07:36:18 CST)
• Ty Curtis
  • RE: AMBER: rmsd over residues using ptraj (Wed May 19 2004 - 11:23:50 CDT)
• uddhavesh bhaskar sonavane
  • AMBER: protein - fractional native contacts (Mon Feb 23 2004 - 05:50:06 CST)
  • AMBER: AMBER 5 (sander) Parallel PME on IBM p630 (Fri Feb 06 2004 - 02:01:24 CST)
• Venkata S Koppuravuri
  • AMBER: Phosphoserine (Mon Oct 04 2004 - 14:26:28 CDT)
  • AMBER: Phosphoserine parameters (Tue Sep 28 2004 - 15:41:23 CDT)
  • AMBER: question on minimization (Thu Aug 26 2004 - 10:41:48 CDT)
  • AMBER: question on simulated annealing (Tue Jul 27 2004 - 13:21:52 CDT)
  • AMBER: atom out of bounds (fwd) (Thu Jul 22 2004 - 14:52:13 CDT)
  • AMBER: atom out of bounds (Wed Jul 21 2004 - 08:25:25 CDT)
  • Re: AMBER: restraints error (Fri Jun 25 2004 - 13:11:20 CDT)
  • AMBER: restraints error (Fri Jun 25 2004 - 12:10:35 CDT)
  • Re: AMBER: Simulated annealing ...vlimit problem (Mon May 17 2004 - 12:00:44 CDT)
  • AMBER: Simulated annealing ...vlimit problem (Fri May 14 2004 - 09:22:44 CDT)
  • AMBER: question on simulated annealing (Wed Apr 28 2004 - 11:00:39 CDT)
  • AMBER: how to check metal ion bonding ? (Tue Apr 13 2004 - 14:13:52 CDT)
  • AMBER: vlimit and vmax problem (Wed Mar 24 2004 - 12:25:31 CST)
• Vidit Kumar
  • AMBER: Amber7: (Thu Jun 03 2004 - 14:55:21 CDT)
  • AMBER: Re: AMBER (Wed Jun 02 2004 - 20:19:08 CDT)
  • AMBER: Amber7: pdb format file (Tue Jun 01 2004 - 13:13:03 CDT)
• Viktor Hornak
  • Re: AMBER: restraintmask problem in ptraj (Mon Nov 15 2004 - 07:37:24 CST)
  • Re: AMBER: ptraj questions (Sun Oct 31 2004 - 13:39:48 CST)
  • Re: AMBER: question about ptraj's Mask (Thu Oct 28 2004 - 16:03:45 CDT)
  • Re: AMBER: Ptraj data (Tue Sep 21 2004 - 13:43:44 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 10:18:01 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 09:52:04 CDT)
  • Re: AMBER: Intel Fortran Compiler Problem (Wed Sep 15 2004 - 09:33:44 CDT)
  • Re: AMBER: target rmsd (Mon Sep 13 2004 - 17:15:56 CDT)
  • Re: AMBER: target rmsd (Mon Sep 13 2004 - 15:57:07 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 14:26:27 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Mon Aug 16 2004 - 13:45:08 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 16:22:30 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:41:27 CDT)
  • Re: AMBER: Moil-view, prmtop, inpcrd question (Fri Aug 13 2004 - 15:20:14 CDT)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 15:31:00 CDT)
  • Re: AMBER: amber compilation (Mon Jul 26 2004 - 15:47:33 CDT)
  • Re: AMBER: Namelist problem (Mon Jul 05 2004 - 09:07:36 CDT)
  • Re: AMBER: Atom Labels (Tue Jun 29 2004 - 15:53:41 CDT)
  • Re: AMBER: problem not with sander, but with mpich (Mon Jun 28 2004 - 07:48:51 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 14:30:38 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 13:29:29 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 12:35:51 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 16:14:10 CDT)
  • Re: AMBER: parallel Sander (amber8): run-time error under Irix (Thu Jun 03 2004 - 14:01:40 CDT)
  • Re: AMBER: question about xleap (Thu Jun 03 2004 - 12:31:23 CDT)
  • Re: AMBER: Sander & fix atoms (Thu Jun 03 2004 - 12:22:55 CDT)
  • Re: AMBER: problems with mpich (Fri May 28 2004 - 14:00:15 CDT)
  • Re: AMBER: Amber 8 compilation (Wed May 26 2004 - 12:08:08 CDT)
  • Re: AMBER: Problem compiling amber7 (Tue May 25 2004 - 07:20:40 CDT)
  • Re: AMBER: Problem compiling amber7 (Mon May 24 2004 - 10:19:04 CDT)
  • Re: AMBER: parallel installation problem (Mon May 24 2004 - 09:38:50 CDT)
  • Re: AMBER: tmd questions (Thu May 13 2004 - 07:16:36 CDT)
  • Re: AMBER: any program or tool (Mon May 03 2004 - 07:18:56 CDT)
  • Re: AMBER: problem for compiling amber7 by ifc8 (Sat May 01 2004 - 09:11:49 CDT)
