AMBER Archive (2003) - By Author

Starting: Thu Jan 02 2003 - 04:37:41 CST
Ending: Fri Feb 06 2004 - 10:15:04 CST

• a b
  • AMBER: Basic potential question: (Wed Dec 24 2003 - 03:29:56 CST)
  • AMBER: structure refinement using CNS vs. AMBER (Sat Nov 22 2003 - 15:27:06 CST)
  • AMBER: RNA and Protein questions (also some general questions) (Thu Nov 13 2003 - 04:55:07 CST)
• A. Hungie
  • AMBER: Vibration frequency of nucleobases (Fri Dec 19 2003 - 11:48:03 CST)
  • AMBER: How to use quasih? (Thu Dec 11 2003 - 10:12:23 CST)
  • AMBER: how to calculate vibration frequency? (Wed Dec 03 2003 - 08:46:26 CST)
  • AMBER: DNA helix is not in z-direction (Fri Sep 05 2003 - 04:35:50 CDT)
  • AMBER: Re: methylphosphonate (Tue Jul 15 2003 - 03:31:52 CDT)
  • methylphosphonate (Mon Jul 14 2003 - 08:20:52 CDT)
  • Re: Etot is not constant in NVE ensemble (Fri May 09 2003 - 11:08:56 CDT)
  • Etot is not constant in NVE ensemble (Fri May 09 2003 - 08:46:43 CDT)
  • minimization with restraints (Tue May 06 2003 - 07:57:22 CDT)
  • velocity auto-correlation function (Wed Apr 16 2003 - 11:25:32 CDT)
  • Re: Unit of velocity (Thu Apr 03 2003 - 11:46:18 CST)
  • Unit of velocity (Thu Apr 03 2003 - 07:38:59 CST)
  • Velocity (Mon Feb 17 2003 - 10:01:04 CST)
• A.Madhumalar
  • ANAL in AMBER (Tue May 06 2003 - 02:25:05 CDT)
  • Re: structure image (Mon Jan 27 2003 - 19:51:35 CST)
  • High temperature MD (Sun Jan 19 2003 - 10:02:41 CST)
• Ahammadunny Pathiaseril
  • mm_pbsa and ALA scan (Wed Jan 29 2003 - 10:24:06 CST)
• aini_at_rwja.umdnj.edu
  • AMBER: question about input files for small molecule with fluorine (Mon Nov 03 2003 - 09:45:10 CST)
• aini_at_UMDNJ.EDU
  • AMBER: question about namelist (Mon Dec 15 2003 - 09:42:04 CST)
  • AMBER: Fluorine in GBSA (Mon Nov 24 2003 - 08:38:38 CST)
  • Re: AMBER: problem in tleap (Fri Oct 24 2003 - 14:23:33 CDT)
  • Re: AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 08:11:30 CDT)
  • AMBER: problem in tleap (Fri Oct 17 2003 - 10:41:27 CDT)
  • AMBER: constant pressure in GB (Wed Oct 01 2003 - 20:19:12 CDT)
• Aki Hoji
  • AMBER: Running Amber on MacOSX(XDarwin) (Thu Jul 31 2003 - 09:10:16 CDT)
  • AMBER: (Wed Jul 30 2003 - 16:19:02 CDT)
• Aldo Jongejan
  • RE: RE: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 01:27:41 CST)
• Alexei Valiaev
  • Move the atom with specific velosity (Thu Mar 20 2003 - 14:28:19 CST)
  • File in the tutorial (Tue Feb 18 2003 - 17:18:05 CST)
• Alexey Onufriev
  • Re: AMBER: Fluorine in GBSA (Tue Nov 25 2003 - 15:33:43 CST)
  • Re: AMBER: 1 fs timestep for GB? (Tue Nov 25 2003 - 15:19:04 CST)
  • Re: AMBER: surface code in Amber (Fri Oct 10 2003 - 18:25:45 CDT)
  • Re: AMBER: Is NTC=2 correct for minimization when hydrogens are added? (Sat Aug 16 2003 - 11:37:35 CDT)
• Alfonso Garcia Sosa
  • Re: AMBER: MD simulations on small molecules immersed in sparse water shell (Tue Sep 16 2003 - 12:08:24 CDT)
  • Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling (Tue Aug 05 2003 - 16:12:10 CDT)
  • AMBER: zero free energy change for nonbond leg of electrst. decoupling (Tue Aug 05 2003 - 09:03:59 CDT)
  • Re: how to restrain water (Mon Jun 23 2003 - 10:42:42 CDT)
  • Re: how to restrain water (Mon Jun 23 2003 - 10:14:02 CDT)
  • posphinic acid parameters (Sun Jan 26 2003 - 10:28:11 CST)
• Amber Administration
  • Re: AMBER: aminoacid mutation (Tue Oct 28 2003 - 16:34:47 CST)
  • Re: AMBER: Implicit precision in sander vs architecture (Mon Oct 20 2003 - 18:18:02 CDT)
  • AMBER: ibelly (Fri Oct 03 2003 - 13:55:02 CDT)
  • AMBER: nstlim (Mon Sep 29 2003 - 18:55:42 CDT)
• amber_at_heimdal.compchem.ucsf.edu
  • Notes: Compiling Amber 7 on Mac OS X (fwd) (Fri Mar 07 2003 - 11:13:10 CST)
  • pressure variation control (fwd) (Fri Mar 07 2003 - 11:13:16 CST)
  • GRASP (fwd) (Fri Mar 07 2003 - 11:13:49 CST)
  • Re: Max residues (fwd) (Fri Mar 07 2003 - 11:12:29 CST)
  • Re: pressure variation control (fwd) (Fri Mar 07 2003 - 11:12:35 CST)
  • about maxium number of residues read by xleap (fwd) (Fri Mar 07 2003 - 11:13:03 CST)
  • intra-perturbed group (fwd) (Fri Mar 07 2003 - 11:13:57 CST)
  • amber installation problems (fwd) (Fri Mar 07 2003 - 11:12:44 CST)
  • Re: Forwarded mail.... (fwd) (Fri Mar 07 2003 - 11:12:49 CST)
  • install amber7 on Linux (fwd) (Fri Mar 07 2003 - 11:13:40 CST)
  • lanes when solvating in LEAP (fwd) (Fri Mar 07 2003 - 11:14:24 CST)
  • Re: Max residues (fwd) (Fri Mar 07 2003 - 11:12:54 CST)
  • question about dummy atoms? (fwd) (Fri Mar 07 2003 - 11:14:06 CST)
  • amber7 & mpich on sgi (fwd) (Fri Mar 07 2003 - 11:13:22 CST)
  • Re: Forwarded mail.... (fwd) (Fri Mar 07 2003 - 11:12:19 CST)
  • GB simulation on protein (fwd) (Fri Mar 07 2003 - 11:13:34 CST)
  • Re: Protein Reorientation (fwd) (Wed Mar 05 2003 - 12:05:11 CST)
  • nasty npt md problem (fwd) (Wed Mar 05 2003 - 12:05:58 CST)
  • Max residues (fwd) (Wed Mar 05 2003 - 12:05:20 CST)
  • pressure variation control (fwd) (Wed Mar 05 2003 - 12:05:29 CST)
  • Forwarded mail.... (Wed Mar 05 2003 - 12:05:51 CST)
• amkumar_at_post.its.mcw.edu
  • (no subject) (Fri Jan 10 2003 - 11:35:12 CST)
• Andrea Tafi
  • Fourth European Workshop in Drug Design (Mon Mar 10 2003 - 08:12:40 CST)
• Andreas Svrcek-Seiler
  • Re: AMBER: 1 fs timestep for GB? (Tue Nov 25 2003 - 12:32:15 CST)
  • Re: AMBER: Compiling AMBER7 on Suse (Tue Nov 18 2003 - 07:41:47 CST)
  • Re: AMBER: high temperature, 498K, unfolding simulations (Thu Nov 13 2003 - 11:05:46 CST)
  • Re: AMBER: Restraints to maintain base pair planarity (Wed Oct 15 2003 - 11:51:12 CDT)
  • Re: AMBER: monte carlo (Fri Oct 10 2003 - 09:19:41 CDT)
  • Re: AMBER: constant energy simulation (Wed Aug 13 2003 - 08:50:32 CDT)
  • Re: AMBER: please let me know if this is correct (Mon Jul 28 2003 - 11:07:28 CDT)
  • Re: AMBER: AMBER and NAMD (Sun Jul 27 2003 - 11:10:10 CDT)
  • Re: helix movement (Tue Jun 10 2003 - 07:07:49 CDT)
  • Re: unit of output velocity (Fri Jun 06 2003 - 11:49:32 CDT)
  • Re: Xleap: 'triangular' and 'square' bond (Thu May 22 2003 - 08:00:58 CDT)
  • Re: Simulation under physiological conditions (Thu May 15 2003 - 11:11:13 CDT)
  • Re: 10-12 H-bond terms (Sat May 10 2003 - 18:13:08 CDT)
  • Re: Protein - DNA complex simulation - protocol (Tue Apr 29 2003 - 03:50:22 CDT)
  • Re: Algorithm for the motion equations? (Fri Mar 14 2003 - 07:11:07 CST)
  • Re: compatibility of amber with NAMD (Fri Feb 14 2003 - 08:27:27 CST)
  • Re: average structure generated by carnal (Wed Jan 22 2003 - 09:16:53 CST)
  • Re: shake and H-O-H angle (Tue Jan 21 2003 - 13:29:22 CST)
  • Re: electrostatic potential calculations (Sat Jan 11 2003 - 10:43:33 CST)
• Andrei Leitão
  • Temperature control (Wed Jul 09 2003 - 15:25:12 CDT)
  • Questions about output archive and micromolecules (Mon Jun 30 2003 - 15:17:46 CDT)
  • Analysis of Curves program output (Tue Mar 11 2003 - 13:34:13 CST)
  • Minimization after dynamic? (Wed Feb 19 2003 - 18:13:31 CST)
  • Final energy minimization step (Tue Feb 18 2003 - 14:30:08 CST)
  • Carnal problem... (Thu Feb 06 2003 - 16:17:49 CST)
• Andrew Petersen
  • debug sander (Thu Jun 19 2003 - 01:40:04 CDT)
  • Xleap adding torsions (Tue May 20 2003 - 10:32:40 CDT)
  • CMC/MD (Fri Mar 14 2003 - 13:31:29 CST)
• Andy Purkiss
  • Re: AMBER: one more line about the npscal, box size changes and rms (Thu Aug 07 2003 - 10:30:25 CDT)
• Angela Pantelogianis
  • Re: AMBER: Fwd: Minimizing after solvation (Mon Jul 21 2003 - 10:26:30 CDT)
  • Re: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 09:59:24 CDT)
  • AMBER: Fwd: Minimizing after solvation (Fri Jul 18 2003 - 17:34:30 CDT)
• Anke Eisenmann
  • (no subject) (Tue Jan 21 2003 - 08:07:25 CST)
• Annette Höglund
  • AMBER: Zinc parameters (Tue Nov 18 2003 - 07:19:28 CST)
• Anton B. Guliaev
  • AMBER: Coordinate resetting (SHAKE) cannot be accomplished (Tue Jul 15 2003 - 16:35:59 CDT)
• Antonio J.Díaz Quintana
  • AMBER: MIPS R14000 and Machine-file (Tue Sep 02 2003 - 06:49:37 CDT)
  • AMBER: MIPS R14000 and Machine-file (Tue Sep 02 2003 - 03:14:33 CDT)
• aram joel panay
  • information (Thu May 29 2003 - 22:45:48 CDT)
• Arpita Mitra
  • Mg2+ ion parameters (Mon Mar 17 2003 - 18:09:52 CST)
• Artem Mamonov
  • Re: EXTRA_PTS: frtype 2 Should not be here (Tue Feb 25 2003 - 17:49:42 CST)
  • EXTRA_PTS: frtype 2 Should not be here (Tue Feb 25 2003 - 16:09:56 CST)
• Artur Galstyan
  • RESP, constraining Dipole Moment (Mon May 19 2003 - 05:06:51 CDT)
  • RESP-group constraint (Fri Jan 24 2003 - 08:38:53 CST)
• arubin_at_unmc.edu
  • AMBER: Nitrated Tyr (Wed Dec 10 2003 - 10:36:45 CST)
  • AMBER: NO2-TYR (Thu Dec 04 2003 - 11:30:24 CST)
  • xleap in Amber7 (Mon Jan 27 2003 - 18:56:16 CST)
  • xleap in Amber7 (Mon Jan 27 2003 - 18:54:46 CST)
• arun prasad
  • AMBER: Amber parallelisation (Fri Aug 01 2003 - 04:15:05 CDT)
• Arvid Soederhaell
  • AMBER: separate thermostats for different molecules (Mon Aug 04 2003 - 08:13:11 CDT)
  • non bonded pairlist? (Wed May 07 2003 - 02:34:27 CDT)
  • Re: Lipids (Tue Mar 18 2003 - 04:33:15 CST)
  • antechamber and gamess (Wed Jan 29 2003 - 09:08:00 CST)
  • chloroform, dichlormethane f.f. (Tue Jan 14 2003 - 04:24:33 CST)
• Asif Rahaman
  • help me switching from amber5 to amber6 (Wed May 07 2003 - 19:18:01 CDT)
• Asim Okur
  • RE: AMBER: Not getting restrt file on running sanders (Thu Oct 09 2003 - 16:53:37 CDT)
• astrid.maass
  • AMBER: special gaff atom types available? (Fri Dec 19 2003 - 05:58:30 CST)
  • AMBER: gaff atom types for phosphor compouds (Tue Dec 09 2003 - 07:51:33 CST)
  • AMBER: gaff parameters (Fri Sep 12 2003 - 04:10:32 CDT)
• Atchara Wijitkosoom
  • AMBER: saveamberparm (Mon Nov 24 2003 - 19:20:36 CST)
  • AMBER: GROUP (Tue Sep 23 2003 - 15:04:20 CDT)
• atobak_at_eden.rutgers.edu
  • AMBER: atomic clash or structure size? (Tue Sep 02 2003 - 16:08:51 CDT)
  • AMBER: sander minimization (Fri Aug 29 2003 - 15:39:58 CDT)
  • AMBER: "ATTN, need revision" (Thu Aug 28 2003 - 11:31:05 CDT)
• ayongye_at_sunchem.chem.uga.edu
  • AMBER: GLYCAM/AMBER Configurator (Tue Sep 02 2003 - 13:36:51 CDT)
• Balvinder Singh
  • Re: AMBER: RNA and Protein questions (also some general questions) (Thu Nov 13 2003 - 11:21:49 CST)
  • AMBER: FF parameters for BOC - group (Fri Sep 12 2003 - 12:38:34 CDT)
  • Re: Running MD (Mon Jun 23 2003 - 13:02:33 CDT)
  • Running MD (Mon Jun 23 2003 - 12:33:56 CDT)
• Bayly, Christopher
  • RE: AMBER: amber 7 for industrial application (Wed Oct 29 2003 - 10:45:27 CST)
  • RE: parm99 (Thu May 22 2003 - 08:36:18 CDT)
  • force field problem (Mon Feb 10 2003 - 14:01:37 CST)
  • RE: script for H-bonds extracting (Tue Jan 28 2003 - 12:40:53 CST)
  • RE: Intramolecular H-bonds in charge fitting (Tue Jan 28 2003 - 09:35:14 CST)
• Beale, John
  • AMBER: MOPAC from antechamber (Wed Dec 10 2003 - 11:46:02 CST)
• Ben Cossins
  • AMBER: Ewald in Amber 7 (Fri Dec 19 2003 - 09:49:11 CST)
  • AMBER: Ibelly and Ewald error message when ewald should be off (Tue Dec 16 2003 - 17:01:52 CST)
• Bengt Svensson
  • AMBER: Amber 7 - bugfix 42 problem. (Wed Sep 17 2003 - 20:21:08 CDT)
  • AMBER: Scyld cluster amber 7 compile problems (Wed Sep 17 2003 - 20:11:04 CDT)
  • Amber on Parallel Sun? (Mon Apr 28 2003 - 16:59:14 CDT)
  • Resp Charges for large ligand. (Mon Mar 17 2003 - 18:11:42 CST)
• bigbrainstorm
  • Re: AMBER: Antechamber functionality, MOL2 files (Wed Aug 13 2003 - 11:20:09 CDT)
  • AMBER: Antechamber functionality, MOL2 files (Tue Aug 12 2003 - 21:50:40 CDT)
• Bill Ross
  • Re: AMBER: roar topology and coordinate files (Mon Dec 29 2003 - 18:14:53 CST)
  • Re: AMBER: The lost velocities in the restart file generated by Ptraj (Mon Dec 29 2003 - 18:11:54 CST)
  • Re: AMBER: Constant temperature (Sat Dec 27 2003 - 11:14:00 CST)
  • Re: AMBER: using sander without SHAKE (Wed Dec 24 2003 - 13:03:43 CST)
  • Re: AMBER: vlimit? (Sun Dec 21 2003 - 22:04:40 CST)
  • Re: AMBER: minimization on sander (Mon Dec 15 2003 - 14:32:39 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 13:26:29 CST)
  • Re: AMBER: a simple question about HBond energy... (Fri Dec 12 2003 - 16:16:42 CST)
  • Re: AMBER: adding extra salt (Fri Dec 12 2003 - 10:44:07 CST)
  • RE: AMBER: xleap-N/C terminus (Thu Dec 11 2003 - 12:33:09 CST)
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Wed Dec 10 2003 - 12:17:37 CST)
  • Re: AMBER: xleap-N/C terminus (Wed Dec 10 2003 - 12:14:06 CST)
  • Re: AMBER: Mg2+ parameters for RNA usage (Wed Dec 10 2003 - 12:07:49 CST)
  • Re: AMBER: saveamberparm (Mon Nov 24 2003 - 19:31:51 CST)
  • Re: AMBER: torsion problems of dummy atoms (Mon Nov 24 2003 - 17:58:21 CST)
  • Re: AMBER: Cutress %cmass error (Wed Nov 19 2003 - 13:51:04 CST)
  • Re: AMBER: Compiling AMBER7 on Suse (Tue Nov 18 2003 - 12:27:25 CST)
  • Re: AMBER: Problem with MPI_Finalize (Tue Nov 18 2003 - 12:06:13 CST)
  • Re: AMBER: average coordinates (Wed Nov 12 2003 - 12:24:18 CST)
  • Re: AMBER: average coordinates (Wed Nov 12 2003 - 12:12:20 CST)
  • Re: AMBER: Protein Rotation (Tue Nov 11 2003 - 10:35:08 CST)
  • Re: AMBER: RMSd per residue (Tue Nov 11 2003 - 10:20:20 CST)
  • Re: AMBER: Protein Rotation (Tue Nov 11 2003 - 10:06:33 CST)
  • Re: AMBER: large file for carnal (Tue Nov 04 2003 - 14:19:19 CST)
  • Re: AMBER: large file for carnal (Tue Nov 04 2003 - 11:03:44 CST)
  • Re: AMBER: large file for carnal (Mon Nov 03 2003 - 14:14:30 CST)
  • RE: AMBER: Radius of Gyration and RMSD (Tue Oct 28 2003 - 11:21:10 CST)
  • RE: AMBER: aminoacid mutation (Mon Oct 27 2003 - 23:09:23 CST)
  • RE: AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 10:35:53 CDT)
  • Re: AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 10:31:17 CDT)
  • Re: AMBER: SHAKE question (Thu Oct 23 2003 - 17:24:20 CDT)
  • Re: AMBER: frozen x unfrozen (Tue Oct 21 2003 - 14:52:55 CDT)
  • RE: AMBER: memory SC45 (Mon Oct 20 2003 - 23:09:01 CDT)
  • Re: AMBER: memory SC45 (Mon Oct 20 2003 - 22:19:37 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Fri Oct 17 2003 - 13:10:46 CDT)
  • Re: AMBER: a problem with xleap (Thu Oct 16 2003 - 13:22:42 CDT)
  • RE: AMBER: tru64 alpha (Wed Oct 15 2003 - 09:38:45 CDT)
  • Re: AMBER: sander: vlimit problem (Tue Oct 14 2003 - 17:23:59 CDT)
  • RE: AMBER: infinitely long DNA & moil-view? (Tue Oct 14 2003 - 15:36:56 CDT)
  • Re: AMBER: Amber charge problem (Mon Oct 13 2003 - 20:21:00 CDT)
  • Re: AMBER: antechamber (Mon Oct 13 2003 - 19:38:24 CDT)
  • Re: AMBER: problem with pdb files (Mon Oct 13 2003 - 12:12:41 CDT)
  • Re: AMBER: Freezing the residues (Fri Oct 10 2003 - 14:43:38 CDT)
  • Re: AMBER: regarding trajectory input and output with ptraj or Carnal (Thu Oct 02 2003 - 11:28:41 CDT)
  • Re: AMBER: addions/xleap question (Wed Oct 01 2003 - 16:10:44 CDT)
  • Re: AMBER: improper (Wed Oct 01 2003 - 12:38:08 CDT)
  • Re: AMBER: improper (Wed Oct 01 2003 - 12:21:03 CDT)
  • Re: AMBER: improper (Tue Sep 30 2003 - 15:15:28 CDT)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 17:13:47 CDT)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 15:53:39 CDT)
  • Re: AMBER: Carnal Input file (Mon Sep 22 2003 - 18:23:27 CDT)
  • Re: AMBER: plane angle. (Mon Sep 22 2003 - 13:42:40 CDT)
  • Re: AMBER: xleap memory issue (Tue Aug 26 2003 - 19:52:40 CDT)
  • Re: AMBER: CARNAL (Mon Aug 25 2003 - 14:04:56 CDT)
  • RE: AMBER: CARNAL (Mon Aug 25 2003 - 15:45:13 CDT)
  • Re: AMBER: ptraj problem (Mon Aug 25 2003 - 14:14:23 CDT)
  • RE: AMBER: CARNAL (Mon Aug 25 2003 - 14:40:29 CDT)
  • Re: AMBER: united atom weiner force field (Mon Aug 18 2003 - 11:12:49 CDT)
  • Re: AMBER: About the limitation of characters on one line in carnal input fi le (Thu Aug 07 2003 - 16:31:39 CDT)
  • Re: AMBER: About the limitation of characters on one line in carnal input fi le (Thu Aug 07 2003 - 17:01:40 CDT)
  • Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished (Wed Jul 16 2003 - 14:46:44 CDT)
  • Re: carnal in big systems (Tue Jul 08 2003 - 14:22:09 CDT)
  • Re: Distribution Min with truncated octahedron box (Tue Jul 08 2003 - 13:24:09 CDT)
  • Re: question about H-bond in carnal? (Fri Apr 25 2003 - 13:57:20 CDT)
  • Re: velocities (Mon Mar 10 2003 - 15:14:57 CST)
  • Re: Backbone torsional angles' format? (Fri Feb 07 2003 - 22:01:26 CST)
• Bimo Ario Tejo
  • AMBER: non-zero 10-12 coefficient (Sat Dec 13 2003 - 08:44:49 CST)
  • AMBER: Carbohydrate connectivity (Thu Dec 11 2003 - 09:14:05 CST)
  • bugfix ptraj-6.4 (need to confirm) (Thu Jun 12 2003 - 07:51:27 CDT)
  • calculated b-factor higher than x-ray (Wed Jun 11 2003 - 13:23:03 CDT)
  • Re: helix movement (Tue Jun 10 2003 - 07:18:14 CDT)
  • Re: helix movement (Tue Jun 10 2003 - 06:19:05 CDT)
  • helix movement (Tue Jun 10 2003 - 05:10:29 CDT)
  • Re: MM-PBSA error (Tue Feb 04 2003 - 21:05:30 CST)
  • MM-PBSA error (Mon Feb 03 2003 - 23:56:34 CST)
  • script for H-bonds extracting (Tue Jan 28 2003 - 04:00:52 CST)
  • SASA and H-bond over trajectories (Mon Jan 20 2003 - 22:59:12 CST)
• bishop
  • Re: AMBER: infinitely long DNA (to Yong Duan) (Fri Nov 07 2003 - 15:59:46 CST)
  • Re: AMBER: infinitely long DNA & moil-view? (Tue Oct 14 2003 - 14:24:52 CDT)
  • Re: Etot is not constant in NVE ensemble (Fri May 09 2003 - 14:41:34 CDT)
• BlackLoveliness_at_aol.com
  • amber (Sun Mar 30 2003 - 22:47:47 CST)
• by
  • ÓÀ¼Îê±±±ÉÏÃ÷·§Ãų§ (Sat Feb 22 2003 - 23:49:08 CST)
• cailliez
  • Order parameters (Tue May 27 2003 - 03:25:30 CDT)
  • I still have problems with parm99.dat (Wed May 21 2003 - 08:37:19 CDT)
  • parm99 (Tue May 20 2003 - 07:55:17 CDT)
  • force field parameters for torsions (Mon May 19 2003 - 10:19:36 CDT)
  • quasih (Thu Apr 17 2003 - 10:35:26 CDT)
• caldwell_at_heimdal.compchem.ucsf.edu
  • big changes coming (Mon Jul 14 2003 - 10:27:11 CDT)
  • RE: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 16:44:53 CDT)
  • Nancy's leaving (Tue Jun 03 2003 - 21:42:00 CDT)
  • Re: Need help recompiling (Mon Jun 02 2003 - 10:14:06 CDT)
  • Re: water box distortion (Fri May 23 2003 - 16:21:33 CDT)
  • Re: From Dr. Ekaterina Nikitina (Tue May 20 2003 - 11:27:04 CDT)
  • Re: ptraj generated PDB files (Fri May 16 2003 - 08:07:57 CDT)
  • Re: saveAmberParm problems in xleap (Tue May 06 2003 - 07:45:36 CDT)
  • Re: topology file in large systems (Thu Apr 17 2003 - 17:25:49 CDT)
  • Re: CYS and HIS (Wed Apr 16 2003 - 09:55:55 CDT)
  • Re: SSBonds and charge problems (Fri Apr 11 2003 - 14:50:04 CDT)
  • Re: Disulphide bridges (Thu Mar 27 2003 - 12:05:06 CST)
  • Re: waterbox (Fri Mar 21 2003 - 17:33:31 CST)
  • Re: waterbox (Fri Mar 21 2003 - 16:31:07 CST)
  • Re: NTX / INIT inconsistency (Wed Mar 19 2003 - 17:13:15 CST)
  • Re: PBC without solvent (Tue Mar 18 2003 - 10:21:40 CST)
  • Re: Compiling Amber7 for linux (Fri Mar 14 2003 - 10:59:07 CST)
  • Re: AMBER/FEP: RESP charges (Fri Mar 14 2003 - 09:32:48 CST)
  • Amber web page (Wed Mar 12 2003 - 16:28:20 CST)
  • Amber Web page (Wed Mar 12 2003 - 15:48:04 CST)
  • Re: using xleap (Tue Mar 11 2003 - 13:31:47 CST)
  • Re: EWALD (Sun Mar 09 2003 - 21:11:51 CST)
  • Re: EWALD (Sun Mar 09 2003 - 17:41:02 CST)
  • reflector text - please ignore (Tue Mar 04 2003 - 15:46:48 CST)
  • Re: Leap to prep (Mon Mar 03 2003 - 17:03:25 CST)
  • Web site problems. (Wed Feb 19 2003 - 15:47:11 CST)
  • Re: Velocity (Mon Feb 17 2003 - 10:10:06 CST)
  • web page update (Thu Feb 13 2003 - 17:34:45 CST)
  • UCSF moving day. (Mon Feb 10 2003 - 19:29:07 CST)
  • Re: Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 16:42:54 CST)
  • Amber Web page. (Fri Jan 24 2003 - 10:45:00 CST)
  • UCSF Network changes to affect Amber Web site. (Fri Jan 17 2003 - 13:41:19 CST)
  • mail reflector (Thu Jan 16 2003 - 15:07:10 CST)
• Carlos P. Sosa
  • Re: AMBER: Compiling 64-bit version on AIX (Tue Sep 09 2003 - 11:06:39 CDT)
  • Re: parallelisation (Mon Jul 14 2003 - 11:19:00 CDT)
  • Organic solvents (Thu Apr 17 2003 - 10:17:54 CDT)
  • Re: Examples for Energy Minimisation methods (Tue Apr 01 2003 - 12:08:27 CST)
  • Re: Machine for IBM Horizon (Mon Mar 10 2003 - 17:13:49 CST)
  • Re: Info request: Amber on 64-bit CPUs (Tue Feb 25 2003 - 11:43:23 CST)
• Carlos Simmerling
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 11:06:39 CST)
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 10:12:37 CST)
  • Re: AMBER: PMEMD Performance on Beowulf systems (Fri Dec 19 2003 - 08:53:12 CST)
  • Re: AMBER: initial structures (Mon Dec 08 2003 - 09:51:04 CST)
  • Re: AMBER: sander output (Mon Dec 01 2003 - 20:37:06 CST)
  • Re: AMBER: restart MD program (Wed Nov 26 2003 - 11:23:06 CST)
  • Re: AMBER: protein MD - problem (Mon Nov 24 2003 - 08:52:53 CST)
  • Re: AMBER: Restarting MD amber7 (Sun Nov 16 2003 - 08:39:03 CST)
  • Re: AMBER: Any correct way to image a molecule ? (Fri Nov 14 2003 - 04:27:18 CST)
  • Re: AMBER: Any correct way to image a molecule ? (Thu Nov 13 2003 - 18:35:19 CST)
  • Re: AMBER: Separation of a Water molecules (Thu Nov 13 2003 - 07:48:28 CST)
  • Re: AMBER: Separation of a Water molecules (Wed Nov 12 2003 - 06:47:20 CST)
  • Re: AMBER: Separation of a Water molecules (Tue Nov 11 2003 - 20:15:53 CST)
  • Re: AMBER: Protein Rotation (Tue Nov 11 2003 - 09:11:40 CST)
  • Re: AMBER: Protein Rotation (Tue Nov 11 2003 - 07:02:32 CST)
  • Re: AMBER: fix some area (Sun Nov 09 2003 - 19:50:17 CST)
  • Re: AMBER: fix some area (Fri Nov 07 2003 - 06:27:38 CST)
  • Re: AMBER: question about input files for small molecule with fluorine (Mon Nov 03 2003 - 09:53:49 CST)
  • Re: AMBER: RMSD and Radius of Gyration (Sat Oct 25 2003 - 18:28:28 CDT)
  • Re: AMBER: Simulation of small protein (Thu Oct 23 2003 - 17:59:58 CDT)
  • Re: AMBER: Simulation of small protein (Thu Oct 23 2003 - 11:13:09 CDT)
  • Re: AMBER: stable protein (Mon Oct 20 2003 - 12:48:03 CDT)
  • Re: AMBER: infinitely long DNA & moil-view? (Tue Oct 14 2003 - 14:18:30 CDT)
  • Re: AMBER: How can I set ntx=7, but exclude the velocity? (Tue Sep 23 2003 - 10:35:28 CDT)
  • Re: AMBER: slower simulation (Mon Sep 22 2003 - 10:59:02 CDT)
  • Re: AMBER: Suggestion regarding long simulation. (Fri Sep 19 2003 - 07:05:58 CDT)
  • Re: AMBER: Suggestion regarding long simulation. (Thu Sep 18 2003 - 21:12:20 CDT)
  • Re: AMBER: MD simulations on small molecules immersed in sparse water shell (Tue Sep 16 2003 - 14:21:18 CDT)
  • Re: AMBER: MD simulations on small molecules immersed in sparse water shell (Tue Sep 16 2003 - 13:23:53 CDT)
  • Re: AMBER: AMBER error in CHALANGE (Mon Sep 15 2003 - 11:04:26 CDT)
  • Re: AMBER: 'ho' vDW parameters (Mon Sep 08 2003 - 15:10:13 CDT)
  • Re: AMBER: IG value (Fri Sep 05 2003 - 06:57:07 CDT)
  • Re: AMBER: target MD simulation (Wed Aug 27 2003 - 14:59:09 CDT)
  • Re: AMBER: Comparing PE of different conformations (Thu Aug 07 2003 - 14:57:11 CDT)
  • Re: AMBER: Comparing PE of different conformations (Wed Aug 06 2003 - 11:45:53 CDT)
  • Re: AMBER: Comparing PE of different conformations (Wed Aug 06 2003 - 11:33:42 CDT)
  • Re: AMBER: AMBER7 & mpich (Sat Aug 02 2003 - 07:53:26 CDT)
  • Re: AMBER: PMF calculation (Mon Jul 28 2003 - 10:09:45 CDT)
  • Re: AMBER: Dynamics and Simulated Annealing (Fri Jul 25 2003 - 11:53:38 CDT)
  • Re: AMBER: TEMP is not reaching 300K (Thu Jul 24 2003 - 12:35:03 CDT)
  • Re: AMBER: water box problem (Thu Jul 24 2003 - 06:36:29 CDT)