  • Re: AMBER: compile amber8 in linux with ifort (Fri Apr 23 2004 - 16:49:49 CDT)
  • Re: AMBER: restraintmask and ambmask (Thu Apr 22 2004 - 07:27:38 CDT)
  • Re: AMBER: distance dependent dielectric (Wed Apr 21 2004 - 07:23:31 CDT)
  • AMBER: Re: a new question (Mon Apr 12 2004 - 22:02:35 CDT)
  • Re: AMBER: Group in sander (Mon Apr 12 2004 - 14:13:15 CDT)
  • Re: AMBER: Compiling Amber 8 (Mon Apr 12 2004 - 08:53:29 CDT)
  • Re: AMBER: ptraj parser (Wed Apr 07 2004 - 11:20:40 CDT)
  • Re: AMBER: amber8 tutorial (Sun Apr 04 2004 - 21:03:56 CDT)
  • Re: AMBER: LES (Thu Feb 19 2004 - 15:30:32 CST)
  • Re: AMBER: sander and mpich (which compilers/mpich work) (Wed Feb 04 2004 - 13:13:13 CST)
  • Re: AMBER: sander and mpich (which compilers/mpich work) (Fri Jan 30 2004 - 19:23:21 CST)
  • Re: AMBER: ambpdb in AMBER7 (Mon Jan 26 2004 - 13:05:47 CST)
  • Re: AMBER: Intel Fortran Compiler 8.0 / pmemd 3.1 warning (Wed Jan 07 2004 - 07:46:28 CST)
• Vincent Bisetty
  • AMBER: getting new box info (Thu Oct 28 2004 - 09:25:51 CDT)
  • AMBER: RE:sander8 (Tue Oct 12 2004 - 02:19:35 CDT)
  • Re: AMBER: sander8 (Sat Oct 09 2004 - 11:13:55 CDT)
  • AMBER: sander8 (Fri Oct 08 2004 - 09:59:01 CDT)
  • AMBER: AddIons (Thu Oct 07 2004 - 07:15:03 CDT)
  • AMBER: frcmod_dmso (Fri Oct 01 2004 - 16:21:42 CDT)
  • AMBER: amparm (Wed Jul 21 2004 - 15:37:39 CDT)
• Vlad
  • AMBER: Sander-7 for Win32 (Tue Oct 19 2004 - 18:11:38 CDT)
• Vlad Cojocaru
  • AMBER: International PhD Symppozium "DECODING NATURE: HIERARCHY OF INTERACTIONS" (Wed Oct 20 2004 - 11:10:43 CDT)
  • AMBER: modes analysis in ptraj (Thu Oct 14 2004 - 07:13:14 CDT)
  • AMBER: Re: rms fluct and displacement in modes analysis (Tue Oct 12 2004 - 12:39:33 CDT)
  • AMBER: rms fluct and displacement in modes analysis (Tue Oct 12 2004 - 05:47:34 CDT)
  • AMBER: rms fluctuation units from ptraj (Thu Oct 07 2004 - 08:36:03 CDT)
  • AMBER: ptraj analyze modes question (Thu Oct 07 2004 - 08:17:02 CDT)
  • AMBER: how to visualize modes from PCA (Mon Sep 27 2004 - 11:05:35 CDT)
  • AMBER: Principal Component Analysis (Mon Sep 27 2004 - 07:09:50 CDT)
  • AMBER: all_nucleic94 versus all_nucleic02 (Wed Sep 22 2004 - 10:15:12 CDT)
  • AMBER: all_nucleic02 and all_nucleic94 (Wed Sep 22 2004 - 05:40:10 CDT)
  • AMBER: Re: to Francois (Tue Sep 14 2004 - 06:35:13 CDT)
  • Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases (Mon Sep 13 2004 - 05:10:48 CDT)
  • AMBER: Test Calculation of atomic charges (RESP) for RNA bases (Fri Sep 10 2004 - 08:41:26 CDT)
  • AMBER: Differences in RESP charges for G in RG and DG residues (Mon Aug 30 2004 - 10:59:35 CDT)
  • AMBER: RED BUG!!! (Fri Aug 13 2004 - 07:56:25 CDT)
  • AMBER: RED BUG!!!!...perhaps I fixed it (Fri Aug 13 2004 - 07:34:50 CDT)
  • AMBER: RED fails to read g94 output (Fri Aug 13 2004 - 05:35:20 CDT)
  • AMBER: Gaussian in RED (Thu Aug 12 2004 - 07:37:05 CDT)
  • AMBER: RESP charge derivation (Wed Aug 11 2004 - 11:10:19 CDT)
  • Re: AMBER: RNA sequence with DNA backbone? (Wed Jul 14 2004 - 06:09:13 CDT)
  • AMBER: namelist problem solved (Thu Jul 08 2004 - 12:50:10 CDT)
  • AMBER: parameter development for nucleotide analogues (Thu Jul 08 2004 - 12:49:42 CDT)
  • AMBER: Namelist problem solved (Wed Jul 07 2004 - 06:09:16 CDT)
  • AMBER: parameter development for nucleotide analogues (Wed Jul 07 2004 - 05:37:50 CDT)
  • AMBER: details for Namelist problem (Mon Jul 05 2004 - 08:22:33 CDT)
  • Re: AMBER: Namelist problem (Mon Jul 05 2004 - 08:10:51 CDT)
  • AMBER: details for Namelist problem (Mon Jul 05 2004 - 04:48:40 CDT)
  • AMBER: Namelist problem (Mon Jul 05 2004 - 04:25:07 CDT)
  • AMBER: M7G parameters (Tue Mar 23 2004 - 06:43:55 CST)
  • Re: AMBER: Some questions in building a new residue (Wed Mar 10 2004 - 11:28:55 CST)
  • Re: AMBER: MD simulation of a DNA decamer (Tue Mar 09 2004 - 04:35:25 CST)
  • AMBER: LES methodology question (Fri Feb 20 2004 - 06:12:14 CST)
  • Re: AMBER: TER in amber (Fri Feb 13 2004 - 02:35:41 CST)
  • Re: AMBER: TER in amber (Thu Feb 12 2004 - 09:56:04 CST)
  • Re: AMBER: Run calculations for protein in Amber-distance dependent dielectric function (Thu Feb 12 2004 - 08:34:31 CST)
  • Re: AMBER: ptraj (Thu Feb 12 2004 - 05:45:55 CST)
  • Re: AMBER: LES question (Tue Feb 10 2004 - 15:01:12 CST)
  • Re: AMBER: adding ions to nucleic acids (Sun Feb 08 2004 - 06:25:55 CST)
  • Re: AMBER: How to remove Cl- ions (Fri Feb 06 2004 - 05:09:52 CST)
  • Re: AMBER: the uses for Amber FFs (Tue Feb 03 2004 - 08:56:26 CST)
  • AMBER: nucleic acid bases nonplanar during LES sim (Mon Feb 02 2004 - 15:17:09 CST)
  • Re: AMBER: ptraj & LES (Mon Feb 02 2004 - 11:22:09 CST)
  • AMBER: ptraj & LES (Mon Feb 02 2004 - 10:46:08 CST)
  • Re: AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 10:07:49 CST)
  • Re: AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 10:07:12 CST)
  • Re: AMBER: convert restart to mdcrd? (Mon Feb 02 2004 - 09:33:35 CST)
  • Re: AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 13:20:56 CST)
  • AMBER: AMBER on IBM SP cluster (Sat Jan 31 2004 - 13:07:29 CST)
  • AMBER: Installing Amber on IBM AIX cluster (Sat Jan 31 2004 - 12:50:30 CST)
  • Re: AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 11:18:56 CST)
  • AMBER: sander.LES on IBM SP cluster (Sat Jan 31 2004 - 04:40:56 CST)
  • Re: AMBER: (No subject) (Fri Jan 30 2004 - 10:31:10 CST)
  • AMBER: test (Fri Jan 30 2004 - 07:39:14 CST)
  • AMBER: LES error (Thu Jan 29 2004 - 14:49:49 CST)
  • AMBER: LES Simulations (Thu Jan 29 2004 - 11:18:14 CST)
  • AMBER: Moil View on Linux (Thu Jan 29 2004 - 11:13:57 CST)
  • AMBER: question about LES simulation (Thu Jan 29 2004 - 10:43:25 CST)
  • AMBER: B factors --- one more explanation (Mon Jan 26 2004 - 10:25:47 CST)
  • AMBER: B factors from simulation and from cryst (Mon Jan 26 2004 - 10:21:50 CST)
• Vojtech Klusak
  • Re: AMBER: all_amino03.in discrepancy (Mon Jun 21 2004 - 04:36:09 CDT)
• Volodymyr Nechiporuk-Zloy
  • AMBER: Unbinding with different pH (Fri Mar 05 2004 - 08:10:23 CST)
• Volodymyr Zloy
  • RE: AMBER: md problem (Mon Sep 20 2004 - 13:05:25 CDT)
  • AMBER: md problem (Wed Sep 15 2004 - 11:03:29 CDT)
  • AMBER: How many ions? (Fri Sep 10 2004 - 06:23:38 CDT)
• Wanxin Sun
  • AMBER: (Mon Dec 06 2004 - 09:06:25 CST)
• warka_at_il.waw.pl
  • AMBER: Preparing complex in Xleap for Amber calculations (Wed Mar 17 2004 - 10:02:38 CST)
• Wayne Dawson
  • Re: AMBER: Ewald calculation using PME for charged system (Tue Mar 09 2004 - 21:28:36 CST)
  • AMBER: How to remove Cl- ions (Fri Feb 06 2004 - 05:19:33 CST)
  • Re: AMBER: questions parm94/99 ff secondary structure (Fri Feb 06 2004 - 01:50:07 CST)
  • AMBER: Installing Amber on IBM AIX cluster (Tue Feb 03 2004 - 00:11:49 CST)
• Wei Fu
  • Re: AMBER: langevin dynamics (Tue Mar 23 2004 - 20:39:44 CST)
  • AMBER: langevin dynamics (Sun Mar 21 2004 - 21:22:27 CST)
• Wen Li
  • AMBER: trajectory (Thu Sep 23 2004 - 08:35:21 CDT)
  • AMBER: ptraj (Wed Jul 14 2004 - 16:07:11 CDT)
  • AMBER: ptraj (Thu Jul 08 2004 - 11:06:01 CDT)
  • AMBER: cluster MD conformations from sander (Thu Jun 10 2004 - 14:13:14 CDT)
  • AMBER: CARNAL RMS (Mon Jun 07 2004 - 10:25:28 CDT)
  • AMBER: CARNAL- movement of an axis (Thu Jun 03 2004 - 15:34:11 CDT)
  • AMBER: Euclidean distances (Thu Apr 22 2004 - 09:49:45 CDT)
  • AMBER: rdparm: a parameter array overflowed (Wed Apr 21 2004 - 11:04:17 CDT)
  • AMBER: ions94.lib file (Fri Feb 20 2004 - 11:10:06 CST)
  • AMBER: prep files for modified bases (Thu Feb 19 2004 - 10:58:01 CST)
  • AMBER: prep file for zinc finger (Wed Jan 21 2004 - 16:02:54 CST)
  • Re: AMBER: disulfide bonds (Tue Jan 13 2004 - 12:13:50 CST)
  • AMBER: disulfide bonds (Mon Jan 12 2004 - 15:56:26 CST)