  • Re: AMBER question (Fri Jul 11 2003 - 10:24:30 CDT)
  • Re: Temperature control (Wed Jul 09 2003 - 16:15:29 CDT)
  • Re: Temperature control (Wed Jul 09 2003 - 15:38:26 CDT)
  • Re: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 19:50:14 CDT)
  • Re: parallelisation (Mon Jul 07 2003 - 08:38:32 CDT)
  • Re: How to do a rigid solvent model? (Sat Jul 05 2003 - 15:06:39 CDT)
  • Re: How to do a rigid solvent model? (Fri Jul 04 2003 - 12:25:21 CDT)
  • Re: unifying trajectory files (Wed Jun 25 2003 - 11:05:57 CDT)
  • Re: Running MD (Mon Jun 23 2003 - 07:40:24 CDT)
  • Re: Running MD (Mon Jun 23 2003 - 07:10:23 CDT)
  • Re: AMBER7 on linux cluster (Fri Jun 20 2003 - 09:55:10 CDT)
  • Re: mpirun problem: no rsh (Wed Jun 18 2003 - 12:56:48 CDT)
  • Re: Problem with LES topology file (Tue Jun 17 2003 - 17:42:07 CDT)
  • Re: AMBER7 on linux cluster (Tue Jun 17 2003 - 11:54:28 CDT)
  • Re: saving trajectory of solute only (Mon Jun 09 2003 - 11:06:01 CDT)
  • Re: MD problem (Thu May 29 2003 - 15:56:27 CDT)
  • Re: translational and rotational motion (more information) (Thu May 22 2003 - 08:35:13 CDT)
  • Re: rotational and translational motion (Thu May 22 2003 - 07:54:51 CDT)
  • Re: a question about scale factor (Sat May 10 2003 - 23:00:24 CDT)
  • Re: What kind of interactions are ignored for end group interactions (Fri May 09 2003 - 16:07:26 CDT)
  • Re: 2 questions (Fri May 09 2003 - 06:08:51 CDT)
  • Re: RMSD fluctuation too much (Thu May 08 2003 - 10:26:41 CDT)
  • Re: MD steps limit in sander (Amber 6) (Wed May 07 2003 - 10:51:01 CDT)
  • Re: minimization with restraints (Tue May 20 2003 - 08:42:43 CDT)
  • Re: can not minimize (Mon May 05 2003 - 07:00:04 CDT)
  • Re: initial velocity (Fri May 02 2003 - 09:20:09 CDT)
  • Re: problem on MD simulation of damage DNA (Thu May 01 2003 - 15:20:02 CDT)
  • Re: problem about virtual box? (Thu May 01 2003 - 10:46:05 CDT)
  • Re: about molecular dynamics (Tue Apr 29 2003 - 22:30:06 CDT)
  • Re: about molecular dynamics (Tue Apr 29 2003 - 20:14:39 CDT)
  • anyone have AMBER benchmarks with gigabit ethernet? (Wed Apr 23 2003 - 13:37:07 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 14:04:49 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 12:31:41 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 11:17:11 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 10:20:07 CDT)
  • Re: CCL:MPI run problem (Wed Apr 16 2003 - 15:26:42 CDT)
  • Re: addles (Mon Apr 14 2003 - 11:22:29 CDT)
  • Re: A problem in Sander production dynamics (Mon Apr 14 2003 - 06:21:04 CDT)
  • Re: Using MPI, PBS (Wed Apr 02 2003 - 13:29:41 CST)
  • Re: SANDER vs GIBBS equilibration (Thu Mar 27 2003 - 14:58:58 CST)
  • Re: a question about simulation at high temperature (Thu Mar 20 2003 - 13:25:19 CST)
  • Re: GB vs. explicit solvent calculations (Thu Mar 20 2003 - 08:25:12 CST)
  • Re: tip5p water model (Thu Mar 13 2003 - 11:58:31 CST)
  • teleap (Wed Mar 05 2003 - 12:38:42 CST)
  • Re: Protein Reorientation (Mon Mar 03 2003 - 09:39:19 CST)
  • Re: results of MD comparison (Wed Feb 26 2003 - 15:00:20 CST)
  • Re: Velocity (Mon Feb 17 2003 - 12:02:34 CST)
  • Re: energy calculation (Sun Feb 09 2003 - 07:27:03 CST)
  • Re: question about temperature (Mon Feb 03 2003 - 11:31:28 CST)
  • Re: conformational sampling (Thu Jan 23 2003 - 17:45:58 CST)
  • JACS 125th and PAK (Fri Jan 03 2003 - 11:02:12 CST)
• Carolina Salvador-Morales
  • (no subject) (Mon Apr 07 2003 - 08:22:27 CDT)
• case
  • RE: TAUP and density problem (Sun Feb 16 2003 - 19:36:48 CST)
• ch cureton
  • Re: AMBER: ambpdb (Fri Dec 12 2003 - 05:53:17 CST)
  • Re: AMBER: ambpdb (Fri Dec 12 2003 - 04:47:06 CST)
• chandran karunakaran
  • AMBER (Sun Apr 20 2003 - 20:13:32 CDT)
  • Re: AMBER (Tue Apr 15 2003 - 20:25:08 CDT)
  • AMBER (Tue Apr 15 2003 - 18:55:16 CDT)
  • Metalloprotein (Mon Apr 14 2003 - 20:18:39 CDT)
  • Re: Tleap-metalloprotein (Thu Apr 10 2003 - 20:20:40 CDT)
  • Tleap (Tue Apr 08 2003 - 18:01:21 CDT)
  • Nitro group introduction in tyrosine residue (Mon Apr 07 2003 - 14:23:33 CDT)
• Charles Laughton
  • Re: force field parameters for torsions (I am away) (Mon May 19 2003 - 12:49:32 CDT)
• Chen, Ya
  • AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 (Fri Aug 22 2003 - 23:47:21 CDT)
  • AMBER: Odd Problem with PMEMD (Mon Jul 21 2003 - 22:35:23 CDT)
  • Does Anyone Have a Working MACHINE File for Solaris/SPARC? (Wed May 28 2003 - 12:30:53 CDT)
• Chenglong Li
  • [Fwd: AMBER: MM_PB/GB/SA] (Thu Nov 20 2003 - 12:07:19 CST)
  • AMBER: MM_PB/GB/SA (Wed Nov 19 2003 - 12:44:19 CST)
  • AMBER: MD Equil (Mon Nov 03 2003 - 17:07:56 CST)
• chernhoe
  • delphi on linux (Wed Jun 11 2003 - 04:03:13 CDT)
  • mm_pbsa error message (Sun Jun 08 2003 - 04:48:02 CDT)
  • clustering trajectories (Wed May 28 2003 - 22:19:41 CDT)
  • protein dna simulation (Thu Feb 27 2003 - 22:13:58 CST)
  • problem patch files (Tue Feb 25 2003 - 02:15:44 CST)
  • Re: new-style prmtop file (Mon Feb 24 2003 - 00:48:47 CST)
  • new-style prmtop file (Sun Feb 23 2003 - 21:45:46 CST)
  • bugfix.33 not online (Tue Feb 18 2003 - 19:45:12 CST)
• Chris Moth
  • RE: AMBER: Amber - compiler help (Thu Dec 04 2003 - 16:45:10 CST)
  • Re: AMBER: GB/SA (Wed Nov 12 2003 - 14:30:33 CST)
  • AMBER: mddisplay (Thu Oct 30 2003 - 12:29:12 CST)
  • AMBER: mddisplay (Fri Oct 24 2003 - 16:22:18 CDT)
  • AMBER: Simulation of small protein (MD Display tips) (Fri Oct 24 2003 - 13:56:38 CDT)
  • AMBER: MM_PBSA(GBSA) Examples (Thu Sep 25 2003 - 10:56:23 CDT)
  • AMBER: ?small bugs? - 2nd suggestion (Wed Sep 24 2003 - 15:23:41 CDT)
  • AMBER: mm_pbsa - ?small bugs? (Wed Sep 24 2003 - 12:37:37 CDT)
  • RE: AMBER: PMEMD: dual XEON vs SGI cluster (Mon Sep 15 2003 - 20:55:46 CDT)
  • AMBER: PMEMD: dual XEON vs SGI cluster (Tue Sep 16 2003 - 16:46:45 CDT)
• chris switzer
  • parallel sander jobs die with error: "MPI_COMM_RANK : Null communicator" (Sat Jun 14 2003 - 21:00:51 CDT)
  • Carnal processing of binary mdcrd files (IOUTFM=1) Sander 7 (Wed Mar 19 2003 - 21:14:01 CST)
  • Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Fri Jan 03 2003 - 21:18:11 CST)
• Christian Gossens
  • Xleap: 'triangular' and 'square' bond (Thu May 22 2003 - 05:58:51 CDT)
• Christoph Kluck
  • force field parameters for phosphoserine (Tue Apr 29 2003 - 09:07:59 CDT)
• Christophe L M J Verlinde
  • AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. (Tue Sep 02 2003 - 12:57:52 CDT)
• Chuck Schneider
  • Re: installing AMBER 7 (Mon Mar 10 2003 - 14:05:37 CST)
  • Re: Info request: Amber on 64-bit CPUs (Tue Feb 25 2003 - 09:02:49 CST)
  • Re: LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi (Thu Jan 23 2003 - 06:52:41 CST)
• Colin Connelly
  • Force Fields (Fri Jan 10 2003 - 23:44:35 CST)
• Courtney Stanton
  • Problem with LES topology file (Tue Jun 17 2003 - 17:28:10 CDT)
• Craig A Bayse
  • mutating residues (Tue Apr 08 2003 - 11:09:38 CDT)
  • Re: bond command (Wed Feb 12 2003 - 15:36:29 CST)
  • Re: bond command (Wed Feb 05 2003 - 15:30:36 CST)
  • bond command (Tue Feb 04 2003 - 23:46:20 CST)
  • problem with antechamber (Sun Jan 12 2003 - 12:54:05 CST)
• CUI, Guanglei
  • Re: Problem with XLEaP in Mandrake 9.1 (Sun Jun 22 2003 - 12:44:51 CDT)
  • Re: job stopped (Thu Apr 24 2003 - 15:32:29 CDT)
  • Re: job stopped (Thu Apr 24 2003 - 13:06:25 CDT)
  • Re: AMBER (Tue Apr 15 2003 - 19:32:12 CDT)
  • Re: Proper Restraint usage (Tue Apr 15 2003 - 16:30:22 CDT)
  • Re: very important (Tue Apr 08 2003 - 09:47:55 CDT)
  • Re: MM_PBSA (Amber7) and delphi (Fri Mar 21 2003 - 09:04:04 CST)
  • Re: PBC without solvent (Tue Mar 18 2003 - 08:58:41 CST)
  • RE: leap remove command (Sun Mar 16 2003 - 23:30:44 CST)
  • leap remove command (Fri Mar 14 2003 - 16:19:12 CST)
  • Re: sequence (Tue Mar 11 2003 - 22:50:59 CST)
  • RE: adding hydrogens (Wed Feb 19 2003 - 08:06:27 CST)
  • adding hydrogens (Tue Feb 18 2003 - 12:44:13 CST)
  • Re: Question about quasih (Sun Feb 09 2003 - 20:59:11 CST)
  • Re: Moil-view (Tue Jan 14 2003 - 11:48:49 CST)
  • Re: looking for 'pdb_to_mass' (Tue Jan 07 2003 - 08:06:05 CST)
• D Fernandez
  • AMBER parameters (Tue Jun 24 2003 - 00:26:09 CDT)
• Dalmaris, John
  • RE: AMBER: xleap-N/C terminus (Thu Dec 11 2003 - 12:01:35 CST)
  • RE: AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 07:29:28 CDT)
  • AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 06:11:36 CDT)
  • AMBER: input/output error (Fri Oct 10 2003 - 11:32:15 CDT)
  • AMBER: DMSO box (Fri Sep 12 2003 - 04:25:21 CDT)
• Daniel Svozil
  • Info request: Amber on 64-bit CPUs (Tue Feb 25 2003 - 07:34:57 CST)
• Daquan Gao
  • CCL: Amber free energy equation (Tue Jun 17 2003 - 11:33:39 CDT)
• darden
  • Re: AMBER: question about ewald (Thu Oct 09 2003 - 15:38:10 CDT)
  • Re: AMBER: MD problem! (Wed Sep 17 2003 - 10:29:50 CDT)
  • Re: AMBER: more than 100,000 atoms ? (Thu Aug 07 2003 - 16:23:25 CDT)
  • Re: PME (Wed Jun 11 2003 - 10:21:25 CDT)
  • Re: PME (Wed Jun 11 2003 - 09:33:12 CDT)
  • Re: Etot is not constant in NVE ensemble (Fri May 09 2003 - 18:20:24 CDT)
  • Re: Etot is not constant in NVE ensemble (Fri May 09 2003 - 09:38:53 CDT)
  • Re: Ewald: coeff, error estimate (Thu May 01 2003 - 16:30:48 CDT)
  • Re: PME cutoff box size (Tue Mar 25 2003 - 13:49:57 CST)
  • Re: leap remove command (Sun Mar 16 2003 - 15:26:02 CST)
  • Re: polarization + ewald (Mon Jan 27 2003 - 18:58:10 CST)
• Darren Davies
  • Re: AMBER Cutoff (Tue Jul 01 2003 - 05:45:05 CDT)
  • A question of time (Tue Jun 10 2003 - 10:52:31 CDT)
• Dat H. Nguyen
  • Periodic Boundary Condition in AMBER7 (the sander module)! (Tue Apr 08 2003 - 16:44:37 CDT)
• Dave S Walker
  • Re: AMBER: sander output (Thu Dec 04 2003 - 18:41:05 CST)
  • AMBER: sander output (Mon Dec 01 2003 - 20:04:31 CST)
  • AMBER: intermolecular force (Tue Nov 25 2003 - 17:19:15 CST)
  • Re: install problem (Thu Jun 12 2003 - 19:03:21 CDT)
  • install problem (Thu Jun 12 2003 - 16:18:02 CDT)
• David
  • AMBER question (Fri Jul 11 2003 - 08:42:12 CDT)
  • AMBER question (Thu Jul 10 2003 - 01:51:31 CDT)
  • van der Waals term (Thu Jul 10 2003 - 01:47:34 CDT)
  • AMBER question (Fri Jun 20 2003 - 11:31:55 CDT)
• David A. Case
  • Re: Antechamber questions (Fri Mar 28 2003 - 13:58:00 CST)
  • Re: antechamber -rn keyword (Fri Mar 28 2003 - 13:54:46 CST)
  • Re: ambpdb (Fri Mar 28 2003 - 12:42:34 CST)
  • Re: SANDER vs GIBBS equilibration (Thu Mar 27 2003 - 14:44:08 CST)
  • Re: tleap in large systems (Thu Mar 27 2003 - 14:43:01 CST)
  • Re: writing mol2 files using antechamber (Sat Mar 22 2003 - 12:08:29 CST)
  • Re: doubts (Sat Mar 22 2003 - 10:56:11 CST)
  • Re: GB vs. explicit solvent calculations (Thu Mar 20 2003 - 09:46:53 CST)
  • Re: using antechamber (Tue Mar 18 2003 - 10:54:49 CST)
  • Re: Diferences in gibbs (Tue Mar 18 2003 - 09:43:10 CST)
  • Re: PBC without solvent (Tue Mar 18 2003 - 09:38:04 CST)
  • Re: CMC/MD (Fri Mar 14 2003 - 15:01:57 CST)
  • Re: [Fwd: MPI problem in modi4.ncsa.uiuc.edu] (Fri Mar 14 2003 - 10:30:48 CST)
  • Re: tip5p water model (Thu Mar 13 2003 - 13:53:26 CST)
  • Re: The gblambda parameter (Thu Mar 13 2003 - 10:34:08 CST)
  • Re: problem of mass center (Wed Mar 12 2003 - 23:02:10 CST)
  • Re: using xleap (Tue Mar 11 2003 - 13:05:56 CST)
  • Re: Machine for IBM Horizon (Mon Mar 10 2003 - 17:04:09 CST)
  • Re: Parameters: additive, lone pair (Mon Mar 10 2003 - 10:11:35 CST)
  • Re: velocities (Mon Mar 10 2003 - 10:04:58 CST)
  • Re: nasty npt md problem (fwd) (Sun Mar 09 2003 - 23:58:58 CST)
  • Re: EWALD (Sun Mar 09 2003 - 16:10:40 CST)
  • Re: Water density and force output questions (Fri Mar 07 2003 - 18:15:38 CST)
  • Re: surface accesible area (Fri Mar 07 2003 - 18:11:02 CST)
  • Re: three digits in the charges of extPDB (Fri Mar 07 2003 - 15:21:39 CST)
  • Re: amber7 & mpich on sgi (fwd) (Fri Mar 07 2003 - 13:24:00 CST)
  • Re: GB simulation on protein (fwd) (Fri Mar 07 2003 - 12:02:13 CST)
  • Re: lanes when solvating in LEAP (fwd) (Fri Mar 07 2003 - 11:56:39 CST)
  • Re: intra-perturbed group (fwd) (Fri Mar 07 2003 - 11:55:29 CST)
  • Re: install amber7 on Linux (fwd) (Fri Mar 07 2003 - 11:51:55 CST)
  • Re: tautp in gibbs (Mon Mar 03 2003 - 15:59:35 CST)
  • Re: GB/SA (Fri Feb 28 2003 - 20:29:29 CST)
  • Re: new-style prmtop file (Sun Feb 23 2003 - 23:38:29 CST)
  • Re: minimization with fixed UC dimensions (Fri Feb 21 2003 - 14:00:09 CST)
  • Re: AMBER6 problem in Solaris 8 (Fri Feb 21 2003 - 01:56:21 CST)
  • Re: probelms with antechamber (Thu Feb 20 2003 - 19:19:24 CST)
  • Re: How do NTC=2 recognize hydrogen atom? (Thu Feb 20 2003 - 10:19:27 CST)
  • Re: antechamber and its prepin files (Wed Feb 19 2003 - 15:08:55 CST)
  • Re: restrained atoms NTR (Tue Feb 18 2003 - 22:16:50 CST)
  • Re: charge neutralization in DNA (Tue Feb 18 2003 - 16:27:20 CST)
  • Re: Final energy minimization step (Tue Feb 18 2003 - 16:25:05 CST)
  • Re: File in the tutorial (Tue Feb 18 2003 - 16:19:24 CST)
  • Re: (no subject) (Tue Feb 18 2003 - 16:16:34 CST)
  • Re: question on EWALD (Mon Feb 17 2003 - 12:08:53 CST)
  • Re: RE: TAUP and density problem (Mon Feb 17 2003 - 12:06:03 CST)
  • Re: bond command (Fri Feb 14 2003 - 00:38:09 CST)
  • Re: inter & intra-molecular interaction energies (Thu Feb 13 2003 - 17:21:15 CST)
  • Re: xleap crash under Irix (Thu Feb 13 2003 - 14:57:35 CST)
  • Re: Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 07:22:55 CST)
  • Re: decrease a force const. for angle (Mon Feb 10 2003 - 19:04:55 CST)
  • Re: Internal dielectric in MM-GBSA (Mon Feb 10 2003 - 14:29:44 CST)
  • Re: Gibbs: DynamicWin and NSTMEQ? (Fri Feb 07 2003 - 18:12:07 CST)
  • Re: essential dynamics (Fri Feb 07 2003 - 15:19:04 CST)
  • Re: bond command (Thu Feb 06 2003 - 00:13:22 CST)
  • Re: noninteger charge (Wed Feb 05 2003 - 12:59:32 CST)
  • Re: bond command (Wed Feb 05 2003 - 00:30:26 CST)
  • Re: Ptraj problem with small molecules (Tue Feb 04 2003 - 09:20:54 CST)
  • Re: some questions in gibbs calculation (Tue Feb 04 2003 - 09:16:40 CST)
  • Re: Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 15:11:43 CST)
  • Re: question about ligand (Fri Jan 31 2003 - 17:14:41 CST)
  • Re: Gibbs, ewald and ifc (Fri Jan 31 2003 - 15:56:25 CST)
  • Re: Quasi-harmonic analysis (Thu Jan 30 2003 - 19:58:32 CST)
  • Re: new amino acid residues (Thu Jan 30 2003 - 11:46:35 CST)
  • antechamber and gamess (Wed Jan 29 2003 - 10:16:03 CST)
  • Re: gibbs calculation (Tue Jan 28 2003 - 14:03:37 CST)
  • Re: Question: about restarting Energy (Mon Jan 27 2003 - 20:33:14 CST)
  • Re: crystal structure of DNA/RNA homopolymers (Mon Jan 27 2003 - 13:48:35 CST)
  • Re: gibbs run (Mon Jan 27 2003 - 12:38:13 CST)
  • Re: lastrst (Mon Jan 27 2003 - 12:33:12 CST)
  • terminal phosphate group in RNA (Fri Jan 24 2003 - 18:03:06 CST)
  • Re: problems in equilibrating NaCl solution (Fri Jan 24 2003 - 16:20:12 CST)
  • Re: Shake problem in organic solvent (Fri Jan 24 2003 - 15:43:20 CST)
  • Re: Gibbs tutorial question (Wed Jan 22 2003 - 15:54:10 CST)
  • Re: shake and belly (Wed Jan 22 2003 - 12:17:22 CST)
  • Re: How to control box size (Wed Jan 22 2003 - 10:53:02 CST)
  • Re: equilibrated solvent box (Wed Jan 22 2003 - 10:48:12 CST)
  • Re: SCSL (Wed Jan 22 2003 - 10:37:33 CST)
  • Re: octahedral volume (Tue Jan 21 2003 - 11:03:23 CST)
  • Re: Polarization charges -geometry (Tue Jan 21 2003 - 10:56:07 CST)
  • Re: Amber tutorial crown-ether (Tue Jan 21 2003 - 10:48:47 CST)
  • Re: 'hot-solvent' and 'cold solute' problem (Tue Jan 21 2003 - 10:38:14 CST)
  • Re: your mail (Tue Jan 21 2003 - 10:35:52 CST)
  • Re: Ewald error (Mon Jan 20 2003 - 11:31:49 CST)
  • Re: morse potential (Mon Jan 20 2003 - 11:29:59 CST)
  • Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold (Mon Jan 20 2003 - 01:26:16 CST)
  • Re: Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold (Sat Jan 18 2003 - 12:53:54 CST)
  • Re: UCSF Network changes to affect Amber Web site. (Fri Jan 17 2003 - 14:14:59 CST)
  • Re: solvent free energy, GB (Thu Jan 16 2003 - 18:25:16 CST)
  • Re: nscm (Tue Jan 14 2003 - 18:55:14 CST)
  • Re: solvatecap (Tue Jan 14 2003 - 16:29:43 CST)
  • Re: how to stop mapping of N- and C-terminal residues in xleap (Tue Jan 14 2003 - 13:59:52 CST)
  • Re: chloroform, dichlormethane f.f. (Tue Jan 14 2003 - 10:19:24 CST)
  • Re: xleap crashes (Mon Jan 13 2003 - 11:08:15 CST)
  • Re: Dummy atoms in free energy calculation (Mon Jan 13 2003 - 01:37:35 CST)
  • Re: problem with antechamber (Sun Jan 12 2003 - 16:01:06 CST)
  • Re: MM_pbsa prmtop file (Thu Jan 09 2003 - 17:53:53 CST)
  • Re: nmanal & quasih question (Thu Jan 09 2003 - 11:16:11 CST)
  • Re: building molecules by script files for leap (Wed Jan 08 2003 - 11:27:13 CST)
  • Re: the unit of velocity (Wed Jan 08 2003 - 10:09:43 CST)
  • Re: virtual box (Tue Jan 07 2003 - 17:56:29 CST)
  • Re: reducing restrains (Tue Jan 07 2003 - 11:08:24 CST)
  • Re: Small organic molecules (Tue Jan 07 2003 - 10:16:48 CST)
  • Re: water reordering in sander (Tue Jan 07 2003 - 10:03:58 CST)
  • Re: JACS 125th and PAK (Fri Jan 03 2003 - 12:36:47 CST)
  • Re: Sander box error and thanks on previous mdin error (Fri Jan 03 2003 - 09:40:07 CST)
• David A. Case
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Wed Dec 31 2003 - 09:47:46 CST)
  • Re: AMBER: problems with pressure control (Tue Dec 30 2003 - 12:03:06 CST)
  • Re: AMBER: Constant temperature (Sun Dec 28 2003 - 00:46:46 CST)
  • Re: AMBER: vlimit? (Fri Dec 26 2003 - 12:18:16 CST)
  • Re: AMBER: MSE (Wed Dec 24 2003 - 12:08:59 CST)
  • Re: AMBER: using sander without SHAKE (Wed Dec 24 2003 - 12:06:40 CST)
  • Re: AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? (Tue Dec 23 2003 - 13:18:39 CST)
  • Re: AMBER: MSMS (Tue Dec 23 2003 - 12:56:32 CST)
  • Re: AMBER: umbrella sampling with AMBER (Mon Dec 22 2003 - 19:48:30 CST)
  • Re: AMBER: vlimit? (Mon Dec 22 2003 - 11:24:18 CST)
  • Re: AMBER: using sander without SHAKE (Mon Dec 22 2003 - 11:22:09 CST)
  • Re: AMBER: special gaff atom types available? (Sat Dec 20 2003 - 10:25:14 CST)
  • Re: AMBER: Ewald in Amber 7 (Fri Dec 19 2003 - 11:30:23 CST)
  • Re: AMBER: non-zero 10-12 coefficient (Sat Dec 13 2003 - 14:48:12 CST)
  • Re: AMBER: a simple question about HBond energy... (Fri Dec 12 2003 - 15:57:47 CST)
  • Re: AMBER: order parameter (Fri Dec 12 2003 - 15:29:26 CST)
  • Re: AMBER: How to use quasih? (Thu Dec 11 2003 - 10:34:39 CST)
  • Re: AMBER: Carbohydrate connectivity (Thu Dec 11 2003 - 10:09:08 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 12:28:00 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 10:31:38 CST)
  • Re: AMBER: xleap-N/C terminus (Wed Dec 10 2003 - 10:33:52 CST)
  • Re: AMBER: About Temperature Regulation (Wed Dec 10 2003 - 10:30:24 CST)
  • Re: AMBER: Re: initial structures (Mon Dec 08 2003 - 11:30:57 CST)
  • Re: AMBER: Amber - compiler help (Thu Dec 04 2003 - 18:54:07 CST)
  • Re: AMBER: sander output (Thu Dec 04 2003 - 18:51:03 CST)
  • Re: AMBER: Compiling on Suse 9 Pro with ifc... (Thu Dec 04 2003 - 10:42:15 CST)
  • Re: AMBER: segmentation fault (Wed Dec 03 2003 - 11:46:46 CST)
  • Re: AMBER: how to calculate vibration frequency? (Wed Dec 03 2003 - 10:59:41 CST)
  • Re: AMBER: Anal/MMPBSA (Tue Dec 02 2003 - 19:29:46 CST)
  • Re: AMBER: partial charge (Tue Dec 02 2003 - 14:06:02 CST)
  • Re: AMBER: basic questions (Tue Dec 02 2003 - 10:37:42 CST)
  • Re: AMBER: partial charge (Tue Dec 02 2003 - 00:46:04 CST)
  • Re: AMBER: basic questions (Tue Dec 02 2003 - 00:37:59 CST)
  • Re: AMBER: Sander / Anal (Mon Dec 01 2003 - 14:58:32 CST)
  • Re: AMBER: Compiling on Suse 9 Pro with ifc... (Mon Dec 01 2003 - 14:49:33 CST)
  • Re: AMBER: NAD+ and NADH amber parameters (Mon Dec 01 2003 - 10:35:56 CST)
  • Re: AMBER: Pseudouridine force field parameters (Sat Nov 29 2003 - 18:48:59 CST)
  • Re: AMBER: gaff errors? (Wed Nov 26 2003 - 10:40:37 CST)
  • Re: AMBER: saveamberparm (Mon Nov 24 2003 - 19:32:22 CST)
  • Re: AMBER: protein MD - problem (Mon Nov 24 2003 - 10:27:08 CST)
  • Re: AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? (Fri Nov 21 2003 - 17:33:38 CST)
  • Re: AMBER: Compaq Tru64 Unix (Fri Nov 21 2003 - 17:34:43 CST)
  • Re: AMBER: missing of VdW Parameters for N3 (Fri Nov 21 2003 - 10:08:07 CST)
  • Re: AMBER: antechamber test failure (Tue Nov 18 2003 - 16:22:16 CST)
  • Re: AMBER: antechamber test failure (Mon Nov 17 2003 - 21:03:56 CST)
  • Re: AMBER: Pressure during MD (Mon Nov 17 2003 - 21:03:47 CST)
  • Re: AMBER: Pressure during MD (Sun Nov 16 2003 - 16:52:36 CST)
  • Re: AMBER: a problem with memory size (Sun Nov 16 2003 - 16:49:30 CST)
  • Re: AMBER: Diffusion constant (Sat Nov 15 2003 - 14:45:56 CST)
  • Re: AMBER: mgbjsb radii in GBSA (Sat Nov 15 2003 - 11:58:35 CST)
  • Re: AMBER: sander lastist (Sat Nov 15 2003 - 11:40:13 CST)
  • Re: AMBER: rotation removal in sander GB (Fri Nov 14 2003 - 10:34:06 CST)
  • Re: AMBER: Problems restarting with sander (Fri Nov 14 2003 - 10:31:12 CST)
  • Re: AMBER: water prep file needed (Thu Nov 13 2003 - 15:36:38 CST)
  • Re: AMBER: ndfmin in belly runs (Thu Nov 13 2003 - 10:07:14 CST)
  • Re: Re: AMBER: a problem with antechamber and leap (Tue Nov 11 2003 - 19:01:39 CST)
  • Re: AMBER: restraints and reordering water (Tue Nov 11 2003 - 11:21:10 CST)
  • Re: AMBER: change force constants (Mon Nov 10 2003 - 17:56:59 CST)
  • Re: AMBER: AM1-BCC in Amber7 (Mon Nov 10 2003 - 10:12:07 CST)
  • Re: AMBER: mgbjsb radii in GBSA (Mon Nov 10 2003 - 10:10:17 CST)
  • Re: AMBER: a problem with antechamber and leap (Mon Nov 10 2003 - 01:24:41 CST)
  • Re: AMBER: restrain (Fri Nov 07 2003 - 10:34:21 CST)
  • Re: AMBER: Restraints (Thu Nov 06 2003 - 17:26:47 CST)
  • Re: AMBER: absolute vs. relative binding free energy (Wed Nov 05 2003 - 19:45:54 CST)
  • Re: AMBER: MD Equil (Mon Nov 03 2003 - 18:55:59 CST)
  • Re: AMBER: distrance restraints for alpha carbons (Mon Nov 03 2003 - 17:06:57 CST)
  • Re: AMBER: make clean doesn't clean leap (Mon Nov 03 2003 - 16:58:38 CST)
  • Re: AMBER: minimize a covalently bounded protein-ligand complex (Thu Oct 30 2003 - 17:50:11 CST)
  • Re: AMBER: (Thu Oct 30 2003 - 11:23:12 CST)
  • Re: AMBER: surface code in Amber (Tue Oct 28 2003 - 18:15:33 CST)
  • Re: AMBER: amber 7 for industrial application (Tue Oct 28 2003 - 00:21:35 CST)
  • Re: AMBER: surface code in Amber (Mon Oct 27 2003 - 00:45:18 CST)
  • Re: AMBER: problem in tleap (Sat Oct 25 2003 - 22:56:29 CDT)
  • Re: AMBER: Pressure in NVT ensemble (Sat Oct 25 2003 - 22:16:37 CDT)
  • Re: AMBER: antechamber and bond type (Sat Oct 25 2003 - 21:49:05 CDT)
  • Re: AMBER: torsional restraints for groups of atoms (Wed Oct 22 2003 - 19:00:16 CDT)
  • Re: AMBER: frozen x unfrozen (Wed Oct 22 2003 - 18:58:41 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Mon Oct 20 2003 - 19:13:15 CDT)
  • Re: AMBER: more questions about igb (Mon Oct 20 2003 - 18:47:35 CDT)
  • Re: AMBER: ibelly in AMBER 6 (Sat Oct 18 2003 - 11:48:16 CDT)
  • Re: AMBER: ibelly in AMBER 6 (Fri Oct 17 2003 - 19:51:29 CDT)
  • Re: AMBER: a question (Fri Oct 17 2003 - 17:36:08 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Fri Oct 17 2003 - 11:05:15 CDT)
  • Re: AMBER: problem in tleap (Fri Oct 17 2003 - 10:59:27 CDT)
  • Re: AMBER: a problem with xleap (Wed Oct 15 2003 - 09:31:06 CDT)
  • Re: AMBER: tru64 alpha (Wed Oct 15 2003 - 09:25:03 CDT)
  • Re: AMBER: Restraints to maintain base pair planarity (Wed Oct 15 2003 - 09:18:10 CDT)
  • Re: AMBER: sander: vlimit problem (Tue Oct 14 2003 - 17:15:02 CDT)
  • Re: AMBER: MeCNBOX & EWALD bomb (Tue Oct 14 2003 - 17:12:42 CDT)
  • Re: AMBER: nmanal projection (Tue Oct 14 2003 - 17:11:29 CDT)
  • Re: AMBER: polarizability and PME (Sat Sep 27 2003 - 11:17:46 CDT)
  • Re: AMBER: Phase for torsion angle different of 0 or 180 ? (Fri Sep 26 2003 - 15:41:35 CDT)
  • Re: AMBER: FW: Residual dipolar couplings (Fri Sep 26 2003 - 15:36:25 CDT)
  • Re: AMBER: non-bonded cutoffs (Fri Sep 26 2003 - 10:32:09 CDT)
  • Re: AMBER: MeCNBOX (Thu Sep 25 2003 - 15:25:23 CDT)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 16:09:06 CDT)
  • Re: AMBER: problem with file format (Wed Sep 24 2003 - 14:28:22 CDT)
  • Re: AMBER: residues and molecules (Wed Sep 24 2003 - 13:45:40 CDT)
  • Re: AMBER: pair-cutoff (Tue Sep 23 2003 - 10:59:01 CDT)
  • Re: AMBER: Antechamber problem (Tue Sep 23 2003 - 10:19:54 CDT)
  • Re: AMBER: increase size of NATOM or NRES for "ambpdb" (Mon Sep 22 2003 - 14:24:12 CDT)
  • Re: AMBER: slow simulation (Mon Sep 22 2003 - 09:54:46 CDT)
  • Re: AMBER: double bonds in prmtop (Fri Sep 19 2003 - 17:42:23 CDT)
  • Re: AMBER: Amber 7 - bugfix 42 problem. (Fri Sep 19 2003 - 13:17:10 CDT)
  • Re: AMBER: no defined type for atom N atom (Fri Sep 19 2003 - 12:01:29 CDT)
  • Re: AMBER: FEP problem (Thu Sep 18 2003 - 10:08:18 CDT)
  • Re: AMBER: leap/frcmod problem (Wed Sep 17 2003 - 15:57:18 CDT)
  • Re: AMBER: AMBER on LINUX ?? (fwd) (Mon Sep 15 2003 - 15:08:56 CDT)
  • Re: AMBER: AMBER error in CHALANGE (Mon Sep 15 2003 - 15:06:21 CDT)
  • Re: AMBER: sander on cygwin (Mon Sep 15 2003 - 15:03:23 CDT)
  • Re: AMBER: performance vs number of processors (Mon Sep 15 2003 - 14:53:32 CDT)
  • Re: AMBER: minimization error (Fri Sep 12 2003 - 16:19:48 CDT)
  • AMBER: Re: torsional energy (Wed Sep 10 2003 - 17:15:34 CDT)
  • Re: AMBER: TIP5P (Wed Sep 10 2003 - 10:14:18 CDT)
  • Re: AMBER: Compiling 64-bit version on AIX (Tue Sep 09 2003 - 11:36:12 CDT)
  • Re: AMBER: SHAKE poblem with dummy atoms (Tue Sep 09 2003 - 10:38:49 CDT)
  • Re: AMBER: reporting atoms clashed during simple energy minimization (Tue Sep 09 2003 - 10:36:29 CDT)
  • Re: AMBER: TIP5P (Tue Sep 09 2003 - 10:32:58 CDT)
  • Re: AMBER: dielectric constant for blends (Mon Sep 08 2003 - 10:23:34 CDT)
  • AMBER: update to answer about solvateShell (Sat Sep 06 2003 - 15:00:50 CDT)
  • Re: AMBER: solvatebox-solvateshell (Sat Sep 06 2003 - 14:56:39 CDT)
  • Re: AMBER: DNA helix is not in z-direction (Fri Sep 05 2003 - 19:37:20 CDT)
  • Re: AMBER: IG value (Fri Sep 05 2003 - 09:46:58 CDT)
  • Re: AMBER: problems with periodic boundary conditions (Fri Sep 05 2003 - 09:43:29 CDT)
  • Re: AMBER: PMF ethane example: Can someone correct the INPUT? Thanks. (Wed Sep 03 2003 - 10:38:56 CDT)
  • Re: AMBER: atomic clash or structure size? (Wed Sep 03 2003 - 10:32:42 CDT)
  • Re: AMBER: MIPS R14000 and Machine-file (Tue Sep 02 2003 - 09:56:26 CDT)
  • Re: title card? Re: AMBER: what can't I use ibelly? (Mon Sep 01 2003 - 23:18:12 CDT)
  • Re: AMBER: sander minimization (Fri Aug 29 2003 - 16:32:55 CDT)
  • Re: AMBER: what can't I use ibelly? (Thu Aug 28 2003 - 14:40:55 CDT)
  • Re: AMBER: target MD simulation (Wed Aug 27 2003 - 15:39:31 CDT)
  • Re: AMBER: LEaP not compiling (Wed Aug 27 2003 - 10:42:49 CDT)
  • Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space (Tue Aug 26 2003 - 20:32:20 CDT)
  • Re: AMBER: xleap memory issue (Tue Aug 26 2003 - 20:25:29 CDT)
  • Re: AMBER: The FCAP parameter in amber7 (Mon Aug 25 2003 - 18:59:45 CDT)
  • Re: AMBER: gibbs pmf calculation (Mon Aug 25 2003 - 18:07:16 CDT)
  • Re: AMBER: gibbs pmf calculation (Mon Aug 25 2003 - 10:25:27 CDT)
  • Re: Re[2]: AMBER: antechamber problem (Thu Aug 21 2003 - 18:34:17 CDT)
  • Re: AMBER: gibbs pmf calculation (Wed Aug 20 2003 - 17:13:23 CDT)
  • Re: AMBER: antechamber problem (Wed Aug 20 2003 - 17:07:30 CDT)
  • Re: AMBER: temperature does not reach to temp0 (Tue Aug 19 2003 - 10:47:15 CDT)
  • Re: AMBER: prepin file (Tue Aug 19 2003 - 10:45:30 CDT)
  • Re: AMBER: nmanal's rvec file (Tue Aug 19 2003 - 21:00:19 CDT)
  • Re: AMBER: nmanal in amber7 (Mon Aug 18 2003 - 14:54:04 CDT)
  • Re: AMBER: tleap under amber6 (Mon Aug 18 2003 - 13:48:19 CDT)
  • Re: AMBER: nmanal in amber7 (Mon Aug 18 2003 - 13:44:20 CDT)
  • Re: AMBER: united atom weiner force field (Mon Aug 18 2003 - 10:21:03 CDT)
  • Re: AMBER: AMBER 7_make install (Mon Aug 18 2003 - 10:16:20 CDT)
  • Re: AMBER: Problems with extra points on parralellized linux and sgi machine (Mon Aug 18 2003 - 10:08:57 CDT)
  • Re: AMBER: large changes in xyz coordinates (Sat Aug 16 2003 - 23:07:25 CDT)
  • Re: AMBER: NTX 5 or 7 after equilibration in constant pressure? (Sat Aug 16 2003 - 19:04:18 CDT)
  • Re: AMBER: minimum image convention mystery (Sat Aug 16 2003 - 19:02:03 CDT)
  • Re: AMBER: Gibbs pmf calculation (Fri Aug 15 2003 - 11:51:07 CDT)
  • Re: AMBER: Problems with extra points on parralellized linux and sgi machine (Fri Aug 15 2003 - 11:17:15 CDT)
  • Re: AMBER: minimization error (Thu Aug 14 2003 - 13:41:43 CDT)
  • Re: AMBER: simulating a crystal using the unit cell (Thu Aug 14 2003 - 10:40:42 CDT)
  • Re: AMBER: complete pdb structure (Thu Aug 14 2003 - 00:30:08 CDT)
  • Re: AMBER: constant energy simulation (Wed Aug 13 2003 - 17:52:56 CDT)
  • Re: AMBER: ANAL component (Wed Aug 13 2003 - 17:45:36 CDT)
  • Re: AMBER: constant energy simulation (Wed Aug 13 2003 - 10:46:52 CDT)
  • Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. (Tue Aug 12 2003 - 14:23:55 CDT)
  • Re: AMBER: machine dependent? (Mon Aug 11 2003 - 15:46:14 CDT)
  • Re: AMBER: saveamberprep in xLeap (Fri Aug 08 2003 - 11:38:34 CDT)
  • Re: AMBER: Reference for Amber7 heme parameters (Fri Aug 08 2003 - 10:23:46 CDT)
  • Re: AMBER: import pdb file in xleap (Thu Aug 07 2003 - 16:30:51 CDT)
  • Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms (Thu Aug 07 2003 - 13:35:46 CDT)
  • Re: AMBER: 2D periodic box (Thu Aug 07 2003 - 11:28:09 CDT)
  • Re: AMBER: references about AMBER MD simulations (Thu Aug 07 2003 - 01:21:05 CDT)
  • Re: AMBER: SHAKE Problem (Wed Aug 06 2003 - 16:52:21 CDT)
  • AMBER: Re: dynamics of isolated system (fwd) (Wed Aug 06 2003 - 16:43:29 CDT)
  • Re: AMBER: anal - memory problem (Wed Aug 06 2003 - 14:00:32 CDT)
  • Re: AMBER: zero free energy change for nonbond leg of electrst. decoupling (Tue Aug 05 2003 - 14:39:22 CDT)
  • Re: AMBER: (no subject) (Tue Aug 05 2003 - 14:32:56 CDT)
  • Re: AMBER: charge method of antechamber (Tue Aug 05 2003 - 00:24:00 CDT)
  • Re: AMBER: separate thermostats for different molecules (Tue Aug 05 2003 - 00:19:02 CDT)
  • Re: AMBER: normal mode analysis (Tue Aug 05 2003 - 00:12:36 CDT)
  • Re: AMBER: AMBER7 & mpich : (no-attachment version) (Sat Aug 02 2003 - 15:30:00 CDT)
  • Re: AMBER: Problem generating .tpp and .rst files for a complex (Fri Aug 01 2003 - 10:32:24 CDT)
  • Re: AMBER: Amber parallelisation (Fri Aug 01 2003 - 10:18:17 CDT)
  • Re: AMBER: compile problem (Wed Jul 30 2003 - 16:56:58 CDT)
  • Re: AMBER: Ewald problem (Wed Jul 30 2003 - 12:01:49 CDT)
  • Re: AMBER: chemical potential (Wed Jul 30 2003 - 11:31:34 CDT)
  • Re: AMBER: Ewald_Bomb (Wed Jul 30 2003 - 11:30:13 CDT)
  • Re: AMBER: dynamics of isolated system (Tue Jul 29 2003 - 19:35:03 CDT)
  • Re: AMBER: combine prep files (Tue Jul 29 2003 - 19:27:57 CDT)
  • Re: AMBER: chemical potential (Tue Jul 29 2003 - 09:50:23 CDT)
  • Re: AMBER: Question about quasih analysis (Mon Jul 28 2003 - 16:40:48 CDT)
  • Re: AMBER: Question about quasih analysis (Mon Jul 28 2003 - 13:37:20 CDT)
  • Re: AMBER: strange problem with a small system (Mon Jul 28 2003 - 12:12:30 CDT)
  • Re: AMBER: please let me know if this is correct (Mon Jul 28 2003 - 11:55:28 CDT)
  • Re: AMBER: Question about quasih analysis (Mon Jul 28 2003 - 11:16:13 CDT)
  • AMBER: a note on problems with MPI and sander (Sat Jul 26 2003 - 13:50:37 CDT)
  • Re: AMBER: strange problem with a small system (Thu Jul 24 2003 - 23:51:04 CDT)
  • Re: AMBER: /exe/teLeap does not exist (Thu Jul 24 2003 - 19:50:17 CDT)
  • Re: AMBER: strange problem with a small system (Wed Jul 23 2003 - 13:51:59 CDT)
  • Re: AMBER: Non-standard Residue (Wed Jul 23 2003 - 13:31:44 CDT)
  • Re: AMBER: FILE UNITIO.C (Wed Jul 23 2003 - 10:04:54 CDT)
  • Re: AMBER: HB dynamics in water and Ion solvation free energies (Tue Jul 22 2003 - 21:18:51 CDT)
  • Re: AMBER: Non-standard Residue (Tue Jul 22 2003 - 16:06:50 CDT)
  • Re: AMBER: FILE UNITIO.C (Tue Jul 22 2003 - 13:54:14 CDT)
  • Re: AMBER: (no subject) (Tue Jul 22 2003 - 11:30:00 CDT)
  • Re: AMBER: dielectric in sander (Mon Jul 21 2003 - 10:52:57 CDT)
  • Re: AMBER: Fwd: Minimizing after solvation (Mon Jul 21 2003 - 10:50:35 CDT)
  • Re: AMBER: Fwd: Minimizing after solvation (Sat Jul 19 2003 - 23:34:53 CDT)
  • Re: AMBER: neutral N- and C- termini ! (Thu Jul 17 2003 - 11:05:00 CDT)
  • Re: AMBER: RADII in DELPHI (Thu Jul 17 2003 - 11:03:29 CDT)
  • Re: AMBER: Big system in Gibbs (Thu Jul 17 2003 - 11:00:57 CDT)
  • Re: AMBER: curves nomenclature (Wed Jul 16 2003 - 17:29:01 CDT)
  • Re: AMBER: Coordinate resetting (SHAKE) cannot be accomplished (Tue Jul 15 2003 - 20:25:26 CDT)
  • AMBER: Re: methylphosphonate (Mon Jul 14 2003 - 19:22:28 CDT)
  • Re: Sander_classic output: NAN (Mon Jul 14 2003 - 17:27:17 CDT)
  • Re: parallelisation (Mon Jul 14 2003 - 17:24:34 CDT)
  • mail reflector address is changing (Mon Jul 14 2003 - 16:56:21 CDT)
  • Re: effect of forcing neutrality (Mon Jul 14 2003 - 10:49:57 CDT)
  • Re: May I get your help? (Thu Jul 10 2003 - 22:05:21 CDT)
  • Re: memory problem (Thu Jul 10 2003 - 22:03:14 CDT)
  • Re: your mail (Thu Jul 10 2003 - 22:01:51 CDT)
  • Re: Adding missing parameters (Thu Jul 10 2003 - 21:58:21 CDT)
  • Re: npscal (Wed Jul 09 2003 - 15:53:54 CDT)
  • Re: Temperature control (Wed Jul 09 2003 - 15:53:10 CDT)
  • Re: memory shortage with mm_pbsa (Tue Jul 08 2003 - 20:47:55 CDT)
  • Re: constraint + restraint (Tue Jul 08 2003 - 12:33:35 CDT)
  • Re: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 17:04:01 CDT)
  • Re: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 16:23:48 CDT)
  • correction to location of the PMEMD program (Mon Jul 07 2003 - 16:17:44 CDT)
  • New program available: PMEMD (Particle Mesh Ewald Molecular Dynamics) (Mon Jul 07 2003 - 16:13:33 CDT)
  • Re: Machine file available for ICC compiler ? (Fri Jul 04 2003 - 14:14:00 CDT)
  • Re: How to do a rigid solvent model? (Fri Jul 04 2003 - 12:16:51 CDT)
  • Re: sander,ntt=5 (Fri Jul 04 2003 - 12:13:21 CDT)
  • Re: Antechamber (Thu Jul 03 2003 - 12:36:47 CDT)
  • Re: Antechamber (Thu Jul 03 2003 - 11:59:12 CDT)
  • Re: input problem (Tue Jul 01 2003 - 14:24:42 CDT)
  • Re: parallel version amber installation problem (Tue Jul 01 2003 - 12:43:03 CDT)
  • Re: Questions about output archive and micromolecules (Tue Jul 01 2003 - 12:39:33 CDT)
  • Re: protonate (Tue Jul 01 2003 - 12:29:54 CDT)
  • Re: AMBER Cutoff (Tue Jul 01 2003 - 10:00:00 CDT)
  • Re: protonate (Mon Jun 30 2003 - 17:44:18 CDT)
  • Re: pyroglutamic acid (PCA) (Thu Jun 26 2003 - 12:34:25 CDT)
  • Re: Amber6 on RH 9 (Thu Jun 26 2003 - 12:31:56 CDT)
  • Re: Sander problem (Wed Jun 25 2003 - 17:30:21 CDT)
  • Re: Antechamber (Wed Jun 25 2003 - 12:31:31 CDT)
  • Re: AMBER parameters (Tue Jun 24 2003 - 10:25:35 CDT)
  • Re: AMBER question (Fri Jun 20 2003 - 19:59:04 CDT)
  • Re: NOESY restraints (Fri Jun 20 2003 - 19:49:00 CDT)
  • Re: constraint + restraint (Thu Jun 19 2003 - 10:39:44 CDT)
  • Re: Error in minimization using sander_classic of AMBER6 (Tue Jun 17 2003 - 15:53:49 CDT)
  • new tutorial available: introduction to ptraj (Tue Jun 17 2003 - 13:03:54 CDT)
  • Re: LEAP compiling problem (Tue Jun 17 2003 - 11:09:26 CDT)
  • Re: LEAP compiling problem (Tue Jun 17 2003 - 10:51:21 CDT)
  • Re: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI (Mon Jun 16 2003 - 10:12:05 CDT)
  • Re: Problem with a library (Fri Jun 13 2003 - 16:07:37 CDT)
  • Re: glycam force field with amber (Fri Jun 13 2003 - 11:42:31 CDT)
  • Re: install problem (Thu Jun 12 2003 - 17:26:56 CDT)
  • Re: vlimit exceeded when sander calculate free energies using TI (Wed Jun 11 2003 - 10:21:31 CDT)
  • Re: quasih problem (Wed Jun 11 2003 - 10:12:54 CDT)
  • New location for the Amber web site (Wed Jun 11 2003 - 01:04:54 CDT)
  • Re: Minimization does not converge. (Wed Jun 11 2003 - 00:52:29 CDT)
  • Re: A question of time (Tue Jun 10 2003 - 11:34:19 CDT)
  • Re: Superimposed trajectory (Tue Jun 10 2003 - 09:53:42 CDT)
  • Re: saving trajectory of solute only (Mon Jun 09 2003 - 11:24:03 CDT)
  • Re: VdW in FEP (Mon Jun 09 2003 - 10:05:58 CDT)
  • Re: constant volume (Fri Jun 06 2003 - 17:48:16 CDT)
  • Re: keeping pdb residues numbers ? (Wed Jun 04 2003 - 12:40:08 CDT)
  • Re: belly vs. position restraints (Wed Jun 04 2003 - 10:57:02 CDT)
  • Re: angle violation in SANDER simulation (Wed Jun 04 2003 - 10:17:32 CDT)
  • Re: solventbox at constant pressure (Wed Jun 04 2003 - 10:13:37 CDT)
  • Re: pol_h (Tue Jun 03 2003 - 11:26:41 CDT)
  • Re: run sander? (Mon Jun 02 2003 - 12:52:00 CDT)
  • Re: antechamber read gaussian file (Sun Jun 01 2003 - 19:18:54 CDT)
  • Re: IR6 and makeDIST-RST (Sun Jun 01 2003 - 19:14:04 CDT)
  • Re: information (Sun Jun 01 2003 - 19:14:29 CDT)
  • Re: water box distortion (Fri May 23 2003 - 18:13:40 CDT)
  • Re: Questions about statistics output of mm_pbsa? (Thu May 22 2003 - 19:32:15 CDT)
  • Re: Please help on xleap: FATAL ERROR (Thu May 22 2003 - 19:25:07 CDT)
  • Re: Hybdrogen bonds and LJ 10-12 (Thu May 22 2003 - 12:21:18 CDT)
  • Re: From Dr. Ekaterina Nikitina (Thu May 22 2003 - 12:16:58 CDT)
  • Re: Minimization problem w/ counter-ion ! (Thu May 22 2003 - 11:51:28 CDT)
  • Re: parm99 (Tue May 20 2003 - 17:37:32 CDT)
  • Re: off-diagonal VDW term (Tue May 20 2003 - 09:43:33 CDT)
  • Re: Calcium in proteins (Tue May 20 2003 - 09:40:06 CDT)
  • Re: Fluorine atom type in mm_pbsa? (Tue May 20 2003 - 09:30:53 CDT)
  • Re: force field parameters for torsions (Mon May 19 2003 - 12:44:27 CDT)
  • Re: anal, amber7 and resnum 0 (Fri May 16 2003 - 16:57:33 CDT)
  • Re: using distance restraints in Sander (AIX 4.3 RS6000) (Fri May 16 2003 - 15:42:18 CDT)
  • Re: ptraj generated PDB files (Fri May 16 2003 - 10:43:34 CDT)
  • Re: protonate problem (Wed May 14 2003 - 13:36:04 CDT)
  • Re: A question about AMBER, leaprc.ff02EP (Wed May 14 2003 - 01:26:56 CDT)
  • Re: Sander help (Tue May 13 2003 - 19:51:12 CDT)
  • Re: parameters for nitro group (Tue May 13 2003 - 11:45:02 CDT)
  • Re: Heat of Vaporization (Tue May 13 2003 - 10:12:41 CDT)
  • Re: Simple question about sander parameter set (Tue May 13 2003 - 10:00:22 CDT)
  • Re: 10-12 H-bond terms (Mon May 12 2003 - 16:58:52 CDT)
  • Re: ANAL in AMBER (Fri May 09 2003 - 11:11:33 CDT)
  • Re: 2 questions (Fri May 09 2003 - 10:54:41 CDT)
  • Re: current AMBER citation? (Thu May 08 2003 - 10:16:13 CDT)
  • Re: help me switching from amber5 to amber6 (Wed May 07 2003 - 19:59:54 CDT)
  • minimizaiton in vacuum (Mon May 05 2003 - 11:01:16 CDT)
  • Re: Latest Leap Compile Errors (Sun May 04 2003 - 16:02:05 CDT)
  • Re: Residual dipolar couplings (Fri May 02 2003 - 12:21:53 CDT)
  • Re: Simple math of memory calculation for nmode (Thu May 01 2003 - 19:23:06 CDT)
  • Re: problem_namelist_reading (Tue Apr 29 2003 - 10:12:01 CDT)
  • Re: force field parameters for phosphoserine (Tue Apr 29 2003 - 09:56:48 CDT)
  • Re: how to restrain base pair (Mon Apr 28 2003 - 14:14:49 CDT)
  • Re: non bonded pair list (Thu Apr 24 2003 - 18:24:37 CDT)
  • Re: Annealing blown up (Thu Apr 24 2003 - 18:21:53 CDT)
  • Re: Question: Nmode with counter ions. (Thu Apr 24 2003 - 18:16:22 CDT)
  • Re: Problem_to_open_PROTON_INFO_file (Thu Apr 24 2003 - 10:30:32 CDT)
  • Re: How to use GLYCAM force field in AMBER (Wed Apr 23 2003 - 16:51:30 CDT)
  • Re: GB/SA (Wed Apr 23 2003 - 14:36:56 CDT)
  • Re: makeDIST_RST (Thu Apr 17 2003 - 11:50:14 CDT)
  • Re: AMBER (Tue Apr 15 2003 - 19:38:59 CDT)
  • Re: ibelly and ntr (Tue Apr 15 2003 - 18:13:11 CDT)
  • Re: Proper Restraint usage (Tue Apr 15 2003 - 16:04:50 CDT)
  • Re: A problem in opening the file (Tue Apr 15 2003 - 01:50:04 CDT)
  • Re: diffusion coefficients (Mon Apr 14 2003 - 01:03:15 CDT)
  • Re: SSBonds and charge problems (Sat Apr 12 2003 - 00:29:53 CDT)
  • Re: free energy in sander (Thu Apr 10 2003 - 17:45:05 CDT)
  • Re: Groups defenition (Wed Apr 09 2003 - 10:59:11 CDT)
  • Re: Tleap (Tue Apr 08 2003 - 20:09:46 CDT)
  • Re: Periodic Boundary Condition in AMBER7 (the sander module)! (Tue Apr 08 2003 - 17:25:53 CDT)
  • Re: problem with tleap (Tue Apr 08 2003 - 11:12:34 CDT)
  • Re: protonate (Tue Apr 08 2003 - 11:06:21 CDT)
  • Re: please kindly help (Mon Apr 07 2003 - 10:34:21 CDT)
  • Re: sander & prmtop file generated from antechamber input ? (Mon Apr 07 2003 - 00:28:58 CDT)
  • Re: Hydrogen bond energy (Thu Apr 03 2003 - 11:26:04 CST)
  • Re: AMBER pdb help - lost atoms - Part 2 (Thu Apr 03 2003 - 11:23:41 CST)
  • Re: Unit of velocity (Thu Apr 03 2003 - 11:18:11 CST)
  • Re: A weird antechamber error (Wed Apr 02 2003 - 09:24:12 CST)
  • Re: AMBER pdb help - lost atoms (Tue Apr 01 2003 - 20:17:41 CST)
  • Re: Polarizable simulation2 (Tue Apr 01 2003 - 15:49:39 CST)
  • Re: size of a simulation system (Tue Apr 01 2003 - 15:44:14 CST)
  • Re: AMBER pdb help - lost atoms (Tue Apr 01 2003 - 14:19:35 CST)
• David Case
  • Re: AMBER: SHAKE for TIP4P! (Fri Oct 03 2003 - 02:43:43 CDT)
  • Re: AMBER: regarding trajectory input and output with ptraj or Carnal (Thu Oct 02 2003 - 07:54:11 CDT)
  • Re: AMBER: constant pressure in GB (Thu Oct 02 2003 - 06:53:32 CDT)
  • Re: AMBER: density equilibrium & harmonic restrain (Thu Oct 02 2003 - 06:39:05 CDT)
  • Re: AMBER: AMBER quasih question(s) (Thu Oct 02 2003 - 06:34:18 CDT)
  • Re: AMBER: nmanal's error message (Mon Aug 18 2003 - 18:24:11 CDT)
  • Re: xleap crashes (Sat Jan 11 2003 - 00:05:45 CST)
  • Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Fri Jan 03 2003 - 23:46:00 CST)
• David Cowburn
  • Future of structural biology conference (Thu Apr 24 2003 - 13:58:23 CDT)
• David E. Konerding
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 11:04:03 CST)
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 10:57:23 CST)
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 09:53:20 CST)
  • Re: AMBER: mpich problem (Sat Nov 08 2003 - 11:15:34 CST)
  • Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD (Mon Nov 03 2003 - 12:41:08 CST)
  • Re: AMBER: surface code in Amber (Tue Oct 28 2003 - 10:38:56 CST)
  • Re: AMBER: surface code in Amber (Mon Oct 27 2003 - 09:32:41 CST)
  • Re: AMBER: Implicit precision in sander vs architecture (Fri Oct 17 2003 - 12:05:14 CDT)
• David E. Konerding DSD Staff
  • Re: AMBER: sander on cygwin (Mon Sep 15 2003 - 16:21:57 CDT)
  • Re: AMBER: sander on cygwin (Mon Sep 15 2003 - 13:24:29 CDT)
  • AMBER: Using NWCHEM for esp? (Fri Sep 05 2003 - 12:59:45 CDT)
• David Skinner
  • AMBER: PMEMD Performance on IBM SP (Tue Dec 23 2003 - 14:00:45 CST)
• David Smith
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 10:16:26 CST)
  • Re: AMBER: GIBBS - PMF problem: Lambda has not changed (Fri Nov 14 2003 - 04:50:01 CST)
  • Re: AMBER: GIBBS - PMF problem: Lambda has not changed (Thu Nov 13 2003 - 08:00:48 CST)
  • AMBER: frozen x unfrozen and the gibbs tragedy (Thu Oct 23 2003 - 10:56:00 CDT)
  • Re: Re[2]: AMBER: derive corresponding torsional parameters (Fri Aug 08 2003 - 11:20:32 CDT)
  • Re: AMBER: more than 100,000 atoms ? (Fri Aug 08 2003 - 10:17:39 CDT)
  • Re: AMBER: derive corresponding torsional parameters (Fri Aug 08 2003 - 08:39:57 CDT)
  • AMBER: more than 100,000 atoms ? (Thu Aug 07 2003 - 14:44:23 CDT)
  • Re: AMBER: PMF (Wed Jul 16 2003 - 04:37:56 CDT)
  • ifc, gibbs and ewald (Tue Feb 04 2003 - 10:49:53 CST)
  • Gibbs, ewald and ifc (Fri Jan 31 2003 - 16:16:14 CST)
• Derek Smith
  • Problem Finishing Tutorial (Mon Apr 21 2003 - 18:31:00 CDT)
• dianah_at_unm.edu
  • Water density and force output questions (Fri Mar 07 2003 - 17:36:41 CST)
• dicksmit_at_umich.edu
  • Error in minimization using sander_classic of AMBER6 (Tue Jun 17 2003 - 15:20:03 CDT)
  • frcmod file for Free energy perturbation tutorial of valine to alanine (Fri Apr 04 2003 - 12:06:37 CST)
  • (no subject) (Wed Apr 02 2003 - 13:32:37 CST)
• Difei Wang
  • AMBER: gaff errors? (Tue Nov 25 2003 - 18:53:43 CST)
  • AMBER: torsion problems of dummy atoms (Mon Nov 24 2003 - 14:24:11 CST)
• Do Anh Tuan
  • AMBER: segmentation fault (Tue Dec 02 2003 - 22:56:32 CST)
  • AMBER: restart MD program (Wed Nov 26 2003 - 11:12:50 CST)
  • AMBER: MD simulation: enzyme and its substrate (Wed Oct 29 2003 - 13:52:24 CST)
  • AMBER: MD simulation: enzyme and its substrate (Sat Oct 25 2003 - 23:51:20 CDT)
  • AMBER: stable protein (Mon Oct 20 2003 - 12:30:45 CDT)
  • AMBER: C-alpha RMS (Sat Sep 20 2003 - 01:39:42 CDT)
• Dodi Heryadi
  • Re: Increase lastist in the &cntrl namelist (Tue May 13 2003 - 15:14:25 CDT)
• Dominico J Vigil
  • Leap to prep (Mon Mar 03 2003 - 16:26:45 CST)
• Donald Keidel
  • Help with Sander test output error (Fri May 02 2003 - 12:38:11 CDT)
• Donald Thomas
  • Re: AMBER: xLEAP Problem (Sun Sep 21 2003 - 21:37:23 CDT)
• Dr Chris L. Brown
  • LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi (Wed Jan 22 2003 - 21:10:34 CST)
• Dr. Yong Duan
  • Re: AMBER: RNA and Protein questions (also some general questions) (Thu Nov 13 2003 - 09:57:41 CST)
  • Re: AMBER: Separation of a Water molecules (Wed Nov 12 2003 - 23:43:26 CST)
  • Re[2]: AMBER: surface code in Amber (Tue Oct 28 2003 - 08:46:32 CST)
  • Re: AMBER: reporting atoms clashed during simple energy minimization (Tue Sep 09 2003 - 07:18:44 CDT)
  • a bug? Re: AMBER: one more line about the npscal, box size changes and rms (Thu Aug 07 2003 - 10:49:10 CDT)
  • Re: AMBER: dynamics of isolated system (Tue Jul 29 2003 - 15:16:35 CDT)
  • Re: AMBER: dynamics of isolated system (Tue Jul 29 2003 - 14:04:42 CDT)
  • Re: AMBER: Fwd: Minimizing after solvation (Mon Jul 21 2003 - 10:48:00 CDT)
• Dr.K.Veluraja
  • Hydrogen bond energy (Thu Apr 03 2003 - 04:37:02 CST)
• dvira
  • ntx in sander (Sat Jul 12 2003 - 08:00:57 CDT)
• Dvira Segal
  • Ptraj problem with small molecules (Tue Feb 04 2003 - 08:18:11 CST)
  • ptraj on Methane in water box (Fri Jan 31 2003 - 04:45:03 CST)
  • Amber tutorial crown-ether (Tue Jan 21 2003 - 08:06:55 CST)
  • building molecules by script files for leap (Wed Jan 08 2003 - 10:07:57 CST)
  • Small organic molecules (Tue Jan 07 2003 - 09:55:31 CST)
• E.S.
  • nmode on Linux : another memory question (Thu Feb 27 2003 - 16:42:15 CST)
• Eddy
  • [Fwd: MPI problem in modi4.ncsa.uiuc.edu] (Thu Mar 13 2003 - 23:57:23 CST)
• Emmanuel Giudice
  • Re: AMBER: Sander / Anal (Fri Dec 05 2003 - 11:54:20 CST)
  • AMBER: Sander / Anal (Mon Dec 01 2003 - 14:06:00 CST)
  • atom type (Wed Mar 12 2003 - 11:21:18 CST)
• Endres, Robert G.