• Wen-Chi Tseng
  • Re: AMBER: how to correct the charge of oligosaccharides (Thu Aug 12 2004 - 04:16:38 CDT)
  • AMBER: how to correct the charge of oligosaccharides (Mon Aug 09 2004 - 21:28:25 CDT)
  • Re: AMBER: problems in using glycam (Thu Jul 01 2004 - 07:44:27 CDT)
  • AMBER: problems in using glycam (Wed Jun 30 2004 - 06:12:22 CDT)
• William Andrew McLaughlin
  • Re: AMBER: target rmsd (Mon Sep 13 2004 - 16:40:24 CDT)
  • AMBER: target rmsd (Mon Sep 13 2004 - 15:35:51 CDT)
• William Boxford
  • AMBER: Diastereoisomers of ATP (Thu Nov 18 2004 - 09:18:42 CST)
• William Wei
  • RE: AMBER: A Question about RESP (Mon Mar 15 2004 - 09:23:57 CST)
• wish_71
  • Re: AMBER: Running on MPI (Tue Oct 05 2004 - 21:43:16 CDT)
  • Re: AMBER: Running on MPI (Tue Oct 05 2004 - 05:17:55 CDT)
  • AMBER: Running on MPI (Sun Oct 03 2004 - 20:59:58 CDT)
• Wu Lei
  • Re: AMBER: Is it a bug?(in prep file opls_unict.in) (Sat Jul 17 2004 - 00:15:16 CDT)
  • Re: AMBER: NB pairs exceeds? (Fri Jul 16 2004 - 03:07:56 CDT)
  • AMBER: Is it a bug?(in prep file opls_unict.in) (Thu Jul 15 2004 - 22:44:09 CDT)
  • Re: AMBER: How to apply OPLS force field? (Thu Jul 15 2004 - 02:45:31 CDT)
  • Re: AMBER: How to apply OPLS force field? (Wed Jul 14 2004 - 23:12:50 CDT)
  • AMBER: How to apply OPLS force field? (Tue Jul 13 2004 - 22:23:04 CDT)
  • Re: AMBER: Fe parameter (Mon Jul 12 2004 - 02:51:18 CDT)
  • AMBER: About the calculation of non-bond list (Sat Jul 10 2004 - 09:21:57 CDT)
• Wu Yingliang
  • Re: AMBER: error in mm_pbsa (Sat Oct 16 2004 - 04:52:47 CDT)
  • Re: Re: AMBER: Running on MPI (Wed Oct 13 2004 - 08:49:48 CDT)
• xhu1_at_memphis.edu
  • AMBER: question about MGB and PB (Fri Dec 10 2004 - 16:12:30 CST)
  • Re: AMBER: question about mmpbsa (Wed Dec 08 2004 - 16:23:27 CST)
  • AMBER: question about mmpbsa (Tue Dec 07 2004 - 19:20:19 CST)
  • Re: AMBER: problem solved: leap compiling problem on a 64-bit machine (Mon Nov 22 2004 - 17:48:43 CST)
  • Re: AMBER: New problem on our 64bit box: xleap Segmentation fault (Mon Nov 22 2004 - 16:38:37 CST)
  • Re: RE: AMBER: New problem on our 64bit box: xleap Segmentation fault (Mon Nov 22 2004 - 16:37:03 CST)
  • AMBER: New problem on our 64bit box: xleap Segmentation fault (Mon Nov 22 2004 - 15:03:48 CST)
  • AMBER: problem solved: leap compiling problem on a 64-bit machine (Mon Nov 22 2004 - 14:51:28 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Sun Nov 21 2004 - 21:31:53 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Sun Nov 21 2004 - 16:52:02 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Sat Nov 20 2004 - 14:19:27 CST)
  • Re: RE: AMBER: leap compiling problem on a 64-bit machine (Fri Nov 19 2004 - 17:51:58 CST)
  • AMBER: leap compiling problem on a 64-bit machine (Fri Nov 19 2004 - 13:13:22 CST)
  • Re: AMBER: question about delphi and UHBD (Thu Sep 30 2004 - 11:52:01 CDT)
  • Re: AMBER: question about delphi and UHBD (Wed Sep 29 2004 - 14:11:47 CDT)
  • Re: AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 17:06:12 CDT)
  • Re: AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 15:32:51 CDT)
  • AMBER: question about delphi and UHBD (Tue Sep 28 2004 - 11:19:32 CDT)
  • AMBER: question about building initial structure (Mon Jun 07 2004 - 12:19:13 CDT)
  • Re: AMBER: question about NMODE for RNA (Sun May 30 2004 - 20:53:58 CDT)
  • AMBER: question about NMODE for RNA (Sun May 30 2004 - 17:32:22 CDT)
  • AMBER: amber on AMD 64 (Fri May 28 2004 - 13:56:02 CDT)
  • Re: AMBER: questions about NMODE (Thu Apr 29 2004 - 18:34:08 CDT)
  • Re: AMBER: questions about NMODE (Thu Apr 29 2004 - 13:11:41 CDT)
  • Re: AMBER: questions about NMODE (Wed Apr 28 2004 - 18:04:04 CDT)
  • Re: AMBER: questions about NMODE (Wed Apr 28 2004 - 16:47:18 CDT)
  • AMBER: questions about NMODE (Wed Apr 28 2004 - 12:43:34 CDT)