  • AMBER: problems with pressure control (Tue Dec 30 2003 - 08:38:02 CST)
  • AMBER: ptraj and charmm files (Mon Nov 17 2003 - 09:25:04 CST)
  • RE: AMBER: update of BOX dim. (Fri Nov 14 2003 - 14:23:14 CST)
  • AMBER: update of BOX dim. (Fri Nov 14 2003 - 13:53:21 CST)
  • RE: AMBER: infinitely long DNA (to Yong Duan) (Fri Nov 07 2003 - 14:50:17 CST)
  • AMBER: reduce box and delete excess solvent (Wed Oct 29 2003 - 13:31:52 CST)
  • RE: AMBER: Radius of Gyration and RMSD (Tue Oct 28 2003 - 08:36:27 CST)
  • RE: AMBER: aminoacid mutation (Mon Oct 27 2003 - 21:02:15 CST)
  • AMBER: RMSD and Radius of Gyration (Sat Oct 25 2003 - 17:24:07 CDT)
  • RE: AMBER: Simulation of small protein (Thu Oct 23 2003 - 20:28:21 CDT)
  • RE: AMBER: Simulation of small protein (Thu Oct 23 2003 - 12:27:45 CDT)
  • AMBER: Simulation of small protein (Thu Oct 23 2003 - 10:52:52 CDT)
  • AMBER: infinitely long DNA & moil-view? (Tue Oct 14 2003 - 13:57:43 CDT)
  • AMBER: parm. and top. for sugars, charmm? (Mon Sep 08 2003 - 11:05:00 CDT)
  • AMBER: amber-on-cheetah-question (Wed Aug 13 2003 - 14:20:10 CDT)
• ENikitina
  • AMBER: (no subject) (Tue Jul 22 2003 - 10:53:56 CDT)
  • Re: AMBER: Big system in Gibbs (Tue Jul 22 2003 - 10:40:07 CDT)
  • AMBER: Big system in Gibbs (Thu Jul 17 2003 - 01:01:23 CDT)
  • Ar as a solvent (Wed Jul 09 2003 - 06:42:47 CDT)
  • VdW in FEP (Wed Jun 18 2003 - 09:02:14 CDT)
  • Re: VdW in FEP (Tue Jun 10 2003 - 06:56:23 CDT)
  • VdW in FEP (Mon Jun 09 2003 - 02:06:49 CDT)
• Eric Hu
  • AMBER: minimize a covalently bounded protein-ligand complex (Thu Oct 30 2003 - 17:36:53 CST)
  • seperate one trajectory file into two (Thu Feb 27 2003 - 21:02:58 CST)
  • no statistics.out in mm_pbsa binding energy calculations (Wed Feb 19 2003 - 12:27:10 CST)
  • mm_pbsa energy unit (Mon Feb 10 2003 - 13:22:38 CST)
  • noninteger charge (Wed Feb 05 2003 - 12:03:08 CST)
  • Re: desolvation energy in mm_pbsa (Tue Feb 04 2003 - 14:38:18 CST)
  • desolvation energy in mm_pbsa (Mon Feb 03 2003 - 20:36:44 CST)
  • trajectory file in mm_pbsa (Mon Feb 03 2003 - 20:11:21 CST)
  • Re: average structure generated by carnal (Tue Jan 21 2003 - 15:02:34 CST)
  • average structure generated by carnal (Tue Jan 21 2003 - 12:53:49 CST)
  • reduce the disk space (Tue Jan 21 2003 - 12:48:14 CST)
  • scripts for compiling UHBD/MEAD with amber 7.0 (Mon Jan 20 2003 - 11:54:37 CST)
  • Re: virtual box (Wed Jan 08 2003 - 01:35:21 CST)
  • Re: virtual box (Wed Jan 08 2003 - 01:35:09 CST)
  • virtual box (Tue Jan 07 2003 - 17:26:15 CST)
• Fabian Boes
  • ptraj generated PDB files (Fri May 16 2003 - 09:01:38 CDT)
  • unit of vlimit? (Mon May 12 2003 - 09:36:25 CDT)
  • boron parameters (Mon Feb 03 2003 - 11:51:20 CST)
• Fabrice Yerly
  • Compilation error of Amber 7 using pgi and mpich on Linux Cluster (Tue Feb 25 2003 - 07:02:00 CST)
• Fajar Rakhman Wibowo
  • AMBER: lifetime in ptraj hbond (Fri Dec 12 2003 - 03:28:45 CST)
• Fan Gao
  • AMBER: initial velocity (Fri Dec 19 2003 - 18:56:16 CST)
  • one question (Tue Jan 28 2003 - 10:14:56 CST)
• Fernando Martin
  • Pi-Pi stacking (Tue May 06 2003 - 12:35:45 CDT)
• Filip Razga
  • Superimposed trajectory (Tue Jun 10 2003 - 08:59:06 CDT)
• Filip RyjXcek
  • old prmtop format in AMBER 6 differs from what is presented in AMBER 7 manual (Wed Apr 02 2003 - 06:29:07 CST)
• Florent Barbault
  • AMBER: a simple question about HBond energy... (Thu Dec 11 2003 - 02:04:27 CST)
• Florian Barth
  • Amber7 on Opteron (Thu Jul 10 2003 - 05:46:32 CDT)
  • Re: ambpdb (Wed Apr 16 2003 - 06:59:42 CDT)
  • Re: Amber7 & mpich (Tue Feb 04 2003 - 17:39:51 CST)
  • Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Sat Jan 04 2003 - 00:36:27 CST)
• Francesc Corcho
  • Bugfixes (Fri Apr 11 2003 - 06:40:08 CDT)
  • RE: Amber7 and mpirun on Linux (Fri Apr 11 2003 - 06:28:32 CDT)
• Francisco Blanco
  • HBOND energies in sander (Sun May 25 2003 - 06:37:52 CDT)
  • IR6 and makeDIST-RST (Sat May 24 2003 - 14:15:29 CDT)
  • ambpdb and protonate in AMBER7 (Thu Apr 17 2003 - 06:38:29 CDT)
• franck
  • AMBER: Diffusion constant (Sat Nov 15 2003 - 13:00:56 CST)
  • AMBER: Compiling AMBER (Thu Oct 09 2003 - 09:16:17 CDT)
• Franck Chevalier
  • PBC without solvent (Tue Mar 18 2003 - 04:37:55 CST)
  • parameters GB/SA (Mon Mar 03 2003 - 09:41:52 CST)
  • GB/SA (Mon Feb 24 2003 - 03:04:22 CST)
• Frank Boeckler
  • AMBER: usability of mm_pbsa with ligand - membrane protein - complex (Thu Aug 28 2003 - 17:20:09 CDT)
• Frederico.Miranda_at_ibmb.uib.no
  • AMBER: restarted MD and ptraj (Wed Nov 26 2003 - 19:35:35 CST)
  • AMBER: sander lastist (Sat Nov 15 2003 - 04:01:57 CST)
  • AMBER: average coordinates (Wed Nov 12 2003 - 11:47:33 CST)
  • Re: AMBER: Protein Rotation (Tue Nov 11 2003 - 08:52:44 CST)
  • AMBER: Protein Rotation (Tue Nov 11 2003 - 06:47:44 CST)
  • AMBER: Restart a simulation (Tue Nov 04 2003 - 13:21:03 CST)
  • AMBER: carnal (Sun Oct 19 2003 - 14:48:06 CDT)
  • AMBER: Carnal Input file (Mon Sep 22 2003 - 18:06:55 CDT)
  • RE: AMBER: AMBER Carnal files (Sun Sep 21 2003 - 19:09:01 CDT)
  • AMBER: AMBER Carnal files (Sat Sep 20 2003 - 17:24:12 CDT)
  • Problem with Snader (Sat Jun 28 2003 - 08:17:12 CDT)
  • Memory problem (Tue Jun 24 2003 - 19:17:40 CDT)
  • Problem with a library (Fri Jun 13 2003 - 15:27:36 CDT)
  • PROBLEM WITH LIBRARY (Thu Jun 05 2003 - 15:06:27 CDT)
  • Phosphorylated Serine Library (Fri May 30 2003 - 03:01:31 CDT)
  • Does Leap has a problem with Isoleucines? (Wed May 28 2003 - 01:28:21 CDT)
• FUNG WAI KEUNG
  • Question about defining force field (followup) (Tue Jun 24 2003 - 23:14:10 CDT)
  • Question about defining force field (Fri Jun 20 2003 - 22:12:59 CDT)
• FyD
  • Re: AMBER: Basic potential question: (Wed Dec 24 2003 - 12:35:22 CST)
  • AMBER: Resp Esp charge Derive (RED v-1.0) release (Wed Dec 03 2003 - 13:09:39 CST)
  • Re: AMBER: charge fitting (Fri Nov 28 2003 - 12:45:21 CST)
  • Re: AMBER: charge fitting (Tue Nov 25 2003 - 10:42:56 CST)
  • Re: AMBER: Lone pairs and resp (Mon Nov 17 2003 - 20:06:57 CST)
  • Re: AMBER: RESP charge (Mon Nov 17 2003 - 16:27:25 CST)
  • Re: AMBER: RNA and Protein questions (also some general questions) (Thu Nov 13 2003 - 10:45:33 CST)
  • Re: AMBER: addions/xleap question (Wed Oct 01 2003 - 16:24:38 CDT)
  • AMBER: addions/xleap question (Wed Oct 01 2003 - 15:39:47 CDT)
  • Re: AMBER: Using NWCHEM for esp? (Sun Sep 07 2003 - 16:19:33 CDT)
  • AMBER: AmberFFC v1.3 released (Fri Aug 29 2003 - 11:35:12 CDT)
  • Comparative MD (Fri Jul 11 2003 - 08:29:02 CDT)
  • Re: GAFF in GUI MD apps (Wed Jun 25 2003 - 00:50:58 CDT)
  • 2 questions (Fri May 09 2003 - 05:02:41 CDT)
  • Re: Description of ATOM type in GLYCAM (Tue Apr 29 2003 - 16:07:35 CDT)
  • mm_pbsa & nmode (Tue Apr 08 2003 - 10:04:38 CDT)
  • Script and MPICH (Fri Mar 21 2003 - 08:01:40 CST)
  • xleap crash under Irix (Thu Feb 13 2003 - 13:46:07 CST)
  • Re: Amber7 & mpich (Wed Feb 05 2003 - 08:58:25 CST)
  • Amber7 & mpich (Tue Feb 04 2003 - 08:27:23 CST)
  • AMBER7 & mpich (Fri Jan 31 2003 - 08:05:41 CST)
• Gaurav Sahni
  • Re: AMBER: Insight pdb file in xleap (Fri Aug 08 2003 - 01:25:42 CDT)
• Gemma Kinsella
  • Helical Drift (Fri Mar 21 2003 - 10:55:17 CST)
  • Lipids (Tue Mar 18 2003 - 02:43:16 CST)
  • Protein Reorientation (Mon Mar 03 2003 - 07:54:48 CST)
• Ghislain Deslongchamps
  • AMBER/FEP: RESP charges (Fri Mar 14 2003 - 07:37:13 CST)
• Giovanni
  • AMBER: MM-PBSA question (Wed Dec 03 2003 - 12:10:10 CST)
• Giulio Rastelli
  • Re: AMBER: mgbjsb radii in GBSA (Sat Nov 15 2003 - 11:05:49 CST)
  • Re: AMBER: atmtypenumbers for halogens (Fri Nov 14 2003 - 09:00:41 CST)
  • Re: AMBER: mgbjsb radii in GBSA (Mon Nov 10 2003 - 17:02:00 CST)
  • AMBER: mgbjsb radii in GBSA (Mon Nov 10 2003 - 10:39:18 CST)
  • AMBER: mgbjsb Radii in GBSA (Tue Oct 07 2003 - 09:42:34 CDT)
  • protonate (Sun Jun 29 2003 - 16:31:20 CDT)
  • pol_h (Tue Jun 03 2003 - 11:34:23 CDT)
  • antechamber -rn keyword (Tue Mar 25 2003 - 17:06:48 CST)
  • writing mol2 files using antechamber (Sat Mar 22 2003 - 17:41:41 CST)
  • three digits in the charges of extPDB (Fri Mar 07 2003 - 18:27:48 CST)
  • Re: ptraj residue number out of range (Tue Feb 25 2003 - 17:35:24 CST)
  • ptraj residue number out of range (Tue Feb 25 2003 - 11:20:30 CST)
• gold gunaseelan
  • AMBER: parallelisation (Tue Aug 05 2003 - 08:55:31 CDT)
  • AMBER: sanderparallel (Mon Aug 04 2003 - 02:32:48 CDT)
  • AMBER: parallelisation (Fri Aug 01 2003 - 01:12:33 CDT)
  • AMBER: parallelisation (Fri Aug 01 2003 - 01:13:21 CDT)
  • AMBER: parallelisation (Thu Jul 31 2003 - 07:42:32 CDT)
  • AMBER: parallelisation (Thu Jul 31 2003 - 07:42:25 CDT)
  • parallelisation (Mon Jul 14 2003 - 10:48:56 CDT)
  • parallelisation (Fri Jul 11 2003 - 10:06:43 CDT)
  • parallelisation (Mon Jul 07 2003 - 08:32:00 CDT)
• Guanglei Cui
  • Re: delphi with amber 7 (Fri Jul 11 2003 - 15:44:09 CDT)
  • Re: Problem with Snader (Sat Jun 28 2003 - 09:53:59 CDT)
  • Re: any tool to know what functions are being called while sander is being run?? (Wed Jun 11 2003 - 08:53:45 CDT)
  • Re: May I get you help from new user of amber? (Mon Jun 09 2003 - 09:41:07 CDT)
  • Re: MD problem (Thu May 29 2003 - 16:28:07 CDT)
  • Re: MD problem (Thu May 29 2003 - 16:14:14 CDT)
  • Re: saveAmberParm problems in xleap (Tue May 06 2003 - 08:42:13 CDT)
  • Re: can not minimize (Mon May 05 2003 - 09:07:39 CDT)
  • Re: can not minimize (Mon May 05 2003 - 08:42:37 CDT)
  • Re: phi and psi angles analysis (Tue Apr 29 2003 - 22:31:11 CDT)
  • Re: question about lysine? (Wed Feb 26 2003 - 21:20:43 CST)
• GUILBAUD Philippe 153683
  • keeping pdb residues numbers ? (Wed Jun 04 2003 - 07:48:50 CDT)
  • polarization + ewald (Mon Jan 27 2003 - 05:21:44 CST)
• GUILLERMINA L ESTIU
  • AMBER: output frequency (Mon Oct 06 2003 - 08:43:26 CDT)
  • AMBER: residues and molecules (Tue Sep 23 2003 - 16:56:01 CDT)
  • AMBER: performance vs number of processors (Mon Sep 15 2003 - 13:58:37 CDT)
  • Re: AMBER: strange problem with a small system (Mon Jul 28 2003 - 11:00:55 CDT)
  • Re: AMBER: strange problem with a small system (Wed Jul 23 2003 - 14:13:47 CDT)
  • AMBER: addition to: problem with a small system (Wed Jul 23 2003 - 13:36:03 CDT)
  • AMBER: strange problem with a small system (Wed Jul 23 2003 - 12:22:34 CDT)
  • carnal in big systems (Tue Jul 08 2003 - 13:44:21 CDT)
  • Re: water box distortion (Sat May 24 2003 - 10:34:11 CDT)
  • water box distortion (Fri May 23 2003 - 15:36:17 CDT)
  • Re: Increase lastist in the &cntrl namelist (Tue May 13 2003 - 13:37:24 CDT)
  • Increase lastist in the &cntrl namelist (Tue May 13 2003 - 13:16:09 CDT)
  • topology file in large systems (Thu Apr 17 2003 - 16:58:35 CDT)
  • ambpdb (Fri Mar 28 2003 - 11:05:09 CST)
  • Re: tleap in large systems (Thu Mar 27 2003 - 14:57:21 CST)
  • tleap in large systems (Wed Mar 26 2003 - 10:36:11 CST)
  • waterbox (Fri Mar 21 2003 - 16:22:41 CST)
  • Re: shake and belly (Wed Jan 22 2003 - 12:47:30 CST)
  • shake and belly (Tue Jan 21 2003 - 15:38:59 CST)
  • solvatecap (Wed Jan 15 2003 - 08:48:05 CST)
  • solvatecap (Tue Jan 14 2003 - 14:33:16 CST)
• Guoxi Zhang
  • questions about AMBER (Sun Feb 02 2003 - 20:57:21 CST)
• Gus Carri
  • Lennard-Jones A and B coefficients (Tue Jul 08 2003 - 17:53:56 CDT)
  • Nmanal (Wed Jul 02 2003 - 16:26:50 CDT)
  • Nmode doesn't work ? (Tue Jul 01 2003 - 16:09:11 CDT)
• Gustavo A. Carri
  • AMBER: How to develop parameters for metallic atoms (Mon Aug 11 2003 - 16:11:19 CDT)
  • Glycerol Parameters (Wed Mar 26 2003 - 18:20:55 CST)
• hagop demirdjian
  • AMBER: handling non neutral systems (Thu Nov 06 2003 - 09:31:19 CST)
  • AMBER: altering mass in .top file (Thu Sep 11 2003 - 04:07:02 CDT)
  • roar-cp : input for QM part ; output for CM2 charges (Fri Jan 31 2003 - 09:38:29 CST)
  • morse potential (Mon Jan 20 2003 - 10:22:03 CST)
• Hai-Long Wang
  • AMD opteron (Tue May 27 2003 - 10:57:39 CDT)
  • carnal hbond (Wed Apr 30 2003 - 13:03:39 CDT)
  • anal question (Thu Apr 03 2003 - 15:48:11 CST)
• Haizhen Zhong
  • Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms (Thu Aug 07 2003 - 12:54:17 CDT)
  • AMBER: one more line about the npscal, box size changes and rms (Thu Aug 07 2003 - 09:58:31 CDT)
  • AMBER: about the npscal, box size changes and rms (Thu Aug 07 2003 - 09:05:08 CDT)
  • Re: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 13:08:39 CDT)
  • RE: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 11:25:38 CDT)
  • AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 09:16:40 CDT)
  • Re: AMBER: Questions about mm_pbsa and alanine scanning (Wed Jul 16 2003 - 08:04:30 CDT)
  • Re: AMBER: Questions about mm_pbsa and alanine scanning (Tue Jul 15 2003 - 16:01:47 CDT)
  • AMBER: Questions about mm_pbsa and alanine scanning (Tue Jul 15 2003 - 15:34:32 CDT)
• Harikrishnan
  • Re: Protein - DNA complex simulation - protocol (Tue Apr 29 2003 - 08:16:25 CDT)
  • Re: any one has references to parallelization aspects of AMBER (Tue Apr 29 2003 - 06:54:51 CDT)
  • Protein - DNA complex simulation - protocol (Mon Apr 28 2003 - 23:40:39 CDT)
• Heather A.Carlson
  • AMBER: length of deltaG calcs (Mon Dec 15 2003 - 09:32:48 CST)
  • Re: AMBER: MD simulation with ATP and MG (Mon Aug 11 2003 - 07:11:27 CDT)
• Heike Meiselbach
  • Proper torsion parameters missing? (Thu Jan 23 2003 - 13:05:05 CST)
• Helios Chen
  • Re: AMBER: fix some area (Sun Nov 09 2003 - 19:21:42 CST)
  • AMBER: fix some area (Fri Nov 07 2003 - 03:06:06 CST)
  • AMBER: prepin file (Tue Aug 19 2003 - 01:53:27 CDT)
  • Re: AMBER: charge method of antechamber(it's ok) (Mon Aug 18 2003 - 08:15:28 CDT)
  • Re: AMBER: charge method of antechamber (Mon Aug 18 2003 - 07:39:18 CDT)
  • AMBER: charge method of antechamber (Sun Aug 03 2003 - 23:00:35 CDT)
• Herbert de Castro Georg
  • AMBER: Compaq Tru64 Unix (Fri Nov 21 2003 - 15:37:07 CST)
• Herbert Georg
  • Re: AMBER: minimization on sander (Mon Dec 15 2003 - 15:21:13 CST)
  • AMBER: minimization on sander (Mon Dec 15 2003 - 14:05:25 CST)
  • Re: AMBER: Compiling on Suse 9 Pro with ifc... (Thu Dec 04 2003 - 06:56:55 CST)
  • Re: AMBER: Compiling on Suse 9 Pro with ifc... (Wed Dec 03 2003 - 13:13:42 CST)
  • Re: AMBER: Compiling on Suse 9 Pro with ifc... (Wed Dec 03 2003 - 08:04:30 CST)
  • Re: AMBER: Compiling on Suse 9 Pro with ifc... (Wed Dec 03 2003 - 07:26:07 CST)
  • AMBER: Compiling on Suse 9 Pro with ifc... (Mon Dec 01 2003 - 13:17:15 CST)
  • AMBER: Compiling AMBER7 on Suse (Tue Nov 18 2003 - 07:08:06 CST)
  • Re: AMBER: prmtop file format (Fri Oct 24 2003 - 13:51:50 CDT)
  • AMBER: prmtop file format (Fri Oct 24 2003 - 09:37:42 CDT)
  • AMBER: SHAKE question (Thu Oct 23 2003 - 17:17:45 CDT)
  • Re: AMBER: frozen x unfrozen (Thu Oct 23 2003 - 09:25:20 CDT)
  • AMBER: antechamber and bond type (Wed Oct 22 2003 - 07:56:15 CDT)
  • AMBER: frozen x unfrozen (Tue Oct 21 2003 - 14:04:44 CDT)
  • Re: AMBER: double bonds in prmtop (Fri Sep 19 2003 - 16:27:53 CDT)
  • AMBER: double bonds in prmtop (Fri Sep 19 2003 - 15:09:16 CDT)
  • AMBER: processors (Mon Sep 01 2003 - 14:30:04 CDT)
  • Re: AMBER: NTT (Thu Aug 21 2003 - 14:48:17 CDT)
  • AMBER: NTT (Thu Aug 21 2003 - 11:31:06 CDT)
  • AMBER: GLYCAM (Mon Aug 11 2003 - 15:57:37 CDT)
  • Re: AMBER: dynamics of isolated system (Tue Jul 29 2003 - 14:27:15 CDT)
  • Re: AMBER: dynamics of isolated system (Tue Jul 29 2003 - 14:05:45 CDT)
  • AMBER: dynamics of isolated system (Tue Jul 29 2003 - 13:19:18 CDT)
  • input problem (Tue Jul 01 2003 - 14:12:23 CDT)
• Holger Gohlke
  • Re: AMBER: nmode statistics (Thu Dec 18 2003 - 01:09:05 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 10:10:05 CST)
  • Re: AMBER: nmode, trajectory (Sat Dec 13 2003 - 09:42:39 CST)
  • Re: AMBER: ANAL/MMPBSA (Thu Dec 04 2003 - 02:42:06 CST)
  • Re: AMBER: MM-PBSA question (Wed Dec 03 2003 - 12:58:23 CST)
  • Re: AMBER: Re: Nmode problem (Mon Dec 01 2003 - 08:17:37 CST)
  • AMBER: Re: Nmode problem (Sun Nov 30 2003 - 09:24:50 CST)
  • Re: AMBER: Nmode problem (Fri Nov 28 2003 - 09:11:49 CST)
  • Re: AMBER: mm_pbsa and antechamber (Mon Nov 24 2003 - 13:37:02 CST)
  • Re: AMBER: MM_PB/GB/SA (Thu Nov 20 2003 - 06:36:30 CST)
  • Re: AMBER: Nmode Problem (Thu Nov 13 2003 - 13:13:45 CST)
  • Re: AMBER: GB/SA (Tue Nov 11 2003 - 14:47:59 CST)
  • Re: AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD (Fri Nov 07 2003 - 02:23:29 CST)
  • Re: AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs (Thu Nov 06 2003 - 01:24:42 CST)
  • Re: AMBER: charge definition (Sat Sep 06 2003 - 14:00:01 CDT)
  • Re: AMBER: surften value in mm_gbsa/mm_pbsa calculations (Tue Sep 02 2003 - 15:30:15 CDT)
  • Re: AMBER: usability of mm_pbsa with ligand - membrane protein - complex (Thu Aug 28 2003 - 18:01:11 CDT)
  • Re: AMBER: Fxnal form of NMR-style restraints (Thu Aug 28 2003 - 17:41:04 CDT)
  • Re: AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands (Mon Aug 18 2003 - 10:50:49 CDT)
  • Re: AMBER: secondary structure (Wed Aug 13 2003 - 09:55:22 CDT)
  • Re: AMBER: mpi in mm-pbsa (Thu Aug 07 2003 - 14:22:53 CDT)
  • Re: AMBER: monitor vdw along time (Fri Jul 25 2003 - 13:56:28 CDT)
  • Re: AMBER: (no subject) (Thu Jul 24 2003 - 10:38:15 CDT)
  • Re: Another mm_pbsa problem (Tue Jun 24 2003 - 12:08:25 CDT)
  • Re: mm_pbsa problem (Fri Jun 20 2003 - 20:47:21 CDT)
  • Re: jarrod (Thu Jun 12 2003 - 10:18:43 CDT)
  • Re: mm_pbsa error message (Sun Jun 08 2003 - 11:19:24 CDT)
  • Re: unit of output velocity (Fri Jun 06 2003 - 10:46:38 CDT)
  • Re: Does Leap has a problem with Isoleucines? (Wed May 28 2003 - 11:14:47 CDT)
  • Re: mm_gbsa question (Tue May 27 2003 - 20:40:36 CDT)
  • Re: Order parameters (Tue May 27 2003 - 14:15:15 CDT)
  • Re: EWALD BOMB (Mon May 26 2003 - 14:58:00 CDT)
  • Re: HBOND energies in sander (Mon May 26 2003 - 12:24:01 CDT)
  • Re: water box distortion (Sat May 24 2003 - 20:26:21 CDT)
  • Re: Questions about statistics output of mm_pbsa? (Thu May 22 2003 - 16:41:32 CDT)
  • Re: bad atom type f(fluorine) in MM-PBSA? (Wed May 21 2003 - 10:49:20 CDT)
  • Re: mm_pbsa with PBCAL = 0 (Fri May 16 2003 - 16:34:41 CDT)
  • Re: atomic positional fluctuation (Thu May 15 2003 - 15:38:07 CDT)
  • Re: SPC/E water model (Sun May 04 2003 - 18:27:01 CDT)
  • Re: phi and psi angles analysis (Tue Apr 29 2003 - 18:48:50 CDT)
  • Re: nmode and mm_pbsa questions? (Fri Apr 25 2003 - 17:21:05 CDT)
  • Re: mm_pbsa nmode calculation (Wed Apr 23 2003 - 14:12:51 CDT)
  • Re: question about MM-PBSA? (Thu Apr 17 2003 - 20:31:31 CDT)
  • Re: No statistical output for MM-PBSA? (Wed Apr 16 2003 - 13:05:38 CDT)
  • Re: ALA-scan problem with mm_pbsa.pl (Wed Apr 16 2003 - 12:40:44 CDT)
  • Re: Side-chain/main-chain decomposition in MM-GBSA (Thu Apr 03 2003 - 16:46:52 CST)
  • Re: unit of energy (Fri Mar 28 2003 - 18:36:02 CST)
  • Re: sander outputs (Fri Mar 28 2003 - 18:26:10 CST)
  • Re: question about mm_pbsa? (Tue Mar 18 2003 - 15:05:29 CST)
  • Re: Question about mm_pbsa? (Tue Mar 18 2003 - 11:06:20 CST)
  • Barium (Mon Mar 10 2003 - 10:21:20 CST)
  • Re: question about mm_pbsa (Sun Mar 09 2003 - 21:31:10 CST)
  • Re: seperate one trajectory file into two (Thu Feb 27 2003 - 21:45:50 CST)
  • Re: ptraj residue number out of range (Tue Feb 25 2003 - 11:31:14 CST)
  • Re: ptraj residue number out of range (Tue Feb 25 2003 - 10:24:00 CST)
  • Re: Nmode (Thu Feb 20 2003 - 12:35:57 CST)
  • Re: Energy calculation (Wed Feb 19 2003 - 16:54:30 CST)
  • Re: no statistics.out in mm_pbsa binding energy calculations (Wed Feb 19 2003 - 12:48:59 CST)
  • Re: mm_pbsa (Tue Feb 18 2003 - 18:13:51 CST)
  • Re: delphi and charge file (Wed Feb 12 2003 - 16:43:39 CST)
  • Re: mm_pbsa energy unit (Mon Feb 10 2003 - 13:48:51 CST)
  • [Fwd: Re: Backbone torsional angles' format?] (Fri Feb 07 2003 - 18:23:15 CST)
  • Re: Carnal DECLARE of TORSION problem (Fri Feb 07 2003 - 12:34:07 CST)
  • Re: Misaligned Coords from Alanine Scanning (Fri Feb 07 2003 - 10:00:31 CST)
  • Re: desolvation energy in mm_pbsa (Tue Feb 04 2003 - 14:59:21 CST)
  • [Fwd: Re: trajectory file in mm_pbsa] (Tue Feb 04 2003 - 11:47:08 CST)
  • Re: mm-pbsa problem & possible solution (Thu Jan 30 2003 - 11:22:39 CST)
  • Re: MM_PBSA (Wed Jan 29 2003 - 09:24:58 CST)
  • Re: one question (Tue Jan 28 2003 - 10:17:02 CST)
  • Re: script for Potential/kinectic energy (Mon Jan 20 2003 - 10:44:13 CST)
  • Re: mm_pbsa -- COMPT must be specified (correctly) (Mon Jan 13 2003 - 11:01:10 CST)
  • Re: mm_gbsa error message (Wed Jan 08 2003 - 15:52:31 CST)
  • Re: mm_pbsa question (Tue Jan 07 2003 - 18:41:30 CST)
• Huang Zunnan
  • A simple question about offset, want to make sure (Sat May 31 2003 - 11:44:46 CDT)
  • What kind of interactions are ignored for end group interactions (Fri May 09 2003 - 15:41:10 CDT)
• Hyonseok Hwang
  • AMBER: charmm force field in amber (Thu Oct 16 2003 - 13:05:36 CDT)
• ian r gould
  • Opteron Experience (Thu Jul 10 2003 - 08:29:38 CDT)
• Ioana Cozmuta
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 13:14:40 CST)
  • Re: AMBER: What does this error message mean? (Fri Oct 31 2003 - 09:46:46 CST)
  • RE: AMBER: aminoacid mutation (Tue Oct 28 2003 - 14:25:53 CST)
  • AMBER: aminoacid mutation (Mon Oct 27 2003 - 18:46:13 CST)
  • AMBER: force field for hybrid systems (Sun Oct 12 2003 - 12:58:41 CDT)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 17:30:26 CDT)
  • Re: AMBER: double bonds in prmtop (Fri Sep 19 2003 - 15:24:18 CDT)
  • AMBER: forces estimation (Thu Aug 28 2003 - 13:54:52 CDT)
  • AMBER: overlap problem (Mon Aug 18 2003 - 16:26:57 CDT)
  • Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. (Sun Aug 17 2003 - 22:08:00 CDT)
  • Re: AMBER: 2D periodic box (Thu Aug 07 2003 - 12:00:22 CDT)
  • AMBER: chage WATBOX216 (Thu Jul 31 2003 - 16:10:44 CDT)
  • AMBER: question about ptraj (Wed Jul 30 2003 - 17:07:21 CDT)
  • AMBER: HB dynamics in water and Ion solvation free energies (Tue Jul 22 2003 - 17:09:41 CDT)
  • AMBER: question on LJ parameters for molecules (Mon Jul 14 2003 - 19:38:58 CDT)
  • diffusion in ptraj (Mon Jul 07 2003 - 16:56:56 CDT)
  • ptraj (Mon Jul 07 2003 - 14:06:13 CDT)
  • Re: unifying trajectory files (Wed Jun 25 2003 - 14:58:39 CDT)
  • ptraj question (Tue Jun 24 2003 - 02:59:48 CDT)
  • perl question (Fri Jun 20 2003 - 17:28:57 CDT)
  • center command (Fri May 23 2003 - 16:40:50 CDT)
  • Re: non-periodic system (Wed May 21 2003 - 21:47:34 CDT)
  • non-periodic system (Wed May 21 2003 - 17:50:18 CDT)
  • Re: off-diagonal VDW term (Mon May 19 2003 - 20:24:34 CDT)
  • Re: nucgen.dat (Thu May 15 2003 - 15:08:50 CDT)
  • Re: H-O-H angle (Tue May 13 2003 - 23:32:17 CDT)
  • Re: Increase lastist in the &cntrl namelist (Tue May 13 2003 - 15:26:48 CDT)
  • H-O-H angle (Tue May 13 2003 - 15:17:54 CDT)
  • Re: Increase lastist in the &cntrl namelist (Tue May 13 2003 - 13:58:09 CDT)
  • Re: 10-12 H-bond terms (Mon May 12 2003 - 18:32:19 CDT)
  • Re: 10-12 H-bond terms (Mon May 12 2003 - 14:50:40 CDT)
  • 10-12 H-bond terms (Fri May 09 2003 - 17:27:53 CDT)
  • Re: SPC/E water model (Wed May 07 2003 - 03:53:43 CDT)
  • Re: saveAmberParm problems in xleap (Tue May 06 2003 - 15:54:49 CDT)
  • SPC/E model -LJ parameters (Sun May 04 2003 - 16:55:53 CDT)
  • SPC/E water model (Sun May 04 2003 - 16:38:06 CDT)
  • multiple timesteps (Fri May 02 2003 - 17:41:51 CDT)
  • Re: Problem Finishing Tutorial (Mon Apr 21 2003 - 18:41:13 CDT)
  • characteristics of nucleic acids homopolymers (Tue Apr 08 2003 - 13:33:03 CDT)
  • Re: Using MPI, PBS (Wed Apr 02 2003 - 13:13:01 CST)
  • Re: size of a simulation system (Wed Apr 02 2003 - 12:37:40 CST)
  • Re: AMBER pdb help - lost atoms (Tue Apr 01 2003 - 16:21:46 CST)
  • sequence (Tue Mar 11 2003 - 19:23:02 CST)
  • adjust virial (Tue Feb 25 2003 - 02:15:45 CST)
  • RE: failure of minimization (Mon Feb 24 2003 - 17:11:23 CST)
  • RE: failure of minimization (Mon Feb 24 2003 - 13:33:58 CST)
  • Re: minimization with fixed UC dimensions (Fri Feb 21 2003 - 19:24:32 CST)
  • failure of minimization (Fri Feb 21 2003 - 19:10:37 CST)
  • minimization with fixed UC dimensions (Fri Feb 21 2003 - 13:38:01 CST)
  • one time evaluation (Mon Feb 17 2003 - 18:14:32 CST)
  • compatibility of amber with NAMD (Thu Feb 13 2003 - 12:42:41 CST)
  • references (Mon Feb 10 2003 - 20:22:51 CST)
  • Re: crystal structure of DNA/RNA homopolymers (Mon Jan 27 2003 - 13:54:18 CST)
  • crystal structure of DNA/RNA homopolymers (Mon Jan 27 2003 - 13:34:13 CST)
  • question on ptraj (Wed Jan 22 2003 - 15:01:26 CST)
  • nucleic acid structures (Fri Jan 17 2003 - 19:12:35 CST)
• Itziar Maestre Asenjo
  • Re: AMBER: charge fitting (Thu Nov 27 2003 - 03:00:58 CST)
  • AMBER: charge fitting (Tue Nov 25 2003 - 02:28:05 CST)
  • AMBER: mm_pbsa with amber7 (Tue Oct 14 2003 - 11:22:18 CDT)
  • AMBER: Re:mm_pbsa problem (Mon Oct 13 2003 - 04:18:38 CDT)
  • AMBER: FEP problem (Thu Sep 18 2003 - 07:35:37 CDT)
  • AMBER: SHAKE poblem with dummy atoms (Tue Sep 09 2003 - 05:06:57 CDT)
  • Re: AMBER: parm. and top. for sugars, charmm? (Tue Sep 09 2003 - 00:57:27 CDT)
• jackie_at_ibms.sinica.edu.tw
  • AMBER: reporting atoms clashed during simple energy minimization (Tue Sep 09 2003 - 05:19:36 CDT)
• Jagannadh B
  • AMBER: Paramters for beta and gamma peptides (Thu Dec 04 2003 - 06:34:43 CST)