  • Re: AMBER: memory problem in NMODE (Mon Apr 19 2004 - 18:43:47 CDT)
  • AMBER: memory problem in NMODE (Mon Apr 19 2004 - 15:06:46 CDT)
  • AMBER: alignment problem using carnal (Thu Mar 18 2004 - 13:48:55 CST)
  • AMBER: pls forget my first question in my last email (Wed Mar 03 2004 - 14:02:06 CST)
  • AMBER: questions about mmpbsa (Wed Mar 03 2004 - 13:48:12 CST)
  • Re: AMBER: ambpdb in AMBER7 (Tue Jan 27 2004 - 11:48:37 CST)
• Xiang, Tian-Xiang
  • AMBER: anisotropic scaling (Tue Jul 13 2004 - 14:12:32 CDT)
• Xiao He
  • AMBER: About Disulfer bond (Sat Nov 27 2004 - 02:11:00 CST)
  • Re: Re: AMBER: about FEP (Tue Nov 02 2004 - 21:18:22 CST)
  • AMBER: about FEP (Tue Nov 02 2004 - 02:29:43 CST)
  • AMBER: MD after partially solvated (Sat Oct 30 2004 - 21:52:51 CDT)
  • Re: Re: AMBER: sander error (Sat Oct 30 2004 - 03:19:15 CDT)
  • AMBER: sander error (Sat Oct 30 2004 - 01:49:17 CDT)
  • AMBER: Settings about frozen atoms in sander (Fri Oct 29 2004 - 10:17:07 CDT)
  • AMBER: Continued:No skew or curtosis when zero variance in moment (Tue Oct 26 2004 - 00:02:31 CDT)
  • AMBER: No skew or curtosis when zero variance in moment (Mon Oct 25 2004 - 23:55:08 CDT)
  • AMBER: continue for No radius for F atom in MM_PBSA (Sun Oct 24 2004 - 09:40:21 CDT)
  • AMBER: No radius for F atom in MM_PBSA (Sun Oct 24 2004 - 08:30:48 CDT)
  • AMBER: About STD in NMODE (Wed Oct 20 2004 - 11:06:15 CDT)
  • AMBER: error in using AM1-BCC charge by antechamber (Mon Oct 18 2004 - 23:22:04 CDT)
  • Re: Re: AMBER: about AM1-BCC charge method (Mon Oct 18 2004 - 08:59:43 CDT)
  • AMBER: about AM1-BCC charge method (Mon Oct 18 2004 - 08:21:34 CDT)
  • Re: Re: AMBER: error in mm_pbsa (Sat Oct 16 2004 - 10:40:17 CDT)
  • AMBER: error in mm_pbsa (Sat Oct 16 2004 - 04:12:41 CDT)
  • AMBER: difference in GBSOL in amber7 and amber8 (Fri Oct 15 2004 - 06:11:11 CDT)
  • AMBER: question about molsurf (Fri Oct 15 2004 - 03:13:05 CDT)
  • Re: Re: AMBER: errors in SGI (Thu Oct 14 2004 - 11:09:40 CDT)
  • AMBER: errors in SGI (Thu Oct 14 2004 - 02:08:42 CDT)
  • AMBER: About missing residues (Mon Oct 11 2004 - 22:21:47 CDT)
  • AMBER: question about mm_pbsa and nmode (Mon Oct 11 2004 - 02:43:53 CDT)
  • AMBER: nmode error (Mon Oct 11 2004 - 02:10:22 CDT)
  • AMBER: Great help:Analysis mm_pbsa result (Mon Sep 27 2004 - 09:44:03 CDT)
  • AMBER: output of mm_pbsa.log (Sat Sep 25 2004 - 04:30:16 CDT)
  • AMBER: Analysis mm_pbsa result (Fri Sep 24 2004 - 21:53:08 CDT)
  • AMBER: nmode error (Fri Sep 24 2004 - 21:17:24 CDT)
  • AMBER: about mm_pbsa parameter (Thu Sep 23 2004 - 22:56:04 CDT)
  • Re: AMBER: Re: Re: Delphi PATH question (Wed Sep 22 2004 - 10:47:47 CDT)
  • Re: Re: AMBER: about MM-PBSA (Tue Sep 21 2004 - 22:44:51 CDT)
  • Re: RE: AMBER: about MM-PBSA (Tue Sep 21 2004 - 02:49:24 CDT)
  • AMBER: about MM-PBSA (Tue Sep 21 2004 - 00:40:16 CDT)
  • AMBER: More details about free energy (Sun Sep 19 2004 - 03:02:53 CDT)
  • AMBER: About binding energy (Sat Sep 18 2004 - 10:08:54 CDT)
  • Re: Re: Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 10:01:28 CDT)
  • Re: Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 09:29:56 CDT)
  • Re: Re: AMBER: a question about Van der waals radius (Sat May 22 2004 - 08:55:05 CDT)
  • AMBER: a question about Van der waals radius (Sat May 22 2004 - 07:07:05 CDT)
  • Re: Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 08:48:06 CDT)
  • Re: Re: AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 08:05:49 CDT)
  • AMBER: Why are there LENNARD_JONES_COEF A,B zero (Wed Apr 21 2004 - 03:46:29 CDT)
  • AMBER: How to solve these warnings? (Wed Apr 21 2004 - 03:37:40 CDT)
  • AMBER: Problem solved (Fri Mar 26 2004 - 09:35:01 CST)
  • AMBER: a question about anal (Thu Mar 25 2004 - 21:06:10 CST)
• Xiao Jian Tan
  • AMBER: memory prolem of the nmode calculation (Tue Nov 30 2004 - 17:24:18 CST)