  • AMBER: Radius of Gyration and RMSD (Tue Oct 28 2003 - 03:36:55 CST)
• Jake Isaacs
  • current AMBER citation? (Thu May 08 2003 - 09:08:38 CDT)
  • converting amber to gromos format (Wed Apr 23 2003 - 08:59:19 CDT)
  • coordinates for quasih (Mon Jan 13 2003 - 08:43:54 CST)
  • pdb_to_mass (Fri Jan 10 2003 - 14:42:35 CST)
• james tomomi macdonald
  • AMBER: high temperature, 498K, unfolding simulations (Thu Nov 13 2003 - 10:19:05 CST)
  • AMBER: problems with pmemd (Fri Aug 22 2003 - 10:37:34 CDT)
  • Re: AMBER: pmemd (Mon Aug 18 2003 - 14:52:32 CDT)
  • RE: AMBER: large changes in xyz coordinates (Mon Aug 18 2003 - 13:35:18 CDT)
  • Re: AMBER: pmemd (Mon Aug 18 2003 - 11:05:20 CDT)
  • AMBER: pmemd (Mon Aug 18 2003 - 10:18:47 CDT)
• James W. Caldwell
  • Re: AMBER: MeCNBOX (Thu Sep 25 2003 - 16:04:03 CDT)
• Jarrod Smith
  • AMBER mail reflector archive (Mon Feb 10 2003 - 14:37:09 CST)
• Jarrod Wesley Barnes
  • jarrod (Thu Jun 12 2003 - 09:51:33 CDT)
• Jash, Panchatapa
  • Probelm with the generation of topology file (Tue Jan 21 2003 - 12:01:45 CST)
• Javier Cuervo
  • pyroglutamic acid (PCA) (Wed Jun 25 2003 - 20:16:44 CDT)
  • Minimization does not converge. (Tue Jun 10 2003 - 22:14:43 CDT)
  • mm_gbsa question (Tue May 27 2003 - 19:49:18 CDT)
  • Calcium in proteins (Mon May 19 2003 - 19:11:54 CDT)
  • MM-GBSA question (Fri Apr 18 2003 - 15:39:23 CDT)
  • Groups defenition (Tue Apr 08 2003 - 15:31:27 CDT)
• jaw3_at_cec.wustl.edu
  • coordinate files from carnal (Thu May 29 2003 - 09:13:25 CDT)
• Jean-François Taly
  • AMBER: STREAM problems : segmentation fault with CARNAL (Wed Oct 15 2003 - 05:03:35 CDT)
  • translational and rotational motion (more information) (Thu May 22 2003 - 08:25:49 CDT)
  • rotational and translational motion (Thu May 22 2003 - 07:45:18 CDT)
  • non bonded pair list (Thu Apr 24 2003 - 11:22:08 CDT)
• Jeffrey Dyason
  • Solaris Benchmark for Amber7 (Tue Mar 11 2003 - 19:04:53 CST)
• Jessica Swanson
  • AMBER: parmscan (Fri Dec 12 2003 - 12:39:19 CST)
• Jian Zhang
  • Re: AMBER: parallelisation (Wed Aug 06 2003 - 07:39:22 CDT)
  • Re: the unit of velocity (Wed Jan 08 2003 - 20:12:15 CST)
  • the unit of velocity (Tue Jan 07 2003 - 22:36:58 CST)
• Jian Zhang, Dr
  • AMBER: shake constraint on all bonds (Wed Nov 05 2003 - 21:34:24 CST)
• Jiang Pengju
  • AMBER: A problem about xleap (Mon Sep 29 2003 - 21:04:14 CDT)
• Jianhui Wu
  • T in MD vs. T in wet experiments (Tue Jun 24 2003 - 20:34:31 CDT)
  • Domain/Helix movement/MD (Fri Jan 31 2003 - 10:35:18 CST)
• Jim Newhouse
  • Re: Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap (Tue Jan 07 2003 - 13:07:32 CST)
• Jiri Matousek
  • AMBER: GIBBS - PMF question: How to get <dV/d_lam> during TI calculations? (Mon Dec 22 2003 - 03:51:25 CST)
  • AMBER: GIBBS - PMFquestion (Wed Dec 03 2003 - 04:47:41 CST)
  • Re: AMBER: GIBBS - PMF problem: Lambda has not changed (Thu Nov 13 2003 - 11:09:49 CST)
  • AMBER: GIBBS - PMF problem: Lambda has not changed (Thu Nov 13 2003 - 06:32:01 CST)
• Jiri Sponer
  • Re: AMBER: Mg2+ parameters for RNA usage (Wed Dec 10 2003 - 13:32:57 CST)
  • Re: AMBER: Mg2+ parameters for RNA usage (Wed Dec 10 2003 - 08:21:24 CST)
  • Re: AMBER: Re:atomic charges and internal H-bond (Tue Oct 07 2003 - 17:08:09 CDT)
  • Re: AMBER: Re:atomic charges and internal H-bond (Tue Oct 07 2003 - 15:48:00 CDT)
  • Re: AMBER: Atomic charges and internal H-bond (Tue Oct 07 2003 - 09:12:27 CDT)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Thu Sep 25 2003 - 06:59:51 CDT)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 16:41:27 CDT)
  • Re: AMBER: Accuracy of PB solvation energy (Fri Sep 05 2003 - 12:46:04 CDT)
  • Re: Valdiation of Latest Amber parameters (Wed Jul 09 2003 - 12:03:53 CDT)
  • Re: DNA base-step distortion (Mon May 19 2003 - 04:56:00 CDT)
• Jiten
  • Re: AMBER: Carbohydrate connectivity (Thu Dec 11 2003 - 10:04:44 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 11:55:51 CST)
  • Re: AMBER: xleap-N/C terminus (Wed Dec 10 2003 - 07:10:15 CST)
  • Re: AMBER: NAD+ and NADH amber parameters (Sun Dec 07 2003 - 22:17:53 CST)
  • AMBER: NAD+ and NADH amber parameters (Mon Dec 01 2003 - 08:01:17 CST)
  • Re: AMBER: MeCNBOX & EWALD bomb (Fri Oct 10 2003 - 22:29:04 CDT)
  • Re: AMBER: DMSO box (Fri Sep 12 2003 - 20:05:46 CDT)
• Jiyoung Heo
  • off-diagonal VDW term (Mon May 19 2003 - 20:01:13 CDT)
  • format of 'mask' in ptraj (Mon Mar 24 2003 - 00:46:18 CST)
  • how to validate ff parameters obtained from antechamber (Thu Feb 27 2003 - 23:27:54 CST)
• Joachim Reichelt
  • Re: question about mm_pbsa (Mon Mar 10 2003 - 06:43:58 CST)
• Joey Harriman
  • Re: AMBER: MOPAC from antechamber (Wed Dec 10 2003 - 12:08:13 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 12:05:44 CST)
  • AMBER: antechamber mopac7 parameters (Wed Nov 12 2003 - 09:06:41 CST)
  • Re: AMBER: AM1-BCC in Amber7 (Mon Nov 10 2003 - 08:15:25 CST)
  • AMBER: AM1-BCC in Amber7 (Mon Nov 10 2003 - 06:56:23 CST)
  • AMBER: Implicit MD simulations in Amber7 (Mon Oct 27 2003 - 12:53:01 CST)
• Joffre Heredia
  • Re: memory shortage with mm_pbsa - some more thoughts (Sat Jul 12 2003 - 05:26:39 CDT)
  • SCSL (Wed Jan 22 2003 - 14:23:12 CST)
• Johannes Zuegg
  • Re: AMBER: Suggestion regarding long simulation. (Thu Sep 18 2003 - 17:56:39 CDT)
  • Re: AMBER: PMEMD: dual XEON vs SGI cluster (Mon Sep 15 2003 - 18:45:27 CDT)
  • Re: AMBER: Odd Problem with PMEMD (Mon Jul 21 2003 - 23:12:37 CDT)
• John
  • RE: AMBER: xleap-N/C terminus (Wed Dec 10 2003 - 09:46:22 CST)
  • AMBER: xleap-N/C terminus (Wed Dec 10 2003 - 06:34:13 CST)
  • RE: AMBER: TFE solvent box (Fri Dec 05 2003 - 08:25:42 CST)
  • AMBER: TFE solvent box (Thu Dec 04 2003 - 05:16:33 CST)
  • AMBER: ndfmin in belly runs (Thu Nov 13 2003 - 04:50:52 CST)
  • RE: AMBER: carnal iteration deviation from original crd file (Mon Oct 27 2003 - 19:05:28 CST)
• John Bushnell
  • Re: AMBER: A problem about xleap (Tue Sep 30 2003 - 12:13:06 CDT)
  • RE: AMBER: LEaP not compiling (Wed Aug 27 2003 - 16:56:32 CDT)
  • RE: AMBER: Atom type in prepin file - new problem (Wed Aug 13 2003 - 19:01:21 CDT)
  • Re: Problem with XLEaP in Mandrake 9.1 (Sun Jun 22 2003 - 20:04:43 CDT)
  • Re: Please help on xleap: FATAL ERROR (Thu May 22 2003 - 21:04:15 CDT)
  • Re: Request for Amber7 (xleap problem) (Tue Apr 22 2003 - 17:30:41 CDT)
  • Re: Resp Charges for large ligand. (Mon Mar 17 2003 - 18:47:33 CST)
  • Re: Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 15:49:56 CST)
• John D. Chodera
  • Binary output switch (IOUTFM=1) broken in sander? (AMBER7) (Sun Feb 23 2003 - 22:49:56 CST)
  • Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold (Sat Jan 18 2003 - 03:26:12 CST)
• John Finke
  • Periodic Box (Fri Feb 07 2003 - 18:25:10 CST)
• John Lee
  • Re[2]: AMBER: surface code in Amber (Tue Oct 28 2003 - 00:53:49 CST)
  • Re[2]: AMBER: surface code in Amber (Sun Oct 26 2003 - 20:06:56 CST)
  • AMBER: surface code in Amber (Sun Oct 05 2003 - 16:13:43 CDT)
• John Mongan
  • AMBER: HT vs no HT (Mon Dec 22 2003 - 13:18:31 CST)
• johneluwa_at_eircom.net
  • Request (Wed Jan 29 2003 - 20:42:28 CST)
• Jonathan Neidigh
  • Re: AMBER: Installation Problem, xleap can't load pdb files (Wed Oct 29 2003 - 09:54:18 CST)
  • AMBER: Installation Problem, xleap can't load pdb files (Tue Oct 28 2003 - 17:19:59 CST)
• Jones de Andrade
  • RE: Why the NMA discrepancies? (Mon Mar 17 2003 - 08:35:05 CST)
  • Why the NMA discrepancies? (Sun Mar 16 2003 - 19:09:16 CST)
• Jones, Garth A
  • SANDER Source Code Documentation (Thu Apr 10 2003 - 02:07:13 CDT)
• Jorge Vasquez-Kool
  • AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 09:29:55 CST)
• Jory L. Zmuda
  • AMBER: correlated motion (Thu Oct 23 2003 - 13:17:01 CDT)
• Jory Zmuda
  • AMBER: Nmode analysis ptn-ligand complex (Tue Dec 16 2003 - 17:11:13 CST)
  • AMBER: Cutress %cmass error (Wed Nov 19 2003 - 09:17:08 CST)
  • AMBER: mm_pbsa example (Thu Oct 09 2003 - 15:35:21 CDT)
• Jose Gallego
  • RE: AMBER: amber 7 for industrial application (Tue Oct 28 2003 - 08:45:19 CST)
  • AMBER: amber 7 for industrial application (Mon Oct 27 2003 - 07:18:16 CST)
• Jose Ramon Blas
  • Re: AMBER: What does this error message mean? (Fri Oct 31 2003 - 18:29:19 CST)
  • constraint + restraint (Thu Jun 19 2003 - 18:58:41 CDT)
  • Re: leap complains! (Thu May 22 2003 - 17:03:02 CDT)
  • Re: Organic Solvents (Tue Apr 22 2003 - 17:00:58 CDT)
  • Re: Extracting structures (Thu Mar 27 2003 - 10:18:31 CST)
  • Re: format of 'mask' in ptraj (Mon Mar 24 2003 - 10:14:33 CST)
  • Itanium II (Tue Feb 11 2003 - 12:50:58 CST)
  • Re: acetonitrile parameters (Tue Feb 04 2003 - 13:21:39 CST)
  • Re: How to calculate new force field? (Mon Feb 03 2003 - 13:06:24 CST)
  • Re: chloroform, dichlormethane f.f. (Tue Jan 14 2003 - 18:05:34 CST)
  • Predefined Water_cap with xleap (Wed Jan 08 2003 - 12:42:16 CST)
• Joseph Fernandez
  • Re: free energy in sander (Thu Apr 10 2003 - 21:58:30 CDT)
  • free energy in sander (Thu Apr 10 2003 - 16:32:52 CDT)
  • free energy calculations (Fri Apr 04 2003 - 15:18:25 CST)
• Joseph Maxwell
  • Re: AMBER: mfef90 - installation problem (Wed Sep 17 2003 - 13:11:58 CDT)
  • AMBER: mfef90 - installation problem (Wed Sep 17 2003 - 11:34:18 CDT)
  • Amber Installation on Octane (Sun Jun 08 2003 - 16:55:55 CDT)
  • Amber 7.xx installation on FreeBSD (Tue May 20 2003 - 15:27:11 CDT)
• Joseph Nachman
  • AMBER: leap/frcmod problem (Wed Sep 17 2003 - 15:08:37 CDT)
  • Re: AMBER: simulating a crystal using the unit cell (Thu Aug 14 2003 - 11:01:34 CDT)
  • Neutral Arginine (Wed Mar 26 2003 - 15:00:54 CST)
• João Barroso
  • Re: AMBER: Pressure during MD (Mon Nov 17 2003 - 03:36:41 CST)
  • AMBER: Pressure during MD (Sun Nov 16 2003 - 12:12:18 CST)
• Junmei Wang
  • Re: AMBER: RESP charges (Thu Dec 18 2003 - 20:29:45 CST)
  • Re: AMBER: RESP charges (Thu Dec 18 2003 - 15:17:28 CST)
  • Re: AMBER: RESP charges (Thu Dec 11 2003 - 10:55:21 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 17:29:19 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 15:07:24 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 12:38:15 CST)
  • Re: AMBER: gaff atom types for phosphor compouds (Tue Dec 09 2003 - 09:28:08 CST)
  • Re: Re: Re: AMBER: a problem with antechamber and leap (Wed Nov 12 2003 - 14:51:05 CST)
  • Re: Re: AMBER: a problem with antechamber and leap (Wed Nov 12 2003 - 14:46:02 CST)
  • Re: Re: AMBER: a problem with antechamber and leap (Tue Nov 11 2003 - 16:38:32 CST)
  • Re: Re: AMBER: a problem with antechamber and leap (Tue Nov 11 2003 - 16:33:02 CST)
  • Re: AMBER: mgbjsb radii in GBSA (Tue Nov 11 2003 - 16:12:08 CST)
  • Re: AMBER: AM1-BCC in Amber7 (Tue Nov 11 2003 - 15:49:31 CST)
  • RE: AMBER: amber 7 for industrial application (Tue Oct 28 2003 - 09:58:43 CST)
  • Re: AMBER: mopac (Wed Oct 08 2003 - 12:15:18 CDT)
  • Re: AMBER: Compiling antechamber on amber 8 (Fri Oct 03 2003 - 09:50:01 CDT)
  • Re: AMBER: Zn in antechamber (Mon Sep 29 2003 - 11:38:09 CDT)
  • Re: AMBER: Zn in antechamber (Mon Sep 29 2003 - 10:32:52 CDT)
  • Re: AMBER: Zn in antechamber (Fri Sep 26 2003 - 15:24:46 CDT)
  • Re: AMBER: Zn in antechamber (Fri Sep 26 2003 - 12:00:11 CDT)
  • Re: AMBER: Zn in antechamber (Fri Sep 26 2003 - 09:47:45 CDT)
  • RE: AMBER: problem with file format (Wed Sep 24 2003 - 15:34:14 CDT)
  • Re: AMBER: cd-c-os and c3-cd-c angle parameters (Wed Sep 24 2003 - 13:16:18 CDT)
  • AMBER: MD simulations on small molecules immersed in sparse water shell (Tue Sep 16 2003 - 11:42:56 CDT)
  • Re: AMBER: gaff parameters (Fri Sep 12 2003 - 16:46:24 CDT)
  • Re: AMBER: 'ho' vDW parameters (Mon Sep 08 2003 - 15:01:25 CDT)
  • Re: AMBER: Antechamber Problem (Thu Aug 28 2003 - 12:16:24 CDT)
  • Re: AMBER: "ATTN, need revision" (Thu Aug 28 2003 - 12:06:46 CDT)
  • Re: AMBER: Antechamber formal charges with Gasteiger method (Tue Aug 26 2003 - 14:55:14 CDT)
  • Re: Re[2]: AMBER: antechamber problem (Fri Aug 22 2003 - 10:03:23 CDT)
  • Re: Re[2]: AMBER: antechamber problem (Thu Aug 21 2003 - 15:16:02 CDT)
  • Re: AMBER: PARMSET problem (Wed Aug 20 2003 - 13:06:00 CDT)
  • Re: AMBER: charge method of antechamber(it's ok) (Mon Aug 18 2003 - 09:26:41 CDT)
  • Re: AMBER: Antechamber functionality, MOL2 files (Wed Aug 13 2003 - 11:28:03 CDT)
  • Re: AMBER: Antechamber functionality, MOL2 files (Wed Aug 13 2003 - 10:06:47 CDT)
  • Re: AMBER: charge method of antechamber (Mon Aug 04 2003 - 09:39:58 CDT)
  • Re: AMBER: (no subject) (Wed Jul 30 2003 - 14:34:54 CDT)
  • Re: parm99 (Wed May 21 2003 - 13:30:18 CDT)
• k.watanabe
  • About antechamber (Wed Feb 12 2003 - 23:32:18 CST)
  • How to calculate new force field? (Mon Feb 03 2003 - 01:22:31 CST)
• kalyan_at_mbu.iisc.ernet.in
  • Number of water too large (Mon Feb 17 2003 - 10:10:52 CST)
• Karen Haskell
  • AMBER: make clean doesn't clean leap (Mon Nov 03 2003 - 16:47:22 CST)
  • Re: AMBER: make clean doesn't clean leap (Mon Nov 03 2003 - 17:19:23 CST)
• Karl N. Kirschner
  • Heat of Vaporization (Mon May 12 2003 - 09:46:17 CDT)
  • Adding ACE to chopped protein (Wed Apr 16 2003 - 15:08:45 CDT)
  • intel ifc amber5 and mpich-1.2.5 (Wed Mar 12 2003 - 15:25:46 CST)
• Karsten Suhre
  • AMBER: following salt and waterbridges during a simulation (Tue Sep 30 2003 - 01:33:31 CDT)
  • Re: AMBER: modelling a Ca binding site (Fri Aug 15 2003 - 04:44:09 CDT)
  • AMBER: modelling a Ca binding site (Thu Aug 14 2003 - 04:36:53 CDT)
• Karthikeyan Pasupathy
  • AMBER: iam a newbie !!! (Mon Sep 29 2003 - 23:25:05 CDT)
  • Problem with XLEaP in Mandrake 9.1 (Sun Jun 22 2003 - 12:08:23 CDT)
• Kaushik Raha
  • AMBER: parmchk on MAC (Thu Nov 06 2003 - 10:19:52 CST)
• Kazuo Koyano
  • Re: AMBER: MM_PBSA(GBSA) Examples (Fri Sep 26 2003 - 05:37:40 CDT)
  • AMBER: MM_PBSA(GBSA) Examples (Thu Sep 25 2003 - 05:35:50 CDT)
  • Re: AMBER: xLEAP Problem (Sun Sep 21 2003 - 21:18:49 CDT)
  • Re: AMBER: gaff parameters (Fri Sep 12 2003 - 05:31:33 CDT)
• kbyun_at_wesleyan.edu
  • AMBER: nmode statistics (Wed Dec 17 2003 - 13:52:51 CST)
  • AMBER: nmode, trajectory (Fri Dec 12 2003 - 11:05:08 CST)
  • Re: AMBER: mm_pbsa crg file (Tue Oct 14 2003 - 09:09:35 CDT)
  • AMBER: mm_pbsa rna/dna charges (Mon Oct 13 2003 - 15:45:37 CDT)
  • AMBER: mm_pbsa crg file (Mon Oct 13 2003 - 12:24:15 CDT)
  • Re: DNA base-step distortion (Sun May 18 2003 - 18:43:59 CDT)
  • DNA base-step distortion (Sun May 18 2003 - 14:37:12 CDT)
  • Re: mm_pbsa nmode calculation (Wed Apr 23 2003 - 15:33:55 CDT)
  • mm_pbsa nmode calculation (Wed Apr 23 2003 - 13:33:17 CDT)
  • mm_pbsa_statistics.pm (Tue Apr 22 2003 - 11:40:10 CDT)
  • CHARMm force field for AMBER (Thu Mar 27 2003 - 11:18:17 CST)
  • PME cutoff box size (Tue Mar 25 2003 - 11:24:07 CST)
• Khanh KIm Dao
  • AMBER: charge definition (Sat Sep 06 2003 - 13:40:31 CDT)
• Khanh.Dao_at_iac.uib.no
  • Re: problem_namelist_reading (Wed Apr 30 2003 - 00:26:58 CDT)
  • problem_namelist_reading (Tue Apr 29 2003 - 01:19:46 CDT)
  • Problem_to_open_PROTON_INFO_file (Thu Apr 24 2003 - 03:46:10 CDT)
  • (no subject) (Mon Apr 21 2003 - 11:35:02 CDT)
  • PME box information (Tue Apr 15 2003 - 04:56:38 CDT)
  • Re: A problem in opening the file (Tue Apr 15 2003 - 02:19:58 CDT)
  • A problem in opening the file (Tue Apr 15 2003 - 00:01:11 CDT)
• kinsellg
  • Nmode query (Fri Jan 24 2003 - 09:00:40 CST)
• Krishna Bisetty
  • AMBER: AMBER 7_make install (Mon Aug 18 2003 - 02:36:37 CDT)
• Kristina Furse
  • RE: AMBER: mddisplay (Tue Oct 28 2003 - 18:48:30 CST)
  • AMBER: Fxnal form of NMR-style restraints (Thu Aug 28 2003 - 16:41:56 CDT)
  • RE: AMBER: large changes in xyz coordinates (Mon Aug 18 2003 - 13:26:27 CDT)
  • RE: AMBER: PMEMD and EAMBER (Fri Aug 08 2003 - 13:33:28 CDT)
  • RE: AMBER: more than 100,000 atoms ? (Fri Aug 08 2003 - 13:14:10 CDT)
  • AMBER: PMEMD and EAMBER (Thu Aug 07 2003 - 15:32:45 CDT)
  • RE: leap complains! (Thu May 22 2003 - 18:17:16 CDT)
  • RE: ibelly and ntr (Wed Apr 16 2003 - 14:51:43 CDT)
  • RE: size of a simulation system (Tue Apr 01 2003 - 16:36:01 CST)
  • RE: average structure generated by carnal (Tue Jan 21 2003 - 19:55:46 CST)
  • RE: nscm (Wed Jan 15 2003 - 13:13:00 CST)
  • nscm (Tue Jan 14 2003 - 18:21:52 CST)
• Kun Song
  • Re: AMBER: C-alpha RMS (Mon Sep 22 2003 - 08:45:20 CDT)
• kxg2248_at_njit.edu
  • Re: AMBER pdb help - lost atoms - Part 2 (Thu Apr 03 2003 - 11:50:29 CST)
  • AMBER pdb help - lost atoms - Part 2 (Thu Apr 03 2003 - 09:39:23 CST)
  • AMBER pdb help - lost atoms (Tue Apr 01 2003 - 13:39:27 CST)
  • Re: Sander box error and thanks on previous mdin error (Fri Jan 03 2003 - 11:37:05 CST)
  • Sander box error and thanks on previous mdin error (Thu Jan 02 2003 - 21:41:49 CST)
• L Jin
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Wed Dec 31 2003 - 05:44:00 CST)
  • AMBER: Constant temperature (Sat Dec 27 2003 - 05:29:13 CST)
  • AMBER: MD: restrt (Fri Dec 19 2003 - 04:47:55 CST)
  • AMBER: Energy map (Mon Dec 15 2003 - 08:42:52 CST)
  • AMBER: Antechamber:charges missing (Fri Dec 12 2003 - 09:45:35 CST)
  • Re: AMBER: Antechamber & Ptraj/Rdparm (Fri Dec 12 2003 - 05:35:46 CST)
  • Re: AMBER: ambpdb (Fri Dec 12 2003 - 05:24:42 CST)
  • AMBER: ambpdb (Fri Dec 12 2003 - 04:43:36 CST)
  • Re: AMBER: About Temperature Regulation (Wed Dec 10 2003 - 11:06:25 CST)
  • AMBER: Antechamber & Ptraj/Rdparm (Wed Dec 10 2003 - 09:07:25 CST)
  • AMBER: About Temperature Regulation (Wed Dec 10 2003 - 09:09:00 CST)
  • AMBER: Small problems (Mon Dec 08 2003 - 11:47:47 CST)
  • AMBER: MD (Mon Dec 08 2003 - 11:45:01 CST)
• Layi Adekoya
  • AMBER: Hydrogen bond plot from carnal (Mon Aug 18 2003 - 02:51:51 CDT)
  • AMBER: Hydrogen bond plot from carnal (Fri Aug 15 2003 - 05:16:02 CDT)
  • viewing movie with VMD (Mon Jun 23 2003 - 03:00:51 CDT)
  • leap complains! (Thu May 22 2003 - 06:56:11 CDT)
  • serine/tyrosine in charged states (Wed May 14 2003 - 07:26:55 CDT)
  • mm_pbsa (Wed Feb 26 2003 - 04:05:35 CST)
  • script for Potential/kinectic energy (Mon Jan 20 2003 - 10:30:09 CST)
  • xleap crashes (Tue Jan 14 2003 - 02:46:49 CST)
  • xleap crashes (Mon Jan 13 2003 - 01:54:20 CST)
  • xleap crashes (Fri Jan 10 2003 - 06:16:26 CST)
• Lee, Matt
  • AMBER: no "Input orientation" in g98 log (Mon Dec 15 2003 - 17:13:10 CST)
• Lee, Matthew
  • AMBER: molsuf failure with too many intersecting cusps (Tue Nov 18 2003 - 14:24:29 CST)
  • AMBER: sander on cygwin (Mon Sep 15 2003 - 13:14:40 CDT)
  • AMBER: 'ho' vDW parameters (Fri Sep 05 2003 - 17:33:12 CDT)
  • AMBER: Antechamber formal charges with Gasteiger method (Tue Aug 26 2003 - 13:07:14 CDT)
  • AMBER: protonation states of small molecules (Fri Aug 15 2003 - 13:33:40 CDT)
• Lepsa
  • Re: viewing movie with VMD (Mon Jun 23 2003 - 03:09:29 CDT)
  • Re: MD input file for MM-PBSA calculations (Mon May 26 2003 - 04:03:02 CDT)
  • Re: Mainchain.dat (Tue May 20 2003 - 08:34:36 CDT)
  • Re: question about MM-PBSA? (Tue Apr 22 2003 - 01:50:42 CDT)
  • Side-chain/main-chain decomposition in MM-GBSA (Thu Apr 03 2003 - 02:24:35 CST)
  • Polarizable simulation2 (Tue Apr 01 2003 - 06:25:22 CST)
  • Polarization simulation (Thu Mar 20 2003 - 03:55:33 CST)
  • Re: Preparation of RESP input from GAUSSIAN output (Mon Mar 17 2003 - 07:11:41 CST)
  • Re: mm_pbsa (Wed Feb 26 2003 - 06:41:47 CST)
  • Fw: adding hydrogens (Wed Feb 19 2003 - 08:23:54 CST)
  • Re: adding hydrogens (Wed Feb 19 2003 - 02:26:36 CST)
  • Re: interaction between ligand & protein (Tue Feb 18 2003 - 11:28:35 CST)
  • Re: question about partial charge (Tue Feb 18 2003 - 01:56:59 CST)
  • Re: charge determination for polariable ff02 force fields (Mon Feb 17 2003 - 02:16:07 CST)
  • Fw: charge determination for polariable ff02 force fields (Sat Feb 15 2003 - 10:12:02 CST)
  • charges, opt and iops (Sat Feb 15 2003 - 09:59:44 CST)
  • Fw: RESP charge derivation (Wed Feb 05 2003 - 02:33:53 CST)
  • RESP charge derivation (Tue Feb 04 2003 - 11:34:57 CST)
  • Re: Domain/Helix movement/MD (Fri Jan 31 2003 - 10:52:59 CST)
  • Re: ptraj distanse question (Fri Jan 31 2003 - 06:16:25 CST)
  • Re: High temperature MD (Thu Jan 30 2003 - 01:27:19 CST)
  • Re: mm_pbsa and ALA scan (Wed Jan 29 2003 - 10:31:41 CST)
  • MM_PBSA (Wed Jan 29 2003 - 07:12:34 CST)
  • Re: one question (Tue Jan 28 2003 - 10:16:05 CST)
  • Intramolecular H-bonds in charge fitting (Tue Jan 28 2003 - 03:05:58 CST)
  • Re: CARNAL (Tue Jan 21 2003 - 12:07:18 CST)
  • pi-pi in AMBER (Tue Jan 21 2003 - 11:53:27 CST)
  • Re: CARNAL (Tue Jan 21 2003 - 03:33:37 CST)
  • CARNAL (Mon Jan 20 2003 - 09:22:22 CST)
  • Polarization charges -geometry (Fri Jan 17 2003 - 02:21:30 CST)
  • Re: mm_pbsa -- COMPT must be specified (correctly) (Tue Jan 14 2003 - 02:49:55 CST)
  • Dummy atoms in free energy calculation (Sat Jan 11 2003 - 12:18:44 CST)
  • IDSX0 in free energy calculations (Fri Jan 10 2003 - 07:29:04 CST)
  • Re: free energy perturbation (Gibbs/Amber 5)? (Fri Jan 10 2003 - 03:56:50 CST)
• Li Ying
  • Re: AMBER: partial charge (Wed Dec 03 2003 - 12:08:14 CST)
  • Re: AMBER: partial charge (Tue Dec 02 2003 - 13:19:22 CST)
  • AMBER: partial charge (Mon Dec 01 2003 - 11:31:56 CST)
  • AMBER: image question (Tue Nov 25 2003 - 12:13:21 CST)
  • AMBER: improper (Tue Sep 30 2003 - 15:08:11 CDT)
• Lifang Xu
  • (no subject) (Tue Jul 01 2003 - 09:22:43 CDT)
• lil_at_umbi.umd.edu
  • AMBER: antechamber (Mon Oct 13 2003 - 18:30:25 CDT)
  • AMBER: mopac (Wed Oct 08 2003 - 11:19:18 CDT)
• Liliana Wroblewska
  • problems with anal in amber7 (Fri May 23 2003 - 16:53:28 CDT)
• Ling Zhang
  • AMBER: The lost velocities in the restart file generated by Ptraj (Mon Dec 29 2003 - 15:12:47 CST)
  • AMBER: The restart file generated by Ptraj (Mon Dec 29 2003 - 14:49:52 CST)
  • AMBER: monitor vdw along time (Fri Jul 25 2003 - 12:48:26 CDT)
  • Re: Distribution Min with truncated octahedron box (Tue Jul 08 2003 - 13:31:42 CDT)
  • Distribution Min with truncated octahedron box (Tue Jul 08 2003 - 12:24:47 CDT)
  • The error in the trajectory file (Tue Apr 08 2003 - 11:37:58 CDT)
  • The image command of ptraj of Amber 6 is not working. (Wed Feb 12 2003 - 14:36:58 CST)
  • How to put the outside atoms back to the truncated octahedron box? (Wed Feb 12 2003 - 13:49:12 CST)
  • Moil-view (Tue Jan 14 2003 - 11:47:14 CST)
• Lishan Yao
  • AMBER: question about ewald (Thu Oct 09 2003 - 11:03:44 CDT)
  • Re: AMBER: Zn in antechamber (Mon Sep 29 2003 - 15:15:04 CDT)
  • Re: AMBER: Zn in antechamber (Mon Sep 29 2003 - 10:59:09 CDT)
  • Re: AMBER: Zn in antechamber (Mon Sep 29 2003 - 10:13:42 CDT)
  • Re: AMBER: Zn in antechamber (Fri Sep 26 2003 - 14:15:21 CDT)
  • Re: AMBER: Zn in antechamber (Fri Sep 26 2003 - 10:01:41 CDT)
  • AMBER: Zn in antechamber (Fri Sep 26 2003 - 08:48:44 CDT)
  • AMBER: ptraj question (Thu Sep 11 2003 - 14:48:08 CDT)
  • AMBER: target MD simulation (Wed Aug 27 2003 - 13:01:46 CDT)
  • Re: AMBER: gibbs pmf calculation (Wed Aug 27 2003 - 10:34:02 CDT)
  • Re: AMBER: gibbs pmf calculation (Mon Aug 25 2003 - 16:06:29 CDT)
  • AMBER: temperature problem (Mon Aug 25 2003 - 08:37:01 CDT)
  • Re: AMBER: ptraj problem (Mon Aug 25 2003 - 08:23:10 CDT)
  • Re: AMBER: gibbs pmf calculation (Mon Aug 25 2003 - 08:16:03 CDT)
  • AMBER: gibbs pmf calculation (Wed Aug 20 2003 - 14:24:29 CDT)
  • AMBER: ptraj problem (Tue Aug 19 2003 - 16:08:02 CDT)
  • AMBER: ptraj problem (Mon Aug 18 2003 - 13:22:43 CDT)
  • AMBER: Gibbs pmf calculation (Fri Aug 15 2003 - 10:35:51 CDT)
  • Re: AMBER: constant energy simulation (Thu Aug 14 2003 - 10:53:13 CDT)
  • Re: AMBER: constant energy simulation (Wed Aug 13 2003 - 11:09:14 CDT)
  • Re: AMBER: constant energy simulation (Wed Aug 13 2003 - 10:07:29 CDT)
  • Re: AMBER: constant energy simulation (Wed Aug 13 2003 - 08:00:20 CDT)
  • Re: AMBER: constant energy simulation (Tue Aug 12 2003 - 17:25:37 CDT)
  • AMBER: constant energy simulation (Tue Aug 12 2003 - 14:38:49 CDT)
  • AMBER: frequency analysis (Wed Jul 30 2003 - 16:43:16 CDT)
  • Re: AMBER: Question about quasih analysis (Mon Jul 28 2003 - 15:24:19 CDT)
  • Re: AMBER: Question about quasih analysis (Mon Jul 28 2003 - 12:30:26 CDT)
  • AMBER: Question about quasih analysis (Mon Jul 28 2003 - 09:04:26 CDT)
  • AMBER: PMF calculation (Thu Jul 24 2003 - 14:25:48 CDT)
  • AMBER: question about ptraj? (Thu Jul 24 2003 - 11:18:20 CDT)
  • AMBER: question about quasih? (Fri Jul 18 2003 - 17:15:32 CDT)
  • Re: Questions about statistics output of mm_pbsa? (Fri May 23 2003 - 08:31:44 CDT)
  • Re: Questions about statistics output of mm_pbsa? (Fri May 23 2003 - 08:22:07 CDT)
  • Questions about statistics output of mm_pbsa? (Thu May 22 2003 - 16:04:04 CDT)
  • Re: bad atom type f(fluorine) in MM-PBSA? (Wed May 21 2003 - 12:12:17 CDT)
  • bad atom type f(fluorine) in MM-PBSA? (Wed May 21 2003 - 08:29:01 CDT)
  • Re: Fluorine atom type in mm_pbsa? (Tue May 20 2003 - 08:12:04 CDT)
  • Fluorine atom type in mm_pbsa? (Mon May 19 2003 - 16:00:09 CDT)
  • Re: question about H-bond in carnal? (Sun Apr 27 2003 - 19:37:13 CDT)
  • Re: question about H-bond in carnal? (Fri Apr 25 2003 - 10:24:56 CDT)
  • question about H-bond in carnal? (Fri Apr 25 2003 - 09:44:55 CDT)
  • Re: question about MM-PBSA? (Fri Apr 18 2003 - 09:10:24 CDT)
  • question about MM-PBSA? (Thu Apr 17 2003 - 14:15:38 CDT)
  • No statistical output for MM-PBSA? (Tue Apr 15 2003 - 21:25:22 CDT)
  • question about MM-PBSA? (Tue Apr 08 2003 - 12:21:20 CDT)
  • question about mm_pbsa? (Tue Mar 18 2003 - 14:00:46 CST)
  • Question about mm_pbsa? (Tue Mar 18 2003 - 10:43:51 CST)
  • question about mm_pbsa? (Mon Mar 10 2003 - 10:04:17 CST)
  • question about mm_pbsa (Sun Mar 09 2003 - 20:26:47 CST)
  • question about lysine? (Wed Feb 26 2003 - 16:23:38 CST)
  • interaction between ligand & protein (Tue Feb 18 2003 - 10:59:56 CST)
  • question about antechamber (Thu Feb 13 2003 - 16:55:39 CST)
  • question about antechamber (Wed Feb 12 2003 - 14:06:23 CST)
  • Question about quasih (Sun Feb 09 2003 - 17:18:38 CST)
  • essential dynamics (Fri Feb 07 2003 - 10:31:05 CST)
  • about Mg++ (Wed Feb 05 2003 - 11:17:12 CST)
  • question about temperature (Mon Feb 03 2003 - 11:02:13 CST)
  • Re: question about ligand (Sat Feb 01 2003 - 20:24:57 CST)
  • question about ligand (Fri Jan 31 2003 - 16:43:39 CST)
• Luis Gracia
  • Re: AMBER: Restrain of dihedral angle! (Fri Aug 01 2003 - 11:14:21 CDT)
  • Re: H-O-H angle (Tue May 13 2003 - 16:46:05 CDT)
  • Re: ambpdb (Tue Apr 15 2003 - 23:40:57 CDT)
  • Re: compatibility of amber with NAMD (Fri Feb 14 2003 - 12:16:12 CST)
  • SASA calculation (Mon Feb 03 2003 - 16:58:25 CST)
  • shake and H-O-H angle (Tue Jan 21 2003 - 10:57:16 CST)
  • Re: script for Potential/kinectic energy (Mon Jan 20 2003 - 12:16:52 CST)
  • reducing restrains (Tue Jan 07 2003 - 10:14:43 CST)
• M. L. Dodson
  • Re: AMBER: roar topology and coordinate files (Mon Dec 29 2003 - 18:42:49 CST)
  • Re: AMBER: roar topology and coordinate files (Mon Dec 29 2003 - 14:15:57 CST)
  • Re: AMBER: roar topology and coordinate files (Mon Dec 29 2003 - 07:35:42 CST)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 18:53:22 CDT)
  • Re: helix axis for A-RNA (Tue Jun 10 2003 - 08:36:44 CDT)
  • Re: Amber 7.xx installation on FreeBSD (Tue May 20 2003 - 16:19:21 CDT)
  • Re: trouble with OFF files (Mon Apr 21 2003 - 15:13:24 CDT)
• Mac Brown
  • trouble with OFF files (Mon Apr 21 2003 - 14:07:32 CDT)
  • solvents aren't loading (Tue Apr 15 2003 - 15:20:15 CDT)
• Mahadevan Seetharaman
  • AMBER: Restraints to maintain base pair planarity (Tue Oct 14 2003 - 22:10:29 CDT)
  • AMBER: xplor2amber (Sat Aug 02 2003 - 21:34:24 CDT)
  • AMBER: xplor2amber (Sat Aug 02 2003 - 21:35:48 CDT)
  • water residence time analysis (Tue May 13 2003 - 12:18:14 CDT)
  • charge neutralization in DNA (Tue Feb 18 2003 - 13:08:55 CST)
  • terminal phosphate group in RNA (Thu Jan 16 2003 - 16:10:13 CST)
  • mm_gbsa error message (Wed Jan 08 2003 - 12:17:23 CST)
• Mahesh Chandran
  • AMBER: Freezing of water with TIP3P potential. (Mon Nov 03 2003 - 05:41:21 CST)
• Mail System Internal Data
  • DON'T DELETE THIS MESSAGE -- FOLDER INTERNAL DATA (Fri Feb 06 2004 - 10:15:04 CST)
• Majid moghaddam
  • AMBER: solvatebox-solvateshell (Sat Sep 06 2003 - 06:42:55 CDT)
  • AMBER: temperature does not reach to temp0 (Tue Aug 19 2003 - 07:32:43 CDT)
  • AMBER: Is NTC=2 correct for minimization when hydrogens are added? (Sat Aug 16 2003 - 03:00:04 CDT)
  • AMBER: NTX 5 or 7 after equilibration in constant pressure? (Sat Aug 16 2003 - 02:08:38 CDT)
  • namelist read: variable not in namelist (Tue Mar 18 2003 - 04:18:46 CST)
  • (no subject) (Sun Feb 16 2003 - 07:57:21 CST)
• Malone, Scott
  • AMBER: Amber - compiler help (Thu Dec 04 2003 - 16:11:53 CST)
• Manuel Rueda
  • Amber parameters for Netropsin (Wed Jan 08 2003 - 17:48:12 CST)
• Mao Xiang
  • how to restrain water (Mon Jun 23 2003 - 09:59:23 CDT)
  • help on solvatecap (Wed Jun 18 2003 - 20:47:36 CDT)
• Marc Dobler
  • metallic ions (Tue Feb 18 2003 - 03:10:29 CST)
• Marcela Madrid
  • AMBER: normal mode analysis (Mon Aug 04 2003 - 13:03:23 CDT)
• Marco Aurelio Correia Preto
  • RE: AMBER: Restrain of dihedral angle! (Mon Aug 04 2003 - 04:15:22 CDT)
  • AMBER: Restrain of dihedral angle! (Fri Aug 01 2003 - 05:59:08 CDT)
  • RE: AMBER question (Fri Jul 11 2003 - 09:29:11 CDT)
  • RE: AMBER question (Thu Jul 10 2003 - 03:04:08 CDT)
  • RE: How to do a rigid solvent model? (Mon Jul 07 2003 - 03:25:27 CDT)
  • How to do a rigid solvent model? (Fri Jul 04 2003 - 09:30:00 CDT)
  • Algorithm for the motion equations? (Fri Mar 14 2003 - 06:20:41 CST)
• Marco Preto
  • Re: NVT system implosion!!! (Wed Oct 30 2002 - 12:46:07 CST)
  • NVT system implosion!!! (Wed Oct 30 2002 - 18:29:24 CST)
  • Re: Minimization problem w/ counter-ion ! (Wed Oct 30 2002 - 13:11:58 CST)
  • Minimization problem w/ counter-ion ! (Wed Oct 30 2002 - 20:54:27 CST)
  • Re: no MD output (Wed Oct 30 2002 - 12:33:30 CST)
  • Re: MD steps limit in sander (Amber 6) (Wed Oct 30 2002 - 21:41:01 CST)
  • MD steps limit in sander (Amber 6) (Wed Oct 30 2002 - 20:09:14 CST)
• Margaret S. Cheung
  • AMBER: How can I set ntx=7, but exclude the velocity? (Tue Sep 23 2003 - 10:30:28 CDT)
  • Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. (Tue Aug 12 2003 - 14:46:24 CDT)
  • AMBER: question to calculate diffusion coefficient under periodic boundary conditions. (Tue Aug 12 2003 - 13:56:47 CDT)
• Margaret Shun Cheung
  • web link for PLEP is not available. (Tue Jun 17 2003 - 15:28:40 CDT)
  • A question of how to choose a appropriate box size for imposing periodic boundary conditions in the simulations. (Fri May 23 2003 - 10:18:39 CDT)
  • Re: Please help on xleap: FATAL ERROR (Fri May 23 2003 - 09:06:10 CDT)
  • Please help on xleap: FATAL ERROR (Thu May 22 2003 - 17:20:42 CDT)
  • a question about constructing a periodic box by PLEP. (Tue May 20 2003 - 10:48:56 CDT)
• Maria Zavodszky
  • nucgen.dat (Thu May 15 2003 - 13:37:14 CDT)
• Mark K. Dean
  • AMBER: Addles (Wed Oct 08 2003 - 09:46:41 CDT)
• Markus Drumm
  • Re: Analysis of close waters (Thu Feb 27 2003 - 06:24:13 CST)
  • Analysis of close waters (Wed Feb 26 2003 - 06:23:25 CST)
• Martin Klvana
  • Preparation of RESP input from GAUSSIAN output (Mon Mar 17 2003 - 06:55:24 CST)
• Martin Lepsik
  • Re: AMBER: lifetime in ptraj hbond (Fri Dec 12 2003 - 07:29:28 CST)
  • Re: AMBER: Reverse TI run (Tue Oct 14 2003 - 08:02:22 CDT)
  • AMBER: Reverse TI run (Mon Oct 13 2003 - 11:55:03 CDT)
  • Re: AMBER: Atomic charges and internal H-bond (Wed Oct 08 2003 - 03:44:21 CDT)
  • AMBER: Atomic charges and internal H-bond (Tue Oct 07 2003 - 06:41:19 CDT)
  • Re: AMBER: calculation of LJ 12-6 from .dat file (fwd)-CORRECTION!!! (Fri Oct 03 2003 - 04:56:07 CDT)
  • Re: AMBER: calculation of LJ 12-6 from .dat file (fwd) (Fri Oct 03 2003 - 04:53:50 CDT)
  • Re: AMBER: FF parameters for BOC - group (Fri Sep 12 2003 - 09:57:24 CDT)
  • AMBER: MM-GB/PBSA:Main-chain/side-chain decomposition in ligands (Mon Aug 18 2003 - 08:12:51 CDT)
  • ALAscan of Proline (Mon Jul 07 2003 - 16:14:09 CDT)
• Martin Mucha
  • AMBER: polarizability and PME (Sat Sep 27 2003 - 09:46:08 CDT)
  • AMBER: minimum image convention mystery (Sat Aug 16 2003 - 15:42:37 CDT)
• Marvin Rich
  • Re: tip5p water model (Thu Mar 13 2003 - 12:35:22 CST)
  • tip5p water model (Thu Mar 13 2003 - 11:44:04 CST)
• Masaki Tomimoto
  • RE: Question about BELLY NMODE (Fri May 02 2003 - 10:46:36 CDT)
  • Question about BELLY NMODE (Fri May 02 2003 - 10:30:36 CDT)
  • Simple math of memory calculation for nmode (Thu May 01 2003 - 13:26:08 CDT)
  • Question: Nmode with counter ions. (Thu Apr 24 2003 - 12:09:02 CDT)
• Matheus Froeyen
  • Re: jarrod (Fri Jun 13 2003 - 02:36:14 CDT)
• Mauro Carlos Costa Ribeiro
  • using antechamber (Tue Mar 18 2003 - 10:39:44 CST)
  • Re: using xleap (Wed Mar 12 2003 - 11:29:23 CST)
  • using xleap (Tue Mar 11 2003 - 12:33:47 CST)
  • installing AMBER 7 (Mon Mar 10 2003 - 13:11:46 CST)
• Maverick
  • Questoin about temperature (Fri May 02 2003 - 00:27:29 CDT)
• McAteer, Kathleen
  • AMBER: FW: Residual dipolar couplings (Fri Sep 26 2003 - 14:44:57 CDT)
  • RE: Residual dipolar couplings (Wed May 21 2003 - 12:49:18 CDT)
  • Residual dipolar couplings (Tue May 20 2003 - 16:03:58 CDT)
  • Residual dipolar couplings (Wed Apr 30 2003 - 12:56:34 CDT)
• Mcneils
  • VXllig Legal geld Verdienen Ohne Risiko! (Tue Jul 01 2003 - 02:30:43 CDT)
• Meg McCarrick
  • RE: AMBER: antechamber test failure (Tue Nov 18 2003 - 11:06:12 CST)
  • AMBER: antechamber test failure (Mon Nov 17 2003 - 14:39:58 CST)
• meiselba
  • Dummy-parameters in Amber? (Thu Jan 23 2003 - 04:39:17 CST)
  • free energy perturbation (Gibbs/Amber 5)? (Thu Jan 09 2003 - 10:49:09 CST)
• Mengjuei Hsieh
  • Re: AMBER: Compiling antechamber on amber 8 (Fri Oct 03 2003 - 19:42:32 CDT)
  • AMBER: Compiling antechamber on amber 8 (Fri Oct 03 2003 - 05:10:35 CDT)
  • Re: AMBER: Compiling sander with single precision (Wed Sep 17 2003 - 16:56:34 CDT)
  • AMBER: Benchmark of AMBER on Apple G5 machine (Mon Sep 15 2003 - 15:56:43 CDT)
  • Re: amber web site (Wed Feb 12 2003 - 14:59:11 CST)
• Mey Khalili
  • AMBER: umbrella sampling with AMBER (Mon Dec 22 2003 - 17:14:24 CST)
• MF Yang
  • GB model (Tue Jun 10 2003 - 14:54:33 CDT)
• Mi-Kyung Seo
  • AMBER: complete pdb structure (Wed Aug 13 2003 - 17:41:52 CDT)
  • AMBER: "irstrnt=1"in input file for RESP (Mon Aug 11 2003 - 17:26:30 CDT)
  • AMBER: saveamberprep and saveoff in xLeap (Fri Aug 08 2003 - 12:39:37 CDT)
  • AMBER: saveamberprep in xLeap (Thu Aug 07 2003 - 22:38:24 CDT)
  • AMBER: Insight pdb file in xleap (Thu Aug 07 2003 - 18:09:47 CDT)
  • AMBER: import pdb file in xleap (Thu Aug 07 2003 - 14:07:17 CDT)
  • AMBER: (no subject) (Wed Jul 30 2003 - 14:00:49 CDT)
  • AMBER: combine prep files (Tue Jul 29 2003 - 16:14:52 CDT)
• Michael Crowley
  • Re: AMBER: Reverse TI run (Wed Oct 15 2003 - 04:55:39 CDT)
  • Re: AMBER: mfef90 - installation problem (Wed Sep 17 2003 - 12:28:19 CDT)
  • Re: AMBER: problems with periodic boundary conditions (Fri Sep 05 2003 - 09:32:29 CDT)
  • Re: AMBER: machine dependent? (Tue Aug 12 2003 - 09:24:58 CDT)
  • Re: mpirun problem: no rsh (Wed Jun 18 2003 - 14:04:52 CDT)
  • Re: run sander? (Tue Jun 03 2003 - 07:42:53 CDT)
  • Re: EWALD BOMB (Tue May 27 2003 - 10:45:22 CDT)
  • Re: non-periodic system (Wed May 21 2003 - 18:27:03 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 12:30:53 CDT)
  • Re: mpi/sander help (Fri Feb 07 2003 - 16:05:10 CST)
  • Re: Amber7 & mpich (Tue Feb 04 2003 - 11:56:22 CST)
• Michael Dolan
  • Re: AMBER: non-bonded cutoffs (Fri Sep 26 2003 - 10:39:34 CDT)
  • AMBER: non-bonded cutoffs (Fri Sep 26 2003 - 10:17:16 CDT)
• Michael Ford
  • Re: desolvation energy in mm_pbsa (Tue Feb 04 2003 - 08:21:15 CST)
  • Re: SASA calculation (Mon Feb 03 2003 - 17:22:26 CST)
  • Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution) (Wed Jan 15 2003 - 12:02:52 CST)
  • Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in (Wed Jan 15 2003 - 12:00:34 CST)
  • how to stop mapping of N- and C-terminal residues in xleap (Tue Jan 14 2003 - 13:37:27 CST)
  • Re: mm_gbsa: Unit 5 Error on OPEN: sander_com.in (Tue Jan 14 2003 - 11:34:33 CST)
• Michael Trieb
  • profec (Mon Mar 10 2003 - 08:46:40 CST)
  • water reordering in sander (Tue Jan 07 2003 - 07:43:38 CST)
• Michal Otyepka
  • AMBER: calculation of LJ 12-6 from .dat file (fwd) (Thu Oct 02 2003 - 09:53:27 CDT)
  • Hybdrogen bonds and LJ 10-12 (Wed May 21 2003 - 04:49:47 CDT)
  • Re: Simulation under physiological conditions (Thu May 15 2003 - 10:50:44 CDT)
  • Simulation under physiological conditions (Thu May 15 2003 - 10:02:34 CDT)
  • decrease a force const. for angle (Mon Feb 10 2003 - 06:47:35 CST)
• Michele Lunelli
  • Re: AMBER: TEMP is not reaching 300K (Fri Jul 25 2003 - 10:27:09 CDT)
  • AMBER: dielectric in sander (Mon Jul 21 2003 - 10:36:19 CDT)
• Miguel de Federico
  • Diferences in gibbs (Tue Mar 18 2003 - 03:37:21 CST)
  • Compiling Amber7 for linux (Fri Mar 14 2003 - 10:49:06 CST)
  • GIBBS - Non periodic simulations. (Mon Mar 03 2003 - 12:08:03 CST)
  • Re: Proper torsion parameters missing? (Fri Jan 24 2003 - 03:27:21 CST)
  • Re: Dummy-parameters in Amber? (Thu Jan 23 2003 - 05:07:14 CST)
  • Ewald error (Mon Jan 20 2003 - 09:32:21 CST)
  • GIBBS - Routine TORCON failed. Required change is too large. (Thu Jan 09 2003 - 04:11:41 CST)
• Ming Lei
  • RE: AMBER: make clean doesn't clean leap (Tue Nov 04 2003 - 10:01:26 CST)
  • RE: AMBER: Carnal Input file (Mon Sep 22 2003 - 22:34:05 CDT)
  • RE: AMBER: charge of IRON in HEME!! (Fri Sep 05 2003 - 13:15:32 CDT)
  • RE: AMBER: CARNAL (Mon Aug 25 2003 - 15:12:50 CDT)
  • RE: AMBER: CARNAL (Mon Aug 25 2003 - 14:27:42 CDT)
  • AMBER: About the limitation of characters on one line in carnal input fi le (Thu Aug 07 2003 - 16:16:26 CDT)
• Mithun Mitra
  • AMBER: problem with pdb files (Sun Oct 12 2003 - 15:12:45 CDT)
• Miyashita, Osamu
  • Re: Quasi-harmonic analysis (Fri Jan 31 2003 - 12:25:23 CST)
• Mizuguchi Mineyuki
  • AMBER: /exe/teLeap does not exist (Thu Jul 24 2003 - 02:23:55 CDT)
• Monica
  • unit of energy (Thu Mar 27 2003 - 02:01:56 CST)
• Monika Fuxreiter
  • AMBER: problems with periodic boundary conditions (Fri Sep 05 2003 - 04:17:40 CDT)
  • sander,ntt=5 (Fri Jul 04 2003 - 06:17:33 CDT)
• Mu Yuguang (Dr)
  • AMBER: rotation removal in sander GB (Fri Nov 14 2003 - 09:40:56 CST)
  • AMBER: SC45 (Mon Oct 27 2003 - 19:12:29 CST)
  • RE: AMBER: memory SC45 (Tue Oct 21 2003 - 20:19:45 CDT)
  • RE: AMBER: memory SC45 (Mon Oct 20 2003 - 22:46:50 CDT)
  • AMBER: memory SC45 (Mon Oct 20 2003 - 21:39:29 CDT)
  • RE: AMBER: tru64 alpha (Thu Oct 16 2003 - 21:08:14 CDT)
  • RE: AMBER: tru64 alpha (Thu Oct 16 2003 - 20:52:41 CDT)
  • RE: AMBER: tru64 alpha (Thu Oct 16 2003 - 19:40:56 CDT)
  • RE: AMBER: tru64 alpha (Wed Oct 15 2003 - 21:59:29 CDT)
  • RE: AMBER: tru64 alpha (Wed Oct 15 2003 - 02:07:45 CDT)
  • AMBER: tru64 alpha (Tue Oct 14 2003 - 20:19:06 CDT)
• myang
  • AMBER: order parameter (Fri Dec 12 2003 - 14:25:17 CST)
  • RE: AMBER: one more question (Sat Oct 18 2003 - 13:51:33 CDT)
  • RE: AMBER: charmm force field in amber (Thu Oct 16 2003 - 15:57:47 CDT)
  • RE: AMBER: H-bond analysis (Fri Oct 03 2003 - 13:08:49 CDT)
• N. Jiten Singh
  • Isotropic Solvent Box (Thu Feb 13 2003 - 05:28:55 CST)
  • Including the Peroidiic Box info ?? (Wed Feb 12 2003 - 21:21:41 CST)
  • Re: Re: Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 08:13:17 CST)
  • Error Massage in Sander amber7 in Linux (Wed Feb 12 2003 - 07:07:26 CST)
  • Acetonitrile parameters (Mon Feb 03 2003 - 23:52:16 CST)
  • Chloroform Parameters (Thu Jan 23 2003 - 23:27:24 CST)
• nabe
  • Re: AMBER: Separation of a Water molecules (Wed Nov 12 2003 - 20:32:45 CST)
  • Re: AMBER: Correction [Separation of a Water molecules] (Wed Nov 12 2003 - 02:53:49 CST)
  • Re: AMBER: Separation of a Water molecules (Wed Nov 12 2003 - 02:43:59 CST)
  • AMBER: Separation of a Water molecules (Tue Nov 11 2003 - 18:59:22 CST)
• Narang Manpreet Kaur
  • AMBER: (no subject) (Tue Aug 05 2003 - 08:55:57 CDT)
• Narang Manpreet Kaur
  • AMBER: Dynamics and Simulated Annealing (Fri Jul 25 2003 - 08:03:52 CDT)
  • Re: AMBER: (no subject) (Thu Jul 24 2003 - 23:36:54 CDT)
  • AMBER: (no subject) (Thu Jul 24 2003 - 06:57:36 CDT)
  • (no subject) (Sat May 03 2003 - 00:02:20 CDT)
• Natasja Brooijmans
  • Re[2]: AMBER: antechamber problem (Wed Aug 20 2003 - 17:26:58 CDT)
  • Re: AMBER: AMBER7 & mpich : (no-attachment version) (Sat Aug 02 2003 - 13:24:59 CDT)
  • Re: AMBER: Questions about mm_pbsa and alanine scanning (Tue Jul 15 2003 - 15:42:40 CDT)
  • Re: unifying trajectory files (Wed Jun 25 2003 - 11:25:41 CDT)
  • Re: electrostatic interaction energ. /delphi (Tue Jun 24 2003 - 14:45:22 CDT)
  • Re: Sander error (Tue Jun 17 2003 - 13:44:53 CDT)
  • Re: MD input file for MM-PBSA calculations (Sat May 24 2003 - 11:28:39 CDT)
  • Re: initial velocity (Fri May 02 2003 - 09:18:26 CDT)
  • Re: job stopped (Thu Apr 24 2003 - 13:55:06 CDT)
  • Re: ALA-scan problem with mm_pbsa.pl (Wed Apr 16 2003 - 13:14:55 CDT)
  • ALA-scan problem with mm_pbsa.pl (Sun Apr 13 2003 - 17:21:03 CDT)
  • Re: Bugfixes (Fri Apr 11 2003 - 11:49:59 CDT)
  • Re: Forwarded mail.... (Wed Mar 05 2003 - 13:02:42 CST)
  • Re: How to put the outside atoms back to the truncated octahedron box? (Wed Feb 12 2003 - 14:00:50 CST)
• Nathan A. Baker
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 20:14:47 CDT)
  • AMBER: NaCl ion pairs in TIP3P water box (Wed Sep 24 2003 - 15:13:11 CDT)
  • Re: CCL:electrostatic potential calculations (Mon Jan 13 2003 - 16:27:00 CST)
• Ndubuisi Emmanuel Okoro
  • Polymers (Wed Jan 29 2003 - 15:40:53 CST)
  • Polymers (Thu Jan 23 2003 - 21:12:10 CST)
• Nicholson, James D Mr ARO
  • Antechamber Manual (Fri Mar 28 2003 - 14:17:12 CST)
• Nick Polfer
  • Flag for antechamber (Wed Jun 18 2003 - 03:59:01 CDT)
  • Annealing blown up (Thu Apr 24 2003 - 14:02:38 CDT)
  • new amino acid residues (Thu Jan 30 2003 - 06:58:41 CST)
• Nicolas Le Novere
  • Postdoctoral position available in Molecular Modeling (Fri Feb 14 2003 - 04:27:56 CST)
• Nicolas Grima
  • Re: AMBER: Compiling 64-bit version on AIX (Tue Sep 09 2003 - 02:11:03 CDT)
• Nicole A Rutkowski
  • Amber Documents (Mon Feb 17 2003 - 13:42:26 CST)
• nie beining
  • Re: AMBER: What does this error message mean? (Fri Oct 31 2003 - 11:41:27 CST)
  • AMBER: What does this error message mean? (Fri Oct 31 2003 - 09:34:40 CST)
  • AMBER: pair-cutoff (Tue Sep 23 2003 - 10:40:32 CDT)
  • AMBER: Slower simulation and pair-range cutoff? (Mon Sep 22 2003 - 12:11:11 CDT)
  • AMBER: slower simulation (Mon Sep 22 2003 - 10:43:24 CDT)
  • AMBER: slow simulation (Mon Sep 22 2003 - 01:46:21 CDT)
  • AMBER: error message is the same after I added a title (Tue Sep 02 2003 - 10:20:11 CDT)
  • title card? Re: AMBER: what can't I use ibelly? (Mon Sep 01 2003 - 21:39:06 CDT)
  • AMBER: Could you please give me an example? Thanks! (Thu Aug 28 2003 - 15:04:00 CDT)
  • AMBER: what can't I use ibelly? (Thu Aug 28 2003 - 14:30:23 CDT)
• Nikitina Ekaterina
  • Re: From Dr. Ekaterina Nikitina (Sun May 25 2003 - 05:26:09 CDT)
• Niko Jukarainen
  • RE: AMBER: xLEAP Problem (Fri Sep 19 2003 - 16:18:30 CDT)
  • RE: AMBER: LEaP not compiling (Wed Aug 27 2003 - 23:58:24 CDT)
  • RE: AMBER: LEaP not compiling (Wed Aug 27 2003 - 10:58:52 CDT)
  • AMBER: LEaP not compiling (Wed Aug 27 2003 - 09:50:01 CDT)
• Nikolai Smolin
  • AMBER: about H-bond definition for TIP3P (Tue Dec 02 2003 - 07:44:19 CST)
  • AMBER: missing of VdW Parameters for N3 (Fri Nov 21 2003 - 03:45:09 CST)
  • about urea and glycerol (Fri Feb 21 2003 - 05:04:33 CST)
• Nori
  • Re: delphi with amber 7 (Fri Jul 11 2003 - 21:15:30 CDT)
• Noriaki Okimoto
  • delphi with amber 7 (Fri Jul 11 2003 - 13:34:34 CDT)
• northrop_at_chem.ucla.edu
  • AMBER: GBSA problem (Thu Dec 11 2003 - 17:28:27 CST)
  • AMBER: MeCNBOX & EWALD bomb (Fri Oct 10 2003 - 19:31:46 CDT)
  • AMBER: TTF parameters (Tue Sep 30 2003 - 01:49:20 CDT)
  • Re: AMBER: MeCNBOX (Thu Sep 25 2003 - 15:47:03 CDT)
  • Re: AMBER: MeCNBOX (Thu Sep 25 2003 - 15:40:37 CDT)
  • AMBER: MeCNBOX (Thu Sep 25 2003 - 14:35:03 CDT)
  • AMBER: EWALD BOMB and solvent density problem (Thu Sep 11 2003 - 13:28:51 CDT)
• Obdulia Rabal
  • AMBER: change force constants (Mon Nov 10 2003 - 11:27:23 CST)
  • RE: AMBER: FILE UNITIO.C (Wed Jul 23 2003 - 02:51:22 CDT)
  • AMBER: FILE UNITIO.C (Tue Jul 22 2003 - 13:15:48 CDT)
  • AMBER: RADII in DELPHI (Thu Jul 17 2003 - 03:58:57 CDT)
  • MGB RADII PARAMETRIZATION (Tue Jun 03 2003 - 06:08:15 CDT)
  • EGB problem in MMPBSA (Mon Jun 02 2003 - 06:11:45 CDT)
  • Phosphotyrosine parametrization (Thu May 08 2003 - 02:51:19 CDT)
• Oliver Hucke
  • Re: adding hydrogens (Wed Feb 19 2003 - 02:02:30 CST)
• Omar Wahab
  • AMBER: water box problem (Thu Jul 24 2003 - 03:32:35 CDT)
  • Minimisation - peek_ewald_inpcrd: SHOULD NOT BE HERE (Mon May 12 2003 - 04:49:52 CDT)
• Osmar Norberto de Souza
  • Re: AMBER: aminoacid mutation (Tue Oct 28 2003 - 14:38:00 CST)
  • Neutral ARG (Mon Feb 03 2003 - 11:19:02 CST)
• pantelo_at_okstate.edu
  • Sander_classic output: NAN (Mon Jul 14 2003 - 11:07:19 CDT)
• Pascal Auffinger
  • Re: AMBER: Mg2+ parameters for RNA usage (Wed Dec 10 2003 - 09:30:47 CST)
  • Re: AMBER: Pseudouridine force field parameters (Sun Nov 30 2003 - 09:58:30 CST)
  • Re: AMBER: NaCl ion pairs in TIP3P water box (Thu Sep 25 2003 - 08:30:08 CDT)
• Pascal Bonnet
  • Re: AMBER: MeCNBOX (Fri Sep 26 2003 - 03:38:03 CDT)
  • AMBER: plane angle. (Mon Sep 22 2003 - 10:14:44 CDT)
  • Re: AMBER: altering mass in .top file (Thu Sep 11 2003 - 05:05:15 CDT)
  • Re: using antechamber (Tue Mar 18 2003 - 10:36:23 CST)
  • Re: MM_PBSA Errors (Wed Feb 12 2003 - 03:50:23 CST)
  • Re: Acetonitrile parameters (Tue Feb 04 2003 - 09:22:04 CST)
• Patricia Burgess
  • gibbs input file (Sun Feb 02 2003 - 18:01:59 CST)
  • Gibbs tutorial question (Wed Jan 22 2003 - 14:27:34 CST)
• Patrizia Rossi
  • barium (Mon Mar 10 2003 - 01:38:13 CST)
• Paula Petrone
  • Ewald: coeff, error estimate (Thu May 01 2003 - 11:05:28 CDT)
  • Gibbs: Electrostatic Decoupling (Tue Feb 18 2003 - 11:31:41 CST)
  • Gibbs: DynamicWin and NSTMEQ? (Thu Feb 06 2003 - 12:48:02 CST)
  • Gibbs dummy atom (Fri Jan 31 2003 - 17:49:52 CST)
• Peng Tao
  • Using GLYCAM in sander with a non-zero 10-12 coefficient (Wed May 14 2003 - 13:54:32 CDT)
  • Re: Simple question about sander parameter set (Tue May 13 2003 - 10:19:50 CDT)
  • Simple question about sander parameter set (Tue May 13 2003 - 09:44:40 CDT)
  • Description of ATOM type in GLYCAM (Tue Apr 29 2003 - 14:14:52 CDT)
  • How to use GLYCAM force field in AMBER (Tue Apr 22 2003 - 10:08:06 CDT)
• pengyo_at_rwja.umdnj.edu
  • atomic positional fluctuation (Thu May 15 2003 - 13:22:25 CDT)
  • Re: problem about virtual box? (Thu May 01 2003 - 11:20:10 CDT)
• Perdita Barran
  • AMBER: Lone pairs and resp (Mon Nov 17 2003 - 10:55:05 CST)
  • AMBER: Lone pairs and resp (Mon Nov 17 2003 - 10:49:35 CST)
• Pete Koladich
  • RE: Software Sales (Tue Jun 24 2003 - 15:41:53 CDT)
• Peter Anderson
  • Strange F.E.P. behavior (Sun Jul 13 2003 - 08:15:49 CDT)
  • Adding missing parameters (Wed Jul 09 2003 - 13:18:33 CDT)
  • memory shortage with mm_pbsa (Tue Jul 08 2003 - 19:36:09 CDT)
  • vlimit exceeded (Sat Jul 05 2003 - 11:39:01 CDT)
  • unifying trajectory files (Wed Jun 25 2003 - 10:57:42 CDT)
  • Another mm_pbsa problem (Tue Jun 24 2003 - 11:47:58 CDT)
  • mm_pbsa problem (Fri Jun 20 2003 - 17:31:17 CDT)
  • mpirun problem: no rsh (Wed Jun 18 2003 - 12:50:26 CDT)
  • saving trajectory of solute only (Mon Jun 09 2003 - 11:01:53 CDT)
  • belly vs. position restraints (Wed Jun 04 2003 - 09:17:05 CDT)
  • Need help recompiling (Mon Jun 02 2003 - 09:23:11 CDT)
  • Use of Mg2+ in AMBER 7 (Thu May 08 2003 - 13:55:06 CDT)
• Peter Gannett
  • AMBER: Curves parameters UU and PP (Fri Dec 19 2003 - 22:08:02 CST)
  • Re: AMBER: Pseudouridine force field parameters (Tue Dec 02 2003 - 06:45:01 CST)
  • Re: AMBER: Pseudouridine force field parameters (Sun Nov 30 2003 - 09:56:28 CST)
  • AMBER: Pseudouridine force field parameters (Sat Nov 29 2003 - 18:27:38 CST)
  • Re: AMBER: how to measure the minor groove widths of a DNA? (Tue Oct 28 2003 - 13:43:22 CST)
  • AMBER: Online model of 2C9 (Thu Sep 25 2003 - 14:23:22 CDT)
  • mm_pbsa and B/Z DNA relative stabilities (Wed May 14 2003 - 06:54:47 CDT)
  • Re: GRASP (fwd) (Fri Mar 07 2003 - 12:50:01 CST)
  • Re: compatibility of amber with NAMD (Thu Feb 13 2003 - 16:05:54 CST)
  • Re: average structure generated by carnal (Tue Jan 21 2003 - 14:14:38 CST)
  • Re: electrostatic potential calculations (Mon Jan 13 2003 - 11:32:19 CST)
• Peter Oelschlaeger
  • Re: AMBER: initial velocity (Fri Dec 19 2003 - 20:08:43 CST)
  • Re: AMBER: Using NWCHEM for esp? (Fri Sep 05 2003 - 23:03:29 CDT)
  • AMBER: Spartan and AMBER7 (Fri Aug 22 2003 - 21:52:21 CDT)
• Peter VARNAI
  • Re: AMBER: Mg2+ parameters for RNA usage (Wed Dec 10 2003 - 10:06:30 CST)
  • AMBER: 1 fs timestep for GB? (Tue Nov 25 2003 - 11:48:35 CST)
  • AMBER: Generalized Born parameters (Thu Sep 18 2003 - 13:51:24 CDT)
  • octahedral volume (Fri Jan 17 2003 - 04:26:58 CST)
• Petrodler_at_aol.com
  • AMBER: radial distribution-function by Ptraj (Tue Sep 09 2003 - 04:15:10 CDT)
  • Re: AMBER: chemical potential (Wed Jul 30 2003 - 02:50:05 CDT)
  • AMBER: chemical potential (Tue Jul 29 2003 - 01:28:57 CDT)
  • solventbox at constant pressure (Wed Jun 04 2003 - 02:19:05 CDT)
  • Organic Solvents (Tue Apr 22 2003 - 05:57:11 CDT)
• Pingna Xu
  • AMBER: about some of the cards in Sander 7 (Wed Nov 12 2003 - 14:09:12 CST)
  • AMBER: more questions about igb (Sun Oct 19 2003 - 22:54:49 CDT)
  • AMBER: one more question (Sat Oct 18 2003 - 13:01:32 CDT)
  • AMBER: a question (Fri Oct 17 2003 - 16:01:12 CDT)
• Piotr Cieplak
  • Re: AMBER: Basic potential question: (Wed Dec 24 2003 - 12:47:57 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 16:02:33 CST)
  • Re: AMBER: charge fitting (Tue Nov 25 2003 - 11:59:59 CST)
  • Re: AMBER: missing of VdW Parameters for N3 (Fri Nov 21 2003 - 12:56:53 CST)
  • Re: AMBER: RNA and Protein questions (also some general questions) (Thu Nov 13 2003 - 11:37:14 CST)
  • Re: AMBER: Re:atomic charges and internal H-bond (Tue Oct 07 2003 - 16:36:10 CDT)
  • Re: AMBER: Atomic charges and internal H-bond (Tue Oct 07 2003 - 12:41:49 CDT)
  • Re: AMBER: frequency analysis (Wed Jul 30 2003 - 16:49:08 CDT)