  • Re: AMBER: recompiling amber8 (Tue Aug 03 2004 - 13:02:12 CDT)
• Xiaobing Tian
  • Re: AMBER: Thank you (Thu Jun 10 2004 - 14:37:37 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 14:21:39 CDT)
  • Re: AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 13:33:43 CDT)
  • AMBER: Compile xleap (amber8) in linux Red Hat 8.0 (Tue Jun 08 2004 - 11:00:06 CDT)
• xiaolin cheng
  • Re: AMBER: question about replica exchange in amber8 (Wed Jun 02 2004 - 09:23:30 CDT)
  • Re: AMBER: LES question (Tue Feb 10 2004 - 18:14:31 CST)
• Xiaowei Li
  • Re: AMBER: (Fri Mar 26 2004 - 21:53:54 CST)
  • AMBER: (Fri Mar 26 2004 - 14:21:08 CST)
• Xiaowei (David) Li
  • AMBER: one question about dielectric dependent model (Sun Dec 05 2004 - 11:42:56 CST)
• xiaowei li
  • AMBER: the energy difference between sander and nmode (Fri Nov 12 2004 - 15:52:57 CST)
  • AMBER: normal mode analysis after energy minimizaiton using sander (Thu Oct 14 2004 - 16:57:30 CDT)
  • AMBER: question about nmode (Tue Oct 05 2004 - 13:09:15 CDT)
  • AMBER: Z-DNA (Thu Jun 17 2004 - 13:43:13 CDT)
  • Re: AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid (Thu Jun 03 2004 - 21:52:16 CDT)
  • AMBER: confusion about epsilon=4r for nmode calclation of nucleic acid (Wed Jun 02 2004 - 22:15:29 CDT)
  • AMBER: separate the longitudinal and transverse vibrations frequencies (Mon May 03 2004 - 23:33:11 CDT)
  • AMBER: Time to minimize the energy by NMODE (Wed Apr 14 2004 - 13:23:02 CDT)
  • AMBER: Group in sander (Mon Apr 12 2004 - 14:05:29 CDT)
  • AMBER: NMODE (Fri Apr 09 2004 - 15:20:23 CDT)
• Xin Chen
  • Re: AMBER: MD at different pH !! (Fri Mar 05 2004 - 14:04:46 CST)
  • AMBER: Build a H+ ion in Leap? (Thu Feb 19 2004 - 13:40:40 CST)
  • Re: AMBER: Segmentation fault in SaveAmberParm (Wed Feb 18 2004 - 13:12:53 CST)
• Xin Hu
  • AMBER: AM1-BCC charges (Tue Oct 26 2004 - 19:19:04 CDT)
  • AMBER: Plot B-factor extracted from PDB file (Wed Oct 13 2004 - 09:41:29 CDT)
  • AMBER: Questions about MD sampling (Tue Oct 12 2004 - 10:03:06 CDT)
  • AMBER: Question about restart MD (Mon Oct 11 2004 - 13:38:38 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 16:15:27 CDT)
  • Re: AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 11:36:06 CDT)
  • AMBER: snapshots of MD trajectory (Fri Aug 27 2004 - 10:23:08 CDT)
  • Re: AMBER: antechamber (Thu Jul 15 2004 - 21:51:26 CDT)
  • Re: AMBER: antechamber (Thu Jul 15 2004 - 15:57:09 CDT)
  • AMBER: antechamber (Thu Jul 15 2004 - 13:03:44 CDT)
  • AMBER: RED (Tue Jun 01 2004 - 18:02:37 CDT)
• xinchen
  • Re: AMBER: Build a H+ ion in Leap? (Thu Feb 19 2004 - 14:19:20 CST)
  • AMBER: Segmentation fault in SaveAmberParm (Tue Feb 17 2004 - 21:31:35 CST)
  • Re: AMBER: How to add H+ ion in leap? (Tue Feb 17 2004 - 14:43:18 CST)
  • AMBER: How to add H+ ion in leap? (Tue Feb 17 2004 - 13:46:10 CST)
• Xioling Chuang
  • AMBER: parallel of sander_classic (Mon Oct 25 2004 - 00:57:16 CDT)
  • AMBER: Using gibbs to calculate free energy (Fri Jun 18 2004 - 08:15:31 CDT)
  • AMBER: water BOX (Mon Jun 07 2004 - 09:09:33 CDT)
• YangPeng
  • AMBER: Xleap (Thu Jun 10 2004 - 03:49:02 CDT)
• Yanze Zhang
  • Re: AMBER: Compiling question (Tue Dec 14 2004 - 14:11:07 CST)
  • AMBER: Compiling question (Tue Dec 14 2004 - 13:27:53 CST)
  • Re: AMBER: How to compile the downloadable RESP in UNIX (Thu Nov 18 2004 - 14:10:13 CST)
  • Re: AMBER: How to compile the downloadable RESP in UNIX (Wed Nov 17 2004 - 17:04:57 CST)
  • AMBER: How to compile the downloadable RESP in UNIX (Tue Nov 16 2004 - 09:33:03 CST)
  • AMBER: parameter set (Wed Nov 10 2004 - 13:56:54 CST)
  • AMBER: AMBER Parameter Database (Wed Nov 10 2004 - 09:35:32 CST)
  • AMBER: gaussian command line (Thu Nov 04 2004 - 13:40:27 CST)
  • AMBER: basis set (Tue Nov 02 2004 - 23:57:19 CST)
  • AMBER: REST (Wed Sep 08 2004 - 15:09:31 CDT)
• Yaroslava Yingling
  • Re: AMBER: restrain one tosion angle (Fri Oct 08 2004 - 14:20:09 CDT)
  • AMBER: restrain one tosion angle (Fri Oct 08 2004 - 14:02:01 CDT)
  • AMBER: intense and spectrum (Wed Aug 04 2004 - 13:15:28 CDT)
• Ye Mei
  • Re: AMBER: AMBER8 compiling error under Itanium 2. (Mon Nov 15 2004 - 19:46:52 CST)
  • Re: AMBER: convert .pdb to .mol2 (Sat Nov 13 2004 - 22:57:32 CST)
  • AMBER: glibc version (Fri Nov 12 2004 - 00:04:00 CST)
  • AMBER: salt bridge detection (Mon Nov 08 2004 - 20:33:21 CST)
  • AMBER: ESP fitting from Gaussian03 cube files (Tue Nov 02 2004 - 03:01:40 CST)
  • AMBER: how to neutralize the peptide (Tue Oct 26 2004 - 21:10:23 CDT)
  • AMBER: information PROTON_INFO (Thu Jun 03 2004 - 22:33:30 CDT)
  • Re: Re: Re: Re: Re: AMBER: a question about Van der waals radius (Mon May 24 2004 - 01:54:30 CDT)
  • AMBER: h bond (Mon May 24 2004 - 01:27:37 CDT)
  • Re: Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 08:26:40 CDT)
  • Re: AMBER: Amber and Linux compilation (Wed Apr 14 2004 - 06:52:55 CDT)
  • Re: AMBER: Antechamber compilation: leap error (Mon Apr 12 2004 - 06:55:11 CDT)
  • Re: AMBER: bug of leap? (Wed Apr 07 2004 - 21:40:29 CDT)
  • AMBER: bug of leap? (Wed Apr 07 2004 - 21:29:07 CDT)
  • AMBER: bug of leap? (Wed Apr 07 2004 - 21:27:11 CDT)
  • AMBER: segmentation fault when running parmchk (Tue Mar 30 2004 - 03:52:14 CST)
  • Re: Re: AMBER: segmentation fault when convert pdb to mol2 (Thu Mar 18 2004 - 18:38:21 CST)
  • AMBER: segmentation fault when convert pdb to mol2 (Thu Mar 18 2004 - 07:02:44 CST)
• yen li
  • AMBER: question about md's (Fri Dec 10 2004 - 09:27:39 CST)
  • AMBER: md's (Mon Dec 06 2004 - 10:08:07 CST)
  • Re: AMBER: Implicit 4r md (Thu Dec 02 2004 - 23:14:06 CST)
  • AMBER: Implicit 4r md (Tue Nov 30 2004 - 10:58:34 CST)
  • AMBER: Adding residues (Mon Aug 09 2004 - 12:47:44 CDT)
  • Re: AMBER: Implicit MD problem (Wed Jul 14 2004 - 11:44:47 CDT)
  • AMBER: Implicit MD problem (Wed Jul 14 2004 - 06:01:39 CDT)
  • AMBER: charge problem in minimization (Wed Jul 07 2004 - 01:33:09 CDT)
  • AMBER: Protein MD (Sat Jul 03 2004 - 11:04:59 CDT)
  • AMBER: Implicit MD simulation (Thu Jul 01 2004 - 06:49:24 CDT)
• ying xiong
  • : AMBER: basis set (Wed Nov 03 2004 - 00:43:52 CST)
  • AMBER: RESTARTED DUE TO LINMIN FAILURE ... (Thu Sep 23 2004 - 03:24:13 CDT)
• yonchen
  • AMBER: Question about RMSD calculation (Wed Mar 03 2004 - 22:25:01 CST)
  • AMBER: Use tleap convert *.pdb file to *.top and *.crd file (Wed Mar 03 2004 - 22:01:04 CST)
  • AMBER: How to use tleap convert *.pdb file to *.crd and *.top files (Tue Mar 02 2004 - 13:08:55 CST)
  • AMBER: A question about RMSD calculation (Tue Mar 02 2004 - 13:05:13 CST)
• Yong Duan
  • RE: AMBER: A torsion parameter in AMBER2003 force field (Fri Oct 08 2004 - 12:41:41 CDT)
  • Re: AMBER: Amber 03 Forcefield discrepancy (Mon Aug 30 2004 - 13:16:21 CDT)
  • RE: AMBER: amber8 performance on linux cluster (Tue Apr 27 2004 - 12:47:21 CDT)
  • RE: AMBER: overlap between HE and OE in GLH (Mon Apr 26 2004 - 12:17:00 CDT)
  • RE: AMBER: neutral residues (Mon Apr 26 2004 - 12:25:46 CDT)
  • RE: AMBER: overlap between HE and OE in GLH (Mon Apr 26 2004 - 12:24:32 CDT)
  • RE: AMBER: understanding SANDER source code (Sun Mar 21 2004 - 20:32:03 CST)
  • RE: AMBER: positive binding free energy (Wed Mar 10 2004 - 09:47:37 CST)
  • RE: AMBER: Close contact warnings (Wed Feb 18 2004 - 13:07:36 CST)
  • RE: AMBER: ambpdb in AMBER7 (Mon Jan 26 2004 - 17:34:41 CST)
• Yong Xu
  • AMBER: RMSD of ligand (Thu Dec 23 2004 - 18:26:14 CST)
  • AMBER: nmode problem (Thu Dec 16 2004 - 22:16:23 CST)
  • Re: Re: AMBER: No radius found for 2412 Zn Zn (Fri Dec 10 2004 - 23:53:18 CST)
  • Re: Re: AMBER: No radius found for 2412 Zn Zn (Fri Dec 10 2004 - 03:15:14 CST)