  • Re: AMBER: Re: methylphosphonate (Tue Jul 15 2003 - 00:01:59 CDT)
  • Re: AMBER: Re: methylphosphonate (Mon Jul 14 2003 - 19:43:14 CDT)
• Pradipta Bandyopadhyay
  • Re: AMBER: MD simulation: enzyme and its substrate!! (Wed Oct 29 2003 - 14:26:17 CST)
  • AMBER: Re:atomic charges and internal H-bond (Tue Oct 07 2003 - 13:24:18 CDT)
  • AMBER: SHAKE for TIP4P! (Thu Oct 02 2003 - 18:25:49 CDT)
  • AMBER: Re:MeCNBOX (Thu Sep 25 2003 - 16:23:09 CDT)
  • AMBER: 'high' temp. simulation!! (Fri Sep 19 2003 - 15:09:05 CDT)
  • AMBER: MD problem!! (Thu Sep 18 2003 - 15:35:36 CDT)
  • AMBER: re: MD problem!! (Thu Sep 18 2003 - 12:36:59 CDT)
  • AMBER: MD problem! (Tue Sep 16 2003 - 19:33:17 CDT)
  • AMBER: charge of IRON in HEME!! (Thu Sep 04 2003 - 19:28:11 CDT)
• Pratul Agarwal
  • Re: Protein - DNA complex simulation - protocol (Tue Apr 29 2003 - 09:39:18 CDT)
  • Re: size of a simulation system (Wed Apr 02 2003 - 14:02:29 CST)
  • Re: size of a simulation system (Wed Apr 02 2003 - 08:32:44 CST)
  • Re: Domain/Helix movement/MD (Fri Jan 31 2003 - 15:00:54 CST)
  • Quasi-harmonic analysis (Thu Jan 30 2003 - 17:48:22 CST)
  • Re: coordinates for quasih (Mon Jan 13 2003 - 09:48:17 CST)
• Pratul K. Agarwal
  • Re: AMBER: Compiling 64-bit version on AIX (Tue Sep 09 2003 - 12:01:13 CDT)
  • Re: AMBER: Compiling 64-bit version on AIX (Tue Sep 09 2003 - 10:45:58 CDT)
  • AMBER: Compiling 64-bit version on AIX (Mon Sep 08 2003 - 21:00:55 CDT)
  • Re: AMBER: Comparing PE of different conformations (Thu Aug 07 2003 - 13:21:07 CDT)
  • Re: AMBER: Comparing PE of different conformations (Wed Aug 06 2003 - 11:40:16 CDT)
  • AMBER: Comparing PE of different conformations (Wed Aug 06 2003 - 11:14:03 CDT)
• Prof.S.B.Rai
  • Regarding the quotation for AMBER 7 Programme (Wed Mar 12 2003 - 01:56:46 CST)
• PSR04996_at_mailstudenti.unimi.it
  • AMBER: roar topology and coordinate files (Mon Dec 29 2003 - 03:11:28 CST)
  • glycam force field with amber (Fri Jun 13 2003 - 06:28:07 CDT)
• ptolonen_at_cc.joensuu.fi
  • 3 simultaneous simulations in one computer (Thu Jul 10 2003 - 06:20:15 CDT)
• pu xuemei
  • hexane parameters (Wed Feb 19 2003 - 06:06:50 CST)
  • hexane parameters (Wed Feb 12 2003 - 04:00:19 CST)
  • How much is minimum distance (Fri Jan 24 2003 - 01:11:29 CST)
  • How to control box size (Wed Jan 22 2003 - 06:58:53 CST)
  • equilibrated solvent box (Mon Jan 20 2003 - 02:55:26 CST)
  • equilibrated solvent box (Mon Jan 20 2003 - 02:54:33 CST)
• Qiang Lu
  • Re[2]: AMBER: mpich problem (Mon Nov 10 2003 - 18:07:06 CST)
  • Re[2]: AMBER: mpich problem (Sun Nov 09 2003 - 20:24:20 CST)
  • Re[2]: AMBER: mpich problem (Sun Nov 09 2003 - 20:27:09 CST)
  • Re[3]: AMBER: mpich problem (Sun Nov 09 2003 - 18:28:37 CST)
  • Re[2]: AMBER: mpich problem (Sun Nov 09 2003 - 16:27:47 CST)
  • AMBER: mpich problem (Sat Nov 08 2003 - 02:23:50 CST)
  • AMBER: mpich problem (Sat Nov 08 2003 - 02:25:08 CST)
  • AMBER: JAC on NCSA titan (Itanium 2 833MHZ) (Wed Oct 29 2003 - 16:09:56 CST)
  • AMBER: nmanal projection (Fri Oct 10 2003 - 17:22:48 CDT)
  • Re: AMBER: charge of IRON in HEME!! (Thu Sep 04 2003 - 19:40:48 CDT)
  • Re: AMBER: atomic clash or structure size? (Tue Sep 02 2003 - 16:20:32 CDT)
  • Re: AMBER: sander minimization (Fri Aug 29 2003 - 16:13:53 CDT)
  • Re[2]: AMBER: antechamber problem (Wed Aug 20 2003 - 17:17:30 CDT)
  • AMBER: antechamber problem (Wed Aug 20 2003 - 13:56:14 CDT)
  • AMBER: nmanal's rvec file (Tue Aug 19 2003 - 18:19:27 CDT)
  • Re[2]: AMBER: nmanal's error message (Mon Aug 18 2003 - 19:10:29 CDT)
  • AMBER: nmanal's error message (Mon Aug 18 2003 - 17:23:20 CDT)
  • Re[2]: AMBER: nmanal in amber7 (Mon Aug 18 2003 - 14:17:30 CDT)
  • AMBER: nmanal in amber7 (Mon Aug 18 2003 - 12:41:42 CDT)
  • AMBER: tleap under amber6 (Mon Aug 18 2003 - 12:32:05 CDT)
• Qing Zhang
  • AMBER: absolute vs. relative binding free energy (Wed Nov 05 2003 - 18:24:45 CST)
  • AMBER: ibelly in AMBER 6 (Fri Oct 17 2003 - 17:32:21 CDT)
  • AMBER: Accuracy of PB solvation energy (Fri Sep 05 2003 - 12:15:15 CDT)
  • AMBER: Re: memory shortage with mm_pbsa - some more thoughts (Mon Jul 14 2003 - 18:10:26 CDT)
  • Newton-Raphson minimization for large systems (Wed May 14 2003 - 18:09:07 CDT)
• quch quch
  • resp for charged molecule? (Thu Jul 10 2003 - 16:09:08 CDT)
  • Re: run sander? (Mon Jun 02 2003 - 13:52:22 CDT)
  • run sander? (Mon Jun 02 2003 - 11:22:35 CDT)
  • antechamber read gaussian file (Thu May 29 2003 - 15:32:10 CDT)
  • antechamber read gaussian file (Thu May 29 2003 - 15:32:14 CDT)
• Rachel Ward
  • AMBER: AMBER quasih question(s) (Mon Sep 29 2003 - 14:39:17 CDT)
• Raghunadha Reddy Burri
  • AMBER: Re: initial structures (Mon Dec 08 2003 - 11:19:10 CST)
  • AMBER: initial structures (Mon Dec 08 2003 - 09:21:28 CST)
• raist_at_mmb.pcb.ub.es
  • AMBER: Restarting MD amber7 (Mon Nov 17 2003 - 12:54:32 CST)
  • Re: AMBER: Problems restarting with sander (Fri Nov 14 2003 - 19:14:42 CST)
  • AMBER: Problems restarting with sander (Fri Nov 14 2003 - 15:26:07 CST)
• Raja Swaminathan
  • parallel version amber installation problem (Tue Jul 01 2003 - 06:09:43 CDT)
  • TFE input (Thu Jan 02 2003 - 04:37:41 CST)
• RAJA SWAMINATHAN
  • AMBER: TFE solvent box (Thu Dec 04 2003 - 22:34:03 CST)
  • AMBER: protein MD - problem (Mon Nov 24 2003 - 08:47:53 CST)
  • AMBER: H-bond analysis (Fri Oct 03 2003 - 11:11:17 CDT)
• Rajendra P. OJHA
  • AMBER: Hello (Sat Nov 29 2003 - 09:51:21 CST)
  • AMBER: mm_pbsa and antechamber (Sat Nov 22 2003 - 13:03:34 CST)
  • AMBER: dual processor (Sun Nov 16 2003 - 11:45:40 CST)
  • AMBER: MM_pbsa (Sun Nov 16 2003 - 11:35:23 CST)
  • AMBER: atomtypenumber (Tue Nov 04 2003 - 15:07:20 CST)
  • Re: Fwd: Re: Request for Amber7 (fwd) (Tue Apr 22 2003 - 04:53:12 CDT)
• Ramón Garduño-Juárez
  • MM_PBSA Errors (Tue Feb 11 2003 - 18:16:00 CST)
  • MM_PBSA for Linux (Wed Jan 22 2003 - 18:53:55 CST)
• Ran Ye
  • AMBER: vlimit? (Sun Dec 21 2003 - 16:15:57 CST)
  • Re: AMBER: add (Thu Jul 31 2003 - 17:03:43 CDT)
  • AMBER: add (Thu Jul 31 2003 - 15:08:30 CDT)
  • Re: AMBER: Non-standard Residue (Wed Jul 23 2003 - 11:08:03 CDT)
  • AMBER: Non-standard Residue (Tue Jul 22 2003 - 14:34:06 CDT)
• resister_at_pchome.com.tw
  • a question~~ (Mon Feb 24 2003 - 18:28:52 CST)
• Rhonda Torres
  • RE: AMBER: image question (Tue Nov 25 2003 - 12:50:36 CST)
  • AMBER: Re: AMBER water mediated contacts (Mon Nov 24 2003 - 11:51:31 CST)
  • Re: AMBER: about some of the cards in Sander 7 (Wed Nov 12 2003 - 14:35:43 CST)
  • AMBER: Re: AM1-BCC in Amber7 (Mon Nov 10 2003 - 12:22:19 CST)
  • RE: AMBER: what is the unit for the energy calculated from MM_PBSA? (Mon Oct 20 2003 - 20:19:09 CDT)
  • Re: AMBER: mm_pbsa example (Thu Oct 09 2003 - 16:09:33 CDT)
  • Re: AMBER: addions/xleap question (Wed Oct 01 2003 - 16:10:00 CDT)
  • Re: AMBER: Zn in antechamber (Fri Sep 26 2003 - 12:24:16 CDT)
  • Re: AMBER: Atom type in prepin file (Wed Aug 13 2003 - 17:38:26 CDT)
  • Re: AMBER: Insight pdb file in xleap (Thu Aug 07 2003 - 18:29:47 CDT)
• Richard Dayton Smith
  • (no subject) (Wed Jul 09 2003 - 12:23:38 CDT)
• Richard Smith
  • AMBER: Removal of Rotational and Translational Motion in AMBER6 (Mon Oct 27 2003 - 14:51:59 CST)
  • RE: AMBER: running sander_classic on multiple processors (Wed Oct 15 2003 - 14:09:57 CDT)
  • AMBER: running sander_classic on multiple processors (Tue Oct 14 2003 - 08:48:23 CDT)
  • RE: AMBER: SHAKE Problem (Thu Aug 07 2003 - 09:42:56 CDT)
  • AMBER: SHAKE Problem (Wed Aug 06 2003 - 15:02:30 CDT)
• rluo_at_uci.edu
  • AMBER: Temperature dependent properties of TIP4P and TIP5P (Mon Dec 08 2003 - 11:00:21 CST)
  • AMBER: Compiling sander with single precision (Tue Sep 16 2003 - 20:37:01 CDT)
  • Re: AMBER: MD simulations on small molecules immersed in sparse water shell (Tue Sep 16 2003 - 14:07:03 CDT)
  • Re: AMBER: MD simulations on small molecules immersed in sparse water shell (Tue Sep 16 2003 - 13:16:41 CDT)
  • Re: AMBER: question about ptraj? (Thu Jul 24 2003 - 11:48:54 CDT)
• Robert Cave
  • (no subject) (Tue Feb 25 2003 - 13:55:51 CST)
• Robert Duke
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 10:44:47 CST)
  • Re: AMBER: PMEMD Performance on Beowulf systems (Thu Dec 18 2003 - 22:35:40 CST)
  • Re: AMBER: Problem with MPI_Finalize (Tue Nov 18 2003 - 08:54:36 CST)
  • Re: AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD (Mon Nov 03 2003 - 13:31:34 CST)
  • AMBER: PMEMD 3.1 Release - High Scalability Update to PMEMD (Fri Oct 31 2003 - 09:40:37 CST)
  • Re: AMBER: memory SC45 (Tue Oct 21 2003 - 21:12:31 CDT)
  • Re: AMBER: memory SC45 (Tue Oct 21 2003 - 08:20:59 CDT)
  • Re: AMBER: memory SC45 (Tue Oct 21 2003 - 07:55:22 CDT)
  • Re: AMBER: memory SC45 (Mon Oct 20 2003 - 22:17:25 CDT)
  • Re: AMBER: ECC vs non-ECC (non-amber issue) (Mon Oct 20 2003 - 21:40:24 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Mon Oct 20 2003 - 20:06:22 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Mon Oct 20 2003 - 08:01:47 CDT)
  • Re: AMBER: tru64 alpha (Thu Oct 16 2003 - 21:50:08 CDT)
  • Re: AMBER: tru64 alpha (Thu Oct 16 2003 - 20:27:27 CDT)
  • Re: AMBER: tru64 alpha (Thu Oct 16 2003 - 20:18:41 CDT)
  • Re: AMBER: tru64 alpha (Thu Oct 16 2003 - 09:17:00 CDT)
  • Re: AMBER: tru64 alpha (Wed Oct 15 2003 - 22:41:57 CDT)
  • Re: AMBER: tru64 alpha (Wed Oct 15 2003 - 21:51:20 CDT)
  • Re: AMBER: Compiling AMBER, ie, number of atoms limit (Thu Oct 09 2003 - 17:18:27 CDT)
  • Re: Re: AMBER: nstlim (Wed Oct 01 2003 - 11:32:48 CDT)
  • Re: AMBER: nstlim (Mon Sep 29 2003 - 20:40:24 CDT)
  • Re: AMBER: residues and molecules (Wed Sep 24 2003 - 14:53:20 CDT)
  • AMBER: PMEMD 3.03 Update available (Tue Sep 23 2003 - 21:13:57 CDT)
  • Re: AMBER: PMEMD: dual XEON vs SGI cluster (Mon Sep 15 2003 - 17:55:28 CDT)
  • Re: AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space (Tue Aug 26 2003 - 20:53:06 CDT)
  • Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 (Mon Aug 25 2003 - 16:33:38 CDT)
  • AMBER: Apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 (Mon Aug 25 2003 - 15:41:08 CDT)
  • AMBER: Re: apparent PMEMD bug -- NTWPRT > 0 & IWRAP = 1 (Mon Aug 25 2003 - 14:20:48 CDT)
  • Fw: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 (Sat Aug 23 2003 - 22:44:06 CDT)
  • Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 (Sat Aug 23 2003 - 09:41:42 CDT)
  • Re: AMBER: Questions on Phi, Psi angles produced by pmemd/sander7 (Sat Aug 23 2003 - 07:41:49 CDT)
  • AMBER: PMEMD BUG ALERT!!! (Fri Aug 22 2003 - 15:50:02 CDT)
  • Re: AMBER: problems with pmemd (Fri Aug 22 2003 - 11:45:47 CDT)
  • AMBER: PMEMD 3.01 Update available (Wed Aug 20 2003 - 13:36:56 CDT)
  • Re: AMBER: pmemd (Mon Aug 18 2003 - 11:51:16 CDT)
  • Re: AMBER: pmemd (Mon Aug 18 2003 - 10:45:47 CDT)
  • Re: Fw: AMBER: PMEMD and EAMBER (Mon Aug 11 2003 - 08:49:36 CDT)
  • AMBER: PMEMD NMR Restraints fix (Fri Aug 08 2003 - 17:13:08 CDT)
  • Re: AMBER: PMEMD and EAMBER (Thu Aug 07 2003 - 16:06:11 CDT)
  • Re: AMBER: more than 100,000 atoms ? (Thu Aug 07 2003 - 15:33:36 CDT)
  • Re: AMBER: PMEMD and sander from AMBER6 performances (Thu Aug 07 2003 - 14:01:39 CDT)
  • Re: AMBER: Odd Problem with PMEMD (Tue Jul 22 2003 - 06:17:25 CDT)
  • Re: AMBER: PMEMD and sander from AMBER6 performances (Wed Jul 16 2003 - 22:11:55 CDT)
  • Mg++ polarizability (Tue Jun 03 2003 - 06:39:25 CDT)
• Robert G. Endres
  • distance-dependent dielectric function (Fri May 23 2003 - 10:44:27 CDT)
  • best force field for Protein+DNA (Fri May 23 2003 - 10:14:51 CDT)
  • Re: mm_pbsa and B/Z DNA relative stabilities (Wed May 14 2003 - 08:36:14 CDT)
  • Re: GB/SA (Wed Apr 30 2003 - 14:57:31 CDT)
  • Re: GB/SA (Mon Apr 28 2003 - 13:10:56 CDT)
  • GB/SA (Wed Apr 23 2003 - 11:26:14 CDT)
  • growing side chains (Mon Apr 07 2003 - 13:37:30 CDT)
  • Re: Zn2+ parameters (Sat Jan 25 2003 - 14:25:36 CST)
  • conformational sampling (Thu Jan 23 2003 - 08:17:57 CST)
  • solvent free energy, GB (Thu Jan 16 2003 - 15:33:36 CST)
• Robert J. Woods
  • Internal dielectric in MM-GBSA (Mon Feb 10 2003 - 13:29:36 CST)
  • Misaligned Coords from Alanine Scanning (Fri Feb 07 2003 - 09:54:07 CST)
• Roberto Gomperts
  • New Machine.sgi_mpi file (Thu Apr 03 2003 - 12:33:35 CST)
  • Re: SCSL (Thu Jan 23 2003 - 09:52:06 CST)
• ronnie
  • about molecular dynamics (Tue Apr 29 2003 - 20:09:25 CDT)
• Ross Walker
  • Re: AMBER: NAD+ and NADH amber parameters (Mon Dec 08 2003 - 00:22:56 CST)
  • RE: AMBER: NAD+ and NADH amber parameters (Mon Dec 01 2003 - 11:07:40 CST)
  • RE: AMBER: Zinc parameters (Tue Nov 18 2003 - 15:26:49 CST)
  • AMBER: Reference for Amber7 heme parameters (Fri Aug 08 2003 - 06:41:30 CDT)
  • RE: Amber7 on Opteron (Thu Jul 10 2003 - 06:58:08 CDT)
  • RE: 3 simultaneous simulations in one computer (Thu Jul 10 2003 - 07:01:57 CDT)
  • RE: viewing movie with VMD (Mon Jun 23 2003 - 17:36:30 CDT)
  • RE: Problem with XLEaP in Mandrake 9.1 (Sun Jun 22 2003 - 12:31:02 CDT)
  • RE: anyone have AMBER benchmarks with gigabit ethernet? (Thu Apr 24 2003 - 08:20:07 CDT)
  • RE: anyone have AMBER benchmarks with gigabit ethernet? (Thu Apr 24 2003 - 04:42:57 CDT)
  • RE: Itanium II (Wed Feb 12 2003 - 17:46:27 CST)
  • RE: amber web site (Wed Feb 12 2003 - 15:13:07 CST)
  • RE: UCSF Network changes to affect Amber Web site. (Fri Jan 17 2003 - 14:07:29 CST)
• Ryan Ye
  • Re: AMBER: vlimit? (Tue Dec 23 2003 - 22:04:45 CST)
• S.Swaminathan
  • problem with tleap (Tue Apr 08 2003 - 20:56:44 CDT)
  • protonate (Tue Apr 08 2003 - 14:14:50 CDT)
  • please kindly help (Mon Apr 07 2003 - 21:03:34 CDT)
  • general minimisation methods (Fri Apr 04 2003 - 18:26:48 CST)
  • Examples for Energy Minimisation methods (Tue Apr 01 2003 - 14:35:41 CST)
  • sander outputs (Fri Mar 28 2003 - 13:47:18 CST)
  • Re: problem with "Example 3" tutorials (Fri Mar 28 2003 - 13:41:20 CST)
  • problem with "Example 3" tutorials (Tue Mar 25 2003 - 16:39:23 CST)
  • abt. Plastocyanin tutorial (Tue Mar 25 2003 - 12:51:50 CST)
  • reg. problem with SM and ICE libraries (Fri Mar 21 2003 - 14:56:59 CST)
  • Re: AMBER6 in Solaris 8 (Fri Mar 21 2003 - 12:37:45 CST)
  • AMBER6 in Solaris 8 (Thu Mar 20 2003 - 18:28:11 CST)
  • Re: AMBER6 problem in Solaris 8 (Wed Feb 26 2003 - 12:10:56 CST)
  • AMBER6 problem in Solaris 8 (Fri Feb 21 2003 - 13:18:19 CST)
• salinthip thipayang
  • which AMBER program to use to get the e-density output? (Wed Jun 11 2003 - 14:24:40 CDT)
• Salma B. Rafi
  • AMBER: MSMS (Tue Dec 23 2003 - 12:36:18 CST)
• samantha hughes
  • Re: AMBER: Calculating solvation energies for MM-PBSA use (Thu Sep 18 2003 - 08:13:04 CDT)
  • Re: Protein Reorientation (Mon Mar 03 2003 - 08:02:11 CST)
• Sameer P. Kawatkar
  • Problem in separating LES copies into different trajectory (Tue Jun 10 2003 - 10:15:18 CDT)
  • LES analysis tool other than Moil-view (Wed May 28 2003 - 13:21:38 CDT)
  • Problem with CMC/MD (Tue May 20 2003 - 10:35:16 CDT)
• Anonymous
  • AMBER: mddisplay (Tue Oct 28 2003 - 18:21:04 CST)
  • AMBER: mddisplay (Thu Oct 23 2003 - 15:57:37 CDT)
  • AMBER: torsional restraints for groups of atoms (Sun Oct 19 2003 - 12:42:59 CDT)
  • addles (Tue Apr 08 2003 - 11:56:44 CDT)
• Sandro Fornili
  • AMBER: solute images (Mon Oct 27 2003 - 09:28:34 CST)
• sangeeta_at_bioinfo.ernet.in
  • AMBER: AMBER on LINUX ?? (fwd) (Mon Sep 15 2003 - 01:57:20 CDT)
• Sanjeev B.S.
  • Re: AMBER: AMBER on LINUX ?? (fwd) (Mon Sep 15 2003 - 04:17:01 CDT)
  • Re: AMBER: MIPS R14000 and Machine-file (Tue Sep 02 2003 - 07:48:33 CDT)
  • Re: Amber on SGI with Itanium compilers for linux (Tue May 27 2003 - 08:58:17 CDT)
  • Amber on SGI with Itanium compilers for linux (fwd) (Tue May 27 2003 - 07:21:20 CDT)
  • Re: anal, amber7 and resnum 0 (Fri May 16 2003 - 17:23:04 CDT)
  • anal, amber7 and resnum 0 (Fri May 16 2003 - 17:15:19 CDT)
  • Re: question about H-bond in carnal? (Tue Apr 29 2003 - 01:59:15 CDT)
  • Re: question about H-bond in carnal? (Fri Apr 25 2003 - 10:53:35 CDT)
  • Re: question about H-bond in carnal? (Fri Apr 25 2003 - 10:35:58 CDT)
  • Re: AMBER6 in Solaris 8 (Fri Mar 21 2003 - 03:44:37 CST)
  • Re: AMBER6 problem in Solaris 8 (Tue Feb 25 2003 - 23:03:55 CST)
• sara nunez
  • velocities (Mon Mar 10 2003 - 04:30:09 CST)
  • extract coord and velocities (Thu Feb 27 2003 - 06:55:18 CST)
• Sarah Wittkopp
  • Re: AMBER: Problems with extra points on parralellized linux and sgi machine (Mon Aug 18 2003 - 02:33:36 CDT)
  • AMBER: Problems with extra points on parralellized linux and sgi machine (Fri Aug 15 2003 - 02:07:11 CDT)
  • AMBER: simulating a crystal using the unit cell (Thu Aug 14 2003 - 06:09:07 CDT)
• Satish Kumar
  • Re: May I get you help from new user of amber?(xmkmf) (Mon Jun 09 2003 - 10:46:53 CDT)
  • Re: unit of output velocity (Fri Jun 06 2003 - 11:25:58 CDT)
  • any one has references to parallelization aspects of AMBER (Tue Apr 29 2003 - 04:59:05 CDT)
• Satish Mummadi
  • Re: debug sander (Thu Jun 19 2003 - 03:32:02 CDT)
  • any tool to know what functions are being called while sander is being run?? (Wed Jun 11 2003 - 08:42:58 CDT)
  • Re: any tool to know what functions are being called while sander is being run?? (Wed Jun 11 2003 - 00:32:11 CDT)
  • Re: May I get you help from new user of amber? (Mon Jun 09 2003 - 10:28:54 CDT)
  • Re: unit of output velocity (Fri Jun 06 2003 - 11:39:45 CDT)
• Scott Brozell
  • Re: AMBER: solute images (Mon Oct 27 2003 - 14:39:21 CST)
  • Re: AMBER: Implicit MD simulations in Amber7 (Mon Oct 27 2003 - 14:20:14 CST)
  • Re: AMBER: problem in tleap (Fri Oct 24 2003 - 21:05:33 CDT)
  • Re: AMBER: a problem with xleap (Thu Oct 16 2003 - 13:19:29 CDT)
  • Re: AMBER: input/output error (Fri Oct 10 2003 - 17:10:08 CDT)
  • Re: AMBER: Freezing the residues (Fri Oct 10 2003 - 14:25:04 CDT)
  • RE: AMBER: Not getting restrt file on running sanders (Thu Oct 09 2003 - 18:25:11 CDT)
  • Re: AMBER: Compiling AMBER, ie, number of atoms limit (Thu Oct 09 2003 - 16:30:02 CDT)
  • Re: AMBER: question about ewald (Thu Oct 09 2003 - 13:11:21 CDT)
  • Re: AMBER: Scyld cluster amber 7 compile problems (Thu Sep 18 2003 - 12:50:08 CDT)
  • Re: AMBER: Compiling sander with single precision (Tue Sep 16 2003 - 20:59:25 CDT)
  • Re: AMBER: minimization error (Fri Sep 12 2003 - 14:24:37 CDT)
  • Re: AMBER: processors (Thu Sep 04 2003 - 11:50:10 CDT)
  • Re: AMBER: import pdb file in xleap (Thu Aug 07 2003 - 18:25:18 CDT)
  • Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) (Thu Aug 07 2003 - 02:40:06 CDT)
  • Re: AMBER: add (Thu Jul 31 2003 - 18:45:54 CDT)
  • Re: AMBER: add (Thu Jul 31 2003 - 16:51:46 CDT)
  • Re: AMBER: compile problem (Wed Jul 30 2003 - 16:58:55 CDT)
  • Re: debug leap (Sat Apr 19 2003 - 18:40:03 CDT)
  • RE: Amber7 and mpirun on Linux (Fri Apr 11 2003 - 14:40:38 CDT)
  • Re: Amber7 and mpirun on Linux (Thu Apr 10 2003 - 14:28:00 CDT)
  • Re: improper torsion for X -CB-CB-X (Mon Mar 24 2003 - 22:16:13 CST)
  • Re: intel ifc amber5 and mpich-1.2.5 (Wed Mar 12 2003 - 16:09:21 CST)
  • Re: installing AMBER 7 (Mon Mar 10 2003 - 13:42:23 CST)
  • Re: Amber under Linux (Tue Feb 25 2003 - 15:13:11 CST)
  • RE: Itanium II (Wed Feb 12 2003 - 18:21:06 CST)
• Scott E. Boesch
  • compiling amber on myrinet (Mon Jan 27 2003 - 14:12:31 CST)
• Scott Shandler
  • Re: Antechamber questions (Mon Mar 31 2003 - 17:42:35 CST)
  • Antechamber questions (Thu Mar 27 2003 - 19:35:32 CST)
• sd233_at_georgetown.edu
  • AMBER: AMBER error in CHALANGE (Mon Sep 15 2003 - 10:58:31 CDT)
  • AMBER: minimization termination (Tue Aug 19 2003 - 12:40:53 CDT)
  • AMBER: ANAL component (Wed Aug 13 2003 - 16:36:56 CDT)
  • Re: AMBER: references about AMBER MD simulations (Thu Aug 07 2003 - 10:04:39 CDT)
  • AMBER: references about AMBER MD simulations (Thu Aug 07 2003 - 00:23:35 CDT)
  • AMBER: anal - memory problem (Wed Aug 06 2003 - 12:02:44 CDT)
  • AMBER: DYNAMICS RUN (Fri Jul 25 2003 - 12:47:44 CDT)
  • AMBER: TEMP is not reaching 300K (Thu Jul 24 2003 - 12:06:49 CDT)
• Sean Mooney
  • CFP: Informatics Approaches in Structural Genomics at PSB 2004 (Wed May 28 2003 - 10:46:17 CDT)
• SEKIJIMA Masakazu
  • AMBER: IG value (Fri Sep 05 2003 - 06:50:05 CDT)
• Seongeun Yang
  • Re: Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 15:42:42 CST)
  • Gibbs stops after a finite number of window runs (Sat Feb 01 2003 - 13:22:16 CST)
  • Re: problems in equilibrating NaCl solution (Fri Jan 24 2003 - 18:13:41 CST)
  • problems in equilibrating NaCl solution (Tue Jan 21 2003 - 16:48:04 CST)
• seraphimo_at_gmx.de
  • hydrogen bonding (Tue Mar 18 2003 - 09:51:48 CST)
  • stress - strain - pressure (Thu Feb 27 2003 - 07:06:32 CST)
• Sergio E. Wong
  • AMBER: surften value in mm_gbsa/mm_pbsa calculations (Tue Sep 02 2003 - 14:34:22 CDT)
• Shafinaz
  • RE: AMBER: problem with file format (Wed Sep 24 2003 - 15:29:10 CDT)
  • AMBER: problem with file format (Wed Sep 24 2003 - 14:05:23 CDT)
  • AMBER: Antechamber problem (Mon Sep 22 2003 - 11:33:58 CDT)
  • very important (Tue Apr 08 2003 - 09:19:18 CDT)
  • Trouble with AMBER 7 (Mon Apr 07 2003 - 15:59:52 CDT)
• Sheldon Holder
  • Re: AMBER: distrance restraints for alpha carbons (Mon Nov 03 2003 - 13:56:49 CST)
  • AMBER: distrance restraints for alpha carbons (Mon Nov 03 2003 - 13:27:48 CST)
• Shiang-Tai Lin
  • Re: AMBER: Pressure in NVT ensemble (Mon Oct 27 2003 - 11:48:48 CST)
  • AMBER: Pressure in NVT ensemble (Fri Oct 24 2003 - 12:44:21 CDT)
• Shixiang Yan
  • Re: distance-dependent dielectric function (Fri May 23 2003 - 11:39:04 CDT)
  • re: parameters for nitro group (Tue May 13 2003 - 10:30:49 CDT)
• Shuang Ding
  • AMBER: Toolchest (Fri Dec 19 2003 - 14:45:08 CST)
  • Re: AMBER: machine dependent? (Tue Aug 12 2003 - 13:48:00 CDT)
  • Re: AMBER: machine dependent? (Mon Aug 11 2003 - 17:01:38 CDT)
  • AMBER: machine dependent? (Mon Aug 11 2003 - 13:39:10 CDT)
  • Re: AMBER: mpi in mm-pbsa (Thu Aug 07 2003 - 15:14:53 CDT)
  • AMBER: mpi in mm-pbsa (Thu Aug 07 2003 - 12:57:03 CDT)
  • AMBER: compile problem? (Tue Aug 05 2003 - 15:51:25 CDT)
  • AMBER: compile problem (Wed Jul 30 2003 - 15:59:08 CDT)
  • Re: AMBER: Ewald problem (Wed Jul 30 2003 - 12:28:31 CDT)
  • AMBER: Ewald problem (Wed Jul 30 2003 - 11:08:55 CDT)
  • npscal (Wed Jul 09 2003 - 15:12:04 CDT)
  • restart MD (Tue Jun 10 2003 - 13:12:08 CDT)
  • shake problem? (Mon Jun 09 2003 - 13:33:50 CDT)
  • constant volume (Thu Jun 05 2003 - 17:26:39 CDT)
  • Re: MD problem (Thu May 29 2003 - 16:30:54 CDT)
  • Re: MD problem (Thu May 29 2003 - 16:04:22 CDT)
  • MD problem (Thu May 29 2003 - 15:47:20 CDT)
  • problem on MD simulation of damage DNA (Thu May 01 2003 - 15:11:04 CDT)
  • how to restrain base pair (Mon Apr 28 2003 - 13:59:58 CDT)
• Shunzhou Wan
  • RMS in carnal (Mon Mar 24 2003 - 05:12:53 CST)
• Shweta Sikri
  • Re: Antechamber (Thu Jul 03 2003 - 12:18:58 CDT)
  • Antechamber (Thu Jul 03 2003 - 11:29:03 CDT)
  • Re: Antechamber (Wed Jun 25 2003 - 14:26:31 CDT)
  • Antechamber (Wed Jun 25 2003 - 11:47:52 CDT)
• Sia Meshkat
  • RE: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 20:40:52 CDT)
  • RE: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 17:19:04 CDT)
  • RE: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 16:48:41 CDT)
  • Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 11:35:57 CDT)
• Sichun Yang
  • Trying to understand parm99.dat (Tue Apr 08 2003 - 19:44:32 CDT)
  • NTX / INIT inconsistency (Wed Mar 19 2003 - 16:31:36 CST)
  • Machine for IBM Horizon (Mon Mar 10 2003 - 16:23:35 CST)
  • Re: Energy calculation (Wed Feb 19 2003 - 20:51:11 CST)
  • Energy calculation (Wed Feb 19 2003 - 16:25:45 CST)
  • Re: restrained atoms NTR (Wed Feb 19 2003 - 11:27:18 CST)
  • restrained atoms NTR (Tue Feb 18 2003 - 15:45:33 CST)
  • RE: question on EWALD (Mon Feb 17 2003 - 17:28:00 CST)
  • RE: question on EWALD (Mon Feb 17 2003 - 16:12:42 CST)
  • Re: question on EWALD (Mon Feb 17 2003 - 13:37:04 CST)
  • Re: question on EWALD (Mon Feb 17 2003 - 13:16:25 CST)
  • question on EWALD (Sun Feb 16 2003 - 17:54:49 CST)
  • ptraj distanse question (Thu Jan 30 2003 - 22:16:06 CST)
  • single point mutations to investigate the conformational change (Mon Jan 27 2003 - 21:43:29 CST)
• Simon Lenzen
  • Antechamber atom types (Tue Mar 25 2003 - 04:41:30 CST)
• Sivakolundu, Sivashankar
  • RE: AMBER: aminoacid mutation (Tue Oct 28 2003 - 09:43:38 CST)
  • RE: AMBER: large changes in xyz coordinates (Mon Aug 18 2003 - 12:51:49 CDT)
  • AMBER: large changes in xyz coordinates (Sat Aug 16 2003 - 20:06:14 CDT)
• smolnar_at_jadeinc.com
  • Latest Leap Compile Errors (Sun May 04 2003 - 06:44:50 CDT)
  • (no subject) (Sat May 03 2003 - 13:19:25 CDT)
• sohail qamar
  • AMBER: united atom weiner force field (Mon Aug 18 2003 - 05:46:18 CDT)
• Soonmin Jang
  • About electrostatic force calculations (Tue Apr 01 2003 - 23:58:38 CST)
• Sophia Kondratova
  • RDPARM problems (ptraj) (Thu Jun 05 2003 - 12:13:35 CDT)
  • ptraj problem (Fri Apr 04 2003 - 08:00:46 CST)
  • SANDER vs GIBBS equilibration (Wed Mar 26 2003 - 07:44:39 CST)
  • tautp in gibbs (Mon Mar 03 2003 - 14:57:03 CST)
• Stefan Jungblut
  • 'hot-solvent' and 'cold solute' problem (Tue Jan 21 2003 - 09:36:37 CST)
• Steph
  • Re: NOESY restraints (Sat Jun 21 2003 - 05:27:35 CDT)
• Stephen P. Molnar, Ph.D.