  • AMBER: how to prepare Zn.lib (Fri Dec 10 2004 - 01:50:16 CST)
  • AMBER: No radius found for 2412 Zn Zn (Fri Dec 10 2004 - 01:13:37 CST)
  • AMBER: calculate ligand's rmsd (Thu Dec 09 2004 - 00:11:15 CST)
• Yongzhi Chen
  • AMBER: atoms not in residue templates (Wed Aug 04 2004 - 12:53:08 CDT)
  • AMBER: RMSD result from GB model (Wed Aug 04 2004 - 12:35:03 CDT)
  • RE: AMBER: What happen when sander reads charge increments from cpin file? (Wed Jul 21 2004 - 16:59:40 CDT)
  • AMBER: What happen when sander reads charge increments from cpin file? (Wed Jul 21 2004 - 15:24:51 CDT)
  • AMBER: A problem regarding constant pH calculation in Amber 8 (Mon Jul 19 2004 - 20:54:43 CDT)
  • Re: AMBER: How to make leap recognise Zn2+? (Tue Jul 06 2004 - 11:00:26 CDT)
  • AMBER: How to make leap recognise Zn2+? (Mon Jul 05 2004 - 20:41:26 CDT)
  • AMBER: A problem about a sander parallel run (Thu Jun 24 2004 - 13:40:37 CDT)
• Your Name
  • AMBER: Problems with CPU scaling on cluster (Mon Jul 12 2004 - 03:12:48 CDT)
• Youyi Peng
  • AMBER: unknown elements (Wed Dec 15 2004 - 10:33:54 CST)
  • AMBER: question about image (Fri Apr 02 2004 - 16:41:36 CST)
  • AMBER: averaged structure with unknown elements (Wed Feb 25 2004 - 15:32:54 CST)
  • AMBER: carnal (Tue Feb 24 2004 - 10:36:11 CST)
  • AMBER: phosphothreonine (Fri Jan 23 2004 - 16:57:06 CST)
  • AMBER: prep file (Mon Jan 05 2004 - 17:40:07 CST)
• yu275197_at_yorku.ca
  • AMBER: compiling software(RESP) (Thu Feb 19 2004 - 00:02:36 CST)
  • AMBER: compiling software(RESP) on MAC G5 (Wed Feb 18 2004 - 22:47:12 CST)
• yuann
  • AMBER: Binding free energy from separate/single trajectory (Sun Dec 12 2004 - 23:01:17 CST)
  • AMBER: Sander problem with different CPU (Fri Mar 05 2004 - 06:29:49 CST)
• Yuhui Cheng
  • AMBER: One more question about the tree structure of looping residues (Wed Aug 25 2004 - 22:11:36 CDT)
  • Re: AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 19:35:13 CDT)
  • AMBER: About tree structure of TRP residue (Wed Aug 25 2004 - 18:46:36 CDT)
  • Re: AMBER: About the Amber constraint constant (Tue Aug 17 2004 - 01:34:24 CDT)
  • AMBER: About the Amber constraint constant (Sun Aug 15 2004 - 03:12:50 CDT)
  • AMBER: about the parameter of the cystein pair in MD simulation (Sun Jul 25 2004 - 21:01:13 CDT)
  • Re: AMBER: Amber8: Vlimit problem again (Wed Jul 21 2004 - 18:44:09 CDT)
  • AMBER: Amber8: Vlimit problem again (Thu Jul 15 2004 - 21:34:58 CDT)
  • AMBER: The parallel problem for umbrella sampling in Amber 8 (Tue Jun 15 2004 - 16:14:07 CDT)
  • AMBER: About umbrella sampling in Amber 8 (Mon Jun 14 2004 - 20:45:44 CDT)
• Yunfeng Hu
  • AMBER: residue insertion (Wed Mar 10 2004 - 18:24:52 CST)
  • Re: AMBER: compiling xleap on MAC OS X.3 (Wed Mar 03 2004 - 16:43:53 CST)
  • AMBER: compiling xleap on MAC OS X.3 (Wed Mar 03 2004 - 16:19:57 CST)
• Yuqin Cai
  • AMBER: Solvent exposure measurement (Fri Nov 05 2004 - 13:32:22 CST)
  • AMBER: Parameters for Inosine (Fri Sep 24 2004 - 13:51:40 CDT)
  • AMBER: Vlimit problem (Thu Jan 08 2004 - 12:15:38 CST)
• Yusuf Abdulghani
  • Re: AMBER: Compiling Amber8 on Mac OS X (Fri Jun 11 2004 - 17:14:12 CDT)
  • Re: AMBER: Mac OSX xleap compilation (Fri Apr 02 2004 - 13:16:14 CST)
• zhaoxc_at_puccini.che.pitt.edu
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Thu Jan 01 2004 - 09:05:31 CST)
• ¬ǿ
  • AMBER: question on NMR restrain (Mon Oct 18 2004 - 17:55:54 CDT)
  • AMBER: how to set up more than 3 groups constrain (Mon Oct 11 2004 - 13:33:51 CDT)
• ÎâÀÚ
  • AMBER: Re: Re: AMBER: Is it a bug?(in prep file opls_unict.in) (Wed Jul 21 2004 - 05:59:13 CDT)
  • AMBER: Leap could not find atom type CK (Tue Jul 20 2004 - 23:35:54 CDT)
• Ülo Lille
  • AMBER: Troubles in the NTP simulation: "vlimit exceeded". (Tue May 04 2004 - 05:16:24 CDT)