  • AMBER: Re: xLEAP Problem (Mon Sep 22 2003 - 11:36:48 CDT)
  • AMBER: xLEAP Problem (Fri Sep 19 2003 - 15:07:14 CDT)
  • Re: Latest Leap Compile Errors (Mon May 05 2003 - 08:18:35 CDT)
• Stephen.Titmuss_at_csiro.au
  • AMBER: PMEMD Performance on Beowulf systems (Thu Dec 18 2003 - 21:19:59 CST)
• Steve Seibold
  • AMBER: Restraints (Thu Nov 06 2003 - 14:28:09 CST)
  • Proper Restraint usage (Tue Apr 15 2003 - 15:42:59 CDT)
  • SSBonds and charge problems (Fri Apr 11 2003 - 14:54:23 CDT)
  • (no subject) (Sat Mar 08 2003 - 13:51:35 CST)
  • antechamber and its prepin files (Wed Feb 19 2003 - 13:11:23 CST)
  • amber web site (Wed Feb 12 2003 - 14:30:40 CST)
  • lastrst (Mon Jan 27 2003 - 11:46:57 CST)
• Subba.Raju
  • Force field ? (Mon Feb 24 2003 - 04:17:54 CST)
• Sue Heavner
  • AMBER: curves nomenclature (Wed Jul 16 2003 - 14:34:13 CDT)
  • MM_PBSA (Amber7) and delphi (Fri Mar 21 2003 - 08:27:00 CST)
  • delphi and charge file (Wed Feb 12 2003 - 14:49:01 CST)
• Sukjoon Yoon
  • Bad atom type: f (Mon Jul 14 2003 - 10:28:58 CDT)
  • Q) vdw radii & GBSA error (Fri Jun 06 2003 - 11:58:03 CDT)
• Surjit Dixit
  • Re: AMBER: Curves parameters UU and PP (Sat Dec 20 2003 - 09:45:28 CST)
• Susanna Monti
  • AMBER: Ewald_Bomb (Wed Jul 30 2003 - 08:37:40 CDT)
• Suse Broyde
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:37:58 CST)
  • Re: AMBER: monitor vdw along time (Fri Jul 25 2003 - 14:57:06 CDT)
• sxzheng
  • Re: Re: can you give me more advice about: vlimit exceeded when sander calculate free energies using TI (Sun Jun 29 2003 - 20:05:55 CDT)
  • can you give me more advice about: vlimit exceeded when sander calculate free energies using TI (Mon Jun 16 2003 - 07:47:53 CDT)
  • how to use profec??? (Sun Jun 08 2003 - 03:04:09 CDT)
• sychen
  • Re[2]: AMBER: derive corresponding torsional parameters (Fri Aug 08 2003 - 10:43:43 CDT)
  • Re: ibelly and ntr (Tue Apr 15 2003 - 22:03:57 CDT)
  • Re: sander & prmtop file generated from antechamber input ? (Sun Apr 06 2003 - 11:12:44 CDT)
  • Re: Problem of Hbond in CARNAL (Tue Apr 01 2003 - 08:23:11 CST)
  • Re: improper torsion for X -CB-CB-X (Mon Mar 24 2003 - 23:16:17 CST)
  • Re: charge neutralization in DNA (Thu Mar 20 2003 - 10:52:38 CST)
  • Re: question about partial charge (Tue Feb 18 2003 - 21:52:32 CST)
  • Re: pdb_to_mass (Fri Jan 10 2003 - 19:53:37 CST)
• Szilveszter Juhos
  • Re: CCL:MEAD on SuSE 8.1 (Tue Jan 14 2003 - 10:22:08 CST)
• Sébastien Canneaux
  • AMBER: PMF calculations (Tue Sep 09 2003 - 07:29:36 CDT)
• Taisung Lee
  • AMBER: Taisung Lee/San Diego/Accelrys is out of the office. (Fri Jul 25 2003 - 12:02:29 CDT)
• takanori.kanazawa_at_pharma.novartis.com
  • Re: AMBER: Re: AMBER7 & mpich : (no-attachment version) (Wed Aug 06 2003 - 23:11:30 CDT)
  • AMBER: Re: AMBER7 & mpich : (no-attachment version) (Mon Aug 04 2003 - 18:51:17 CDT)
  • AMBER: AMBER7 & mpich : (no-attachment version) (Sat Aug 02 2003 - 08:03:06 CDT)
  • AMBER: AMBER7 & mpich (Sat Aug 02 2003 - 07:17:52 CDT)
  • AMBER: MOPAC509mn test jobs on linux (Thu Jul 24 2003 - 18:54:39 CDT)
• Tammy Smith
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 12:47:34 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 12:47:34 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 12:47:34 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 12:47:34 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 12:37:33 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 12:37:33 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 12:37:33 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 12:27:33 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 12:27:33 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 12:27:33 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 12:27:33 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 12:17:33 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 12:17:33 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 12:17:33 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 12:07:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 12:07:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 12:07:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 11:57:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 11:57:32 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 11:57:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 11:57:33 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:47:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:47:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 11:47:32 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 11:37:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 11:37:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 11:37:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 11:37:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:27:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:27:32 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 11:17:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 11:17:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 11:17:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:07:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 11:07:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 11:07:32 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 10:57:31 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 10:57:31 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 10:47:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 10:47:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 10:47:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 10:47:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 10:37:31 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 10:27:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 10:27:32 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 10:27:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 10:27:32 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 10:27:32 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 10:07:31 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 09:57:31 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 09:57:31 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 09:57:31 CST)
  • Re: AMBER: question about namelist (Mon Dec 15 2003 - 09:47:30 CST)
  • Re: AMBER: length of deltaG calcs (Mon Dec 15 2003 - 09:37:30 CST)
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 09:37:30 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 09:37:30 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 09:17:31 CST)
  • Re: AMBER: Energy map (Mon Dec 15 2003 - 08:57:29 CST)
• Taner E. Dirama
  • AMBER: Ptraj-HBOND (Tue Dec 02 2003 - 12:42:58 CST)
  • AMBER: dielectric constant for blends (Mon Sep 08 2003 - 09:21:11 CDT)
• tang kwa
  • constraint + restraint (Tue Jul 08 2003 - 02:05:11 CDT)
  • Re: EWALD BOMB (Tue May 27 2003 - 10:38:31 CDT)
  • EWALD BOMB (Mon May 26 2003 - 09:27:07 CDT)
  • Mainchain.dat (Mon May 19 2003 - 11:16:12 CDT)
  • Re: minimizaiton in vacuum (Tue May 06 2003 - 07:17:03 CDT)
  • Re: can not minimize (Mon May 05 2003 - 09:45:24 CDT)
  • Re: can not minimize (Mon May 05 2003 - 08:57:40 CDT)
  • Re: can not minimize (Mon May 05 2003 - 08:49:31 CDT)
  • can not minimize (Mon May 05 2003 - 06:57:42 CDT)
  • how to generate FF of DNA complex? (Thu Mar 27 2003 - 09:43:47 CST)
• taxquestions_at_nyit.edu
  • Automated response (Wed Feb 26 2003 - 11:11:58 CST)
• Teletchéa Stéphane
  • Re: AMBER: Any correct way to image a molecule ? (Fri Nov 14 2003 - 03:55:36 CST)
  • Re: AMBER: Any correct way to image a molecule ? (Thu Nov 13 2003 - 16:46:48 CST)
  • AMBER: Any correct way to image a molecule ? (Thu Nov 13 2003 - 15:37:40 CST)
  • Re: AMBER: Implicit precision in sander vs architecture (Tue Oct 21 2003 - 03:42:54 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Mon Oct 20 2003 - 03:45:04 CDT)
  • Re: AMBER: Implicit precision in sander vs architecture (Fri Oct 17 2003 - 11:15:13 CDT)
  • AMBER: Implicit precision in sander vs architecture (Fri Oct 17 2003 - 10:42:41 CDT)
  • AMBER: Phase for torsion angle different of 0 or 180 ? (Fri Sep 26 2003 - 11:27:34 CDT)
  • Re: AMBER: PMEMD and sander from AMBER6 performances (Thu Aug 07 2003 - 11:55:03 CDT)
  • Re: AMBER: 2D periodic box (Thu Aug 07 2003 - 11:52:01 CDT)
  • Re: AMBER: Dynamics and Simulated Annealing (Fri Jul 25 2003 - 11:57:53 CDT)
  • Re: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 11:35:46 CDT)
  • AMBER: PMEMD and sander from AMBER6 performances (Wed Jul 16 2003 - 18:37:34 CDT)
  • Machine file available for ICC compiler ? (Fri Jul 04 2003 - 12:08:30 CDT)
  • NOESY restraints (Fri Jun 20 2003 - 06:28:03 CDT)
• Terry Downing
  • AMBER: xleap memory issue (Tue Aug 26 2003 - 19:30:06 CDT)
• thenmalar rathinavelan
  • doubts (Thu Mar 20 2003 - 22:26:50 CST)
  • Nmode (Thu Feb 20 2003 - 00:21:03 CST)
  • energy calculation (Sun Feb 09 2003 - 01:19:59 CST)
  • stacking energy (Wed Feb 05 2003 - 04:19:06 CST)
• Therese Malliavin
  • AMBER: comparing versions 6.0 and 7.0 of AMBER (Mon Oct 27 2003 - 03:30:21 CST)
• Thomas
  • GAFF in GUI MD apps (Tue Jun 24 2003 - 14:07:54 CDT)
• Thomas Cheatham
  • Re: Comparative MD (Fri Jul 11 2003 - 14:32:35 CDT)
  • Re: your mail (IBM runtime problem) (Tue Jul 01 2003 - 11:58:00 CDT)
  • Re: ptraj question (Tue Jun 24 2003 - 15:56:51 CDT)
  • Re: ptraj rdf help (Wed May 21 2003 - 23:12:57 CDT)
  • Re: Etot is not constant in NVE ensemble (Fri May 09 2003 - 10:49:18 CDT)
  • Re: problem about virtual box? (Thu May 01 2003 - 12:07:52 CDT)
  • Re: diffusion coefficients (Mon Apr 14 2003 - 16:34:39 CDT)
  • Re: A problem in Sander production dynamics (Mon Apr 14 2003 - 16:24:31 CDT)
  • Re: The image command of ptraj of Amber 6 is not working. (Wed Feb 12 2003 - 15:40:28 CST)
• Thomas E. Cheatham, III
  • Re: AMBER: water neighborhood of amide hydrogens (Mon Dec 15 2003 - 11:29:00 CST)
  • Re: AMBER: ptraj and charmm files (Mon Nov 17 2003 - 09:50:22 CST)
  • Re: AMBER: Any correct way to image a molecule ? (Thu Nov 13 2003 - 15:58:38 CST)
  • Re: AMBER: Separation of a Water molecules (Wed Nov 12 2003 - 22:16:38 CST)
  • Re: AMBER: Separation of a Water molecules (Tue Nov 11 2003 - 22:13:41 CST)
  • Re: AMBER: how to measure the minor groove widths of a DNA? (Wed Oct 29 2003 - 11:31:09 CST)
  • Re: AMBER: ibelly problem (Wed Oct 29 2003 - 11:23:12 CST)
  • Re: AMBER: solvatebox-solvateshell (Sat Sep 06 2003 - 15:16:38 CDT)
  • Re: AMBER: ptraj problem (Wed Aug 20 2003 - 14:00:57 CDT)
  • Re: AMBER: question to calculate diffusion coefficient under periodic boundary conditions. (Tue Aug 12 2003 - 14:32:36 CDT)
  • Re: AMBER: question about ptraj (Wed Jul 30 2003 - 17:38:52 CDT)
  • Re: AMBER: question about ptraj? (Thu Jul 24 2003 - 11:40:50 CDT)
  • Re: AMBER: (no subject) (Thu Jul 24 2003 - 11:32:28 CDT)
  • Re: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 13:18:50 CDT)
  • Re: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 11:40:29 CDT)
  • Re: AMBER: question about quasih? (Fri Jul 18 2003 - 17:39:15 CDT)
  • AMBER: Re: methylphosphonate (Mon Jul 14 2003 - 21:46:06 CDT)
  • Re: problem about virtual box? (Thu May 01 2003 - 12:33:49 CDT)
• Thomas Steinbrecher
  • AMBER: Calculating solvation energies for MM-PBSA use (Thu Sep 18 2003 - 07:43:37 CDT)
  • AMBER: The FCAP parameter in amber7 (Fri Aug 22 2003 - 04:21:35 CDT)
  • AMBER: MD simulation with ATP and MG (Mon Aug 11 2003 - 04:45:08 CDT)
  • Nmode recompilation (Tue Jul 01 2003 - 03:41:33 CDT)
  • How do I perform an Nmode calculation on a big protein-ligand complex? (Mon Jun 30 2003 - 04:31:38 CDT)
  • MD input file for MM-PBSA calculations (Sat May 24 2003 - 07:36:43 CDT)
  • MM-PBSA results (Fri Mar 21 2003 - 07:15:25 CST)
  • GB vs. explicit solvent calculations (Thu Mar 20 2003 - 07:53:44 CST)
  • DelphiLinux V. 4 Segmentation Fault (Wed Mar 19 2003 - 07:10:16 CST)
  • The gblambda parameter (Thu Mar 13 2003 - 08:29:03 CST)
  • Re: Namelist READ error - solved (Wed Feb 26 2003 - 08:54:54 CST)
  • Namelist READ error (Wed Feb 26 2003 - 06:54:46 CST)
  • mm-pbsa problem & possible solution (Thu Jan 30 2003 - 09:51:57 CST)
  • mm-pbsa error message (Tue Jan 28 2003 - 09:02:04 CST)
• Thomas.Fox_at_bc.boehringer-ingelheim.com
  • AW: AMBER: Problem with MPI_Finalize (Tue Nov 18 2003 - 09:34:36 CST)
  • AMBER: Problem with MPI_Finalize (Tue Nov 18 2003 - 08:10:02 CST)
  • AMBER: atmtypenumbers for halogens (Thu Nov 13 2003 - 02:53:38 CST)
• Thu Zar Lwin
  • mpi/sander help (Fri Feb 07 2003 - 16:01:05 CST)
• Tian-Xiang Xiang
  • inter & intra-molecular interaction energies (Thu Feb 13 2003 - 16:10:07 CST)
• tianxiao yang
  • AMBER: water model (Fri Aug 08 2003 - 10:10:04 CDT)
  • Re: ptraj and rdf help (Wed May 21 2003 - 17:54:59 CDT)
  • ptraj rdf help (Wed May 21 2003 - 17:28:26 CDT)
  • Sander help (Tue May 13 2003 - 18:47:17 CDT)
• Tommi Kajander
  • electrostatic interaction energ. /delphi (Tue Jun 24 2003 - 14:39:51 CDT)
• Tormod Skauge
  • Re: Compilation error of Amber 7 using pgi and mpich on Linux Cluster (Tue Feb 25 2003 - 09:00:19 CST)
• Troy Wymore
  • PSC Summer Workshop: Modeling from Protein Sequence to Structure (Thu Apr 24 2003 - 12:33:39 CDT)
• Tru Huynh
  • g77 on 32 bits cpu (was Re: Nmode recompilation) (Tue Jul 01 2003 - 04:48:15 CDT)
  • Re: AMD opteron (Wed May 28 2003 - 11:52:18 CDT)
  • Re: AMD opteron (Wed May 28 2003 - 08:08:51 CDT)
• uddhavesh bhaskar sonavane
  • Re: Re: AMBER: nstlim (Wed Oct 01 2003 - 10:32:27 CDT)
  • AMBER: Suggestion regarding long simulation. (Thu Sep 18 2003 - 01:50:37 CDT)
• Ulf Johansson
  • Re: AMBER: TIP5P (Wed Sep 10 2003 - 02:37:36 CDT)
  • AMBER: TIP5P (Tue Sep 09 2003 - 08:27:27 CDT)
• Ulf Ryde
  • Re: AMBER: NAD+ and NADH amber parameters (Mon Dec 08 2003 - 05:05:25 CST)
  • Re: AMBER: NAD+ and NADH amber parameters (Tue Dec 02 2003 - 07:20:26 CST)
• vannajan_at_chiangmai.ac.th
  • Question: about restarting Energy (Mon Jan 27 2003 - 19:53:30 CST)
• Vema Aparna
  • AMBER: Heme and Zn parameters (Sun Dec 14 2003 - 08:04:43 CST)
• Venkata S Koppuravuri
  • AMBER: minimization error (Fri Sep 12 2003 - 14:00:05 CDT)
  • AMBER: minimization error (Thu Aug 14 2003 - 13:23:39 CDT)
  • Re: AMBER7 on linux cluster (Fri Jun 20 2003 - 09:53:17 CDT)
  • AMBER7 on linux cluster (Tue Jun 17 2003 - 11:49:06 CDT)
  • protonate problem (Wed May 14 2003 - 12:17:39 CDT)
  • Re: Problem_to_open_PROTON_INFO_file (Thu Apr 24 2003 - 14:43:59 CDT)
  • Re: ambpdb (Fri Apr 18 2003 - 11:14:34 CDT)
  • Using MPI, PBS (Wed Apr 02 2003 - 12:58:23 CST)
  • Re: problem with "Example 3" tutorials (Wed Mar 26 2003 - 11:35:11 CST)
  • Extracting structures (Wed Mar 26 2003 - 11:20:51 CST)
  • extracting structures (Wed Mar 26 2003 - 11:16:17 CST)
• Vikas Varshney
  • AMBER: ibelly problem (Tue Oct 28 2003 - 13:34:00 CST)
  • AMBER: 'vlimit exceeded' (Tue Oct 14 2003 - 14:36:19 CDT)
  • AMBER: sander: vlimit problem (Sun Oct 12 2003 - 21:19:41 CDT)
  • AMBER: Freezing the residues (Thu Oct 09 2003 - 22:37:11 CDT)
  • AMBER: Not getting restrt file on running sanders (Thu Oct 09 2003 - 16:40:15 CDT)
  • AMBER: Resp Problem (Tue Oct 07 2003 - 10:18:39 CDT)
  • AMBER: cd-c-os and c3-cd-c angle parameters (Wed Sep 24 2003 - 10:10:09 CDT)
  • Re: AMBER: import pdb file in xleap (Thu Aug 07 2003 - 14:21:32 CDT)
  • AMBER: 2D periodic box (Thu Aug 07 2003 - 09:50:20 CDT)
  • AMBER: problem regarding surface (Wed Aug 06 2003 - 12:00:09 CDT)
• Viktor Hornak
  • Re: AMBER: PMEMD Performance on Beowulf systems (Mon Dec 22 2003 - 07:47:42 CST)
  • Re: AMBER: mpich problem (Sun Nov 09 2003 - 18:06:53 CST)
  • Re: Problem in separating LES copies into different trajectory (Tue Jun 10 2003 - 10:50:36 CDT)
  • Re: Install Amber7 in linux cluster (Mon Jun 02 2003 - 10:11:10 CDT)
  • Re: Amber on Linux (Sat Apr 12 2003 - 18:41:41 CDT)
  • Re: Amber7 & mpich (Tue Feb 04 2003 - 12:07:47 CST)
  • Re: AMBER7 & mpich (Fri Jan 31 2003 - 09:12:37 CST)
• Vlad
  • Beyond 1,000,000 atoms (Wed Apr 02 2003 - 16:45:21 CST)
  • Beyond 1,000,000 atoms... (Thu Feb 27 2003 - 19:45:14 CST)
• Vlad Cojocaru
  • AMBER: adding extra salt (Fri Dec 12 2003 - 07:34:55 CST)
  • AMBER: Mg2+ parameters for RNA usage (Wed Dec 10 2003 - 07:38:59 CST)
  • AMBER: water mediated contacts (Mon Nov 24 2003 - 10:42:12 CST)
  • Re: AMBER: about some of the cards in Sander 7 (Wed Nov 12 2003 - 14:38:39 CST)
  • AMBER: restraints and reordering water (Tue Nov 11 2003 - 03:42:04 CST)
  • AMBER: restrain (Fri Nov 07 2003 - 09:53:52 CST)
  • Re: AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 07:42:24 CDT)
  • Re: AMBER: carnal iteration deviation from original crd file (Fri Oct 24 2003 - 06:32:17 CDT)
  • Re: AMBER: problem with pdb files (Mon Oct 13 2003 - 03:35:04 CDT)
  • AMBER: monte carlo (Fri Oct 10 2003 - 08:40:11 CDT)
  • AMBER: regarding trajectory input and output with ptraj or Carnal (Thu Oct 02 2003 - 07:37:19 CDT)
  • Re: AMBER: iam a newbie !!! (Tue Sep 30 2003 - 04:12:43 CDT)
  • Re: AMBER: dynamics of isolated system (Tue Jul 29 2003 - 13:50:52 CDT)
  • AMBER: H-O-H angle in TIP3P water model during minimization (Mon Jul 28 2003 - 19:42:10 CDT)
  • AMBER: ambpdb and residue number (Mon Jul 28 2003 - 14:47:26 CDT)
  • AMBER: please let me know if this is correct (Mon Jul 28 2003 - 08:58:55 CDT)
  • AMBER: Impropers from Amber parm files to NAMD (Sun Jul 27 2003 - 12:56:47 CDT)
  • Re: AMBER: AMBER and NAMD (Sun Jul 27 2003 - 12:45:40 CDT)
  • AMBER: AMBER and NAMD (Sun Jul 27 2003 - 08:57:24 CDT)
  • AMBER: running AMBER on an IBM P690 cluster (Thu Jul 24 2003 - 12:46:30 CDT)
  • Re: AMBER: TEMP is not reaching 300K (Thu Jul 24 2003 - 12:35:21 CDT)
  • Re: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 10:16:22 CDT)
  • nab compilation (Thu Jul 10 2003 - 07:02:04 CDT)
  • helix axis for A-RNA (Tue Jun 10 2003 - 07:25:09 CDT)
  • Parameters for Cy3 and Fluorescein (Fri Mar 28 2003 - 06:27:14 CST)
  • Disulphide bridges (Thu Mar 27 2003 - 11:10:24 CST)
  • Hbond analysis with Carnal (Fri Mar 21 2003 - 08:50:36 CST)
  • ptraj html documentation still available? (Fri Mar 21 2003 - 08:39:08 CST)
  • a perl question for Hbond occupancies analysis (Wed Mar 19 2003 - 07:43:30 CST)
  • Re: pressure variation control (Fri Mar 07 2003 - 12:20:38 CST)
  • 2drms command in ptraj (Tue Jan 28 2003 - 06:52:17 CST)
  • freeware to visualize RMSD matrices creatde with Carnal (Mon Jan 27 2003 - 16:41:00 CST)
  • Has anyone ever used MEAD? (Mon Jan 20 2003 - 07:58:30 CST)
  • MEAD on SuSE 8.1 (Tue Jan 14 2003 - 09:10:18 CST)
  • electrostatic potential calculations (Sat Jan 11 2003 - 10:05:07 CST)
  • errors in MD trajectories (Fri Jan 10 2003 - 12:13:03 CST)
• volodya
  • Re: AMBER: Protein Rotation (Sun Oct 12 2003 - 08:40:07 CDT)
  • AMBER: RMSd per residue (Tue Oct 07 2003 - 07:58:20 CDT)
  • Re: AMBER: large file for carnal (Tue Oct 07 2003 - 07:52:04 CDT)
  • Re: AMBER: large file for carnal (Sun Oct 05 2003 - 06:23:44 CDT)
  • AMBER: large file for carnal (Sat Oct 04 2003 - 12:12:37 CDT)
• vze6jslz_at_verizon.net
  • debug leap (Sat Apr 19 2003 - 13:52:40 CDT)
• wangf2
  • AMBER: (Thu Oct 30 2003 - 10:00:15 CST)
• Wayne Dawson
  • Re: AMBER: Basic potential question: (Thu Dec 25 2003 - 21:04:37 CST)
  • Re: AMBER: using sander without SHAKE (Wed Dec 24 2003 - 10:39:43 CST)
  • AMBER: Basic potential question: (Wed Dec 24 2003 - 09:56:37 CST)
  • AMBER: using sander without SHAKE (Mon Dec 22 2003 - 00:38:14 CST)
  • AMBER: compiling amber using gcc on SGI Unix machines (Wed Nov 26 2003 - 07:15:57 CST)
  • AMBER: aminoacid mutation (Mon Oct 27 2003 - 23:47:25 CST)
  • AMBER: Insight pdb file in xleap (Thu Aug 07 2003 - 21:33:26 CDT)
  • using distance restraints in Sander (AIX 4.3 RS6000) (Fri May 16 2003 - 03:33:02 CDT)
  • Re: saveAmberParm problems in xleap (Thu May 08 2003 - 04:02:45 CDT)
  • Re: saveAmberParm problems in xleap (Tue May 06 2003 - 12:04:19 CDT)
  • saveAmberParm problems in xleap (Tue May 06 2003 - 03:14:58 CDT)
  • troubles on RS6000 (Mon Apr 28 2003 - 04:37:50 CDT)
• Wei Wang
  • Re: AMBER: basic questions (Tue Dec 02 2003 - 10:23:13 CST)
  • AMBER: basic questions (Mon Dec 01 2003 - 17:02:52 CST)
• Wen Li
  • AMBER: MSE (Wed Dec 24 2003 - 10:25:33 CST)
  • AMBER: increase size of NATOM or NRES for "ambpdb" (Mon Sep 22 2003 - 14:14:36 CDT)
  • AMBER: CARNAL (Mon Aug 25 2003 - 09:30:19 CDT)
  • Install Amber7 in linux cluster (Mon Jun 02 2003 - 09:20:51 CDT)
  • Re: Amber on Linux (Sun Apr 13 2003 - 10:06:52 CDT)
  • Amber on Linux (Sat Apr 12 2003 - 12:00:46 CDT)
  • Amber7 and mpirun on Linux (Thu Apr 10 2003 - 13:14:59 CDT)
  • frcmod file (Thu Apr 03 2003 - 14:04:34 CST)
  • size of a simulation system (Tue Apr 01 2003 - 09:49:42 CST)
  • Install Amber 7 (Thu Mar 27 2003 - 10:05:53 CST)
  • Install Amber 7 (Thu Mar 27 2003 - 10:01:10 CST)
  • Maximum molecular size for Amber? (Tue Mar 18 2003 - 13:21:16 CST)
• wendy.cornell_at_pharma.novartis.com
  • Re: AMBER: missing of VdW Parameters for N3 (Wed Dec 03 2003 - 09:18:23 CST)
• wentaofu
  • mm_pbsa with PBCAL = 0 (Fri May 16 2003 - 14:14:42 CDT)
  • upper limited of memory for nmode (Fri May 02 2003 - 19:06:06 CDT)
  • nmode and mm_pbsa questions? (Fri Apr 25 2003 - 15:47:48 CDT)
  • nmode for S calculation (Tue Apr 08 2003 - 18:22:47 CDT)
  • MM_pbsa prmtop file (Thu Jan 09 2003 - 17:29:38 CST)
  • mm_pbsa question (Tue Jan 07 2003 - 18:17:08 CST)
• Wiktor Jurkowski
  • amber7 on sgi (Fri Mar 21 2003 - 08:26:54 CST)
• William Wei
  • MPI run problem (Wed Apr 16 2003 - 11:36:31 CDT)
  • a-Helix direction? (Mon Apr 07 2003 - 15:26:40 CDT)
  • Summary: Protein-Inhibitor binding affinity (Fri Mar 28 2003 - 08:51:30 CST)
  • Protein-Inhibitor binding afinity (Mon Mar 24 2003 - 12:02:04 CST)
  • mpirun problem! (Thu Mar 20 2003 - 10:21:17 CST)
  • Parameters for Hyddantoin derivatives? (Mon Mar 10 2003 - 12:13:48 CST)
  • Parameters: additive, lone pair (Mon Mar 10 2003 - 08:57:35 CST)
  • Backbone torsional angles' format? (Fri Feb 07 2003 - 17:35:56 CST)
  • Carnal DECLARE of TORSION problem (Fri Feb 07 2003 - 12:20:37 CST)
  • mm_pbsa Stop at statistics (Fri Jan 17 2003 - 12:52:48 CST)
  • mm_gbsa: Unit 5 Error on OPEN: sander_com.in (Tue Jan 14 2003 - 11:19:36 CST)
  • Summary: mm_pbsa -- COMPT must be specified (correctly) (Tue Jan 14 2003 - 09:31:07 CST)
  • mm_pbsa -- COMPT must be specified (correctly) (Mon Jan 13 2003 - 12:00:10 CST)
  • RE: mm_pbsa -- COMPT must be specified (correctly) (Mon Jan 13 2003 - 11:32:36 CST)
• Wu Yingliang
  • Re: AMBER: GBSA problem (Thu Dec 11 2003 - 22:20:05 CST)
  • Re: Re: AMBER: ANAL/MMPBSA (Thu Dec 04 2003 - 07:29:41 CST)
  • RE: Re: AMBER: ANAL/MMPBSA (Thu Dec 04 2003 - 01:53:25 CST)
  • AMBER: Anal/MMPBSA (Tue Dec 02 2003 - 19:16:02 CST)
  • Re: AMBER: Re: Nmode problem (Mon Dec 01 2003 - 07:34:40 CST)
  • AMBER: Re: Nmode problem (Sat Nov 29 2003 - 21:52:15 CST)
  • AMBER: Nmode problem (Fri Nov 28 2003 - 07:52:31 CST)
  • AMBER: no defined type for atom N atom (Fri Sep 19 2003 - 08:02:31 CDT)
  • AMBER: no defined type for atom N atom (Fri Sep 19 2003 - 07:57:12 CDT)
  • Refining a docked protein complex (Wed Jul 09 2003 - 08:59:26 CDT)
  • May I get your help? (Wed Jul 09 2003 - 07:39:05 CDT)
  • May I get you help from new user of amber? (Mon Jun 09 2003 - 09:21:49 CDT)
• X. Tan
  • AMBER: PMF (Tue Jul 15 2003 - 12:02:47 CDT)
  • PMF (Wed Jul 02 2003 - 14:02:53 CDT)
  • charge fitting for c-term homocysteine. (Thu May 22 2003 - 21:25:19 CDT)
• Xavier Periole
  • Re: AMBER: solvatebox-solvateshell (Mon Sep 08 2003 - 16:46:00 CDT)
  • Re: AMBER: overlap problem (Tue Aug 19 2003 - 11:23:45 CDT)
  • Re: AMBER: minimization error (Thu Aug 14 2003 - 13:38:39 CDT)
  • Re: AMBER: modelling a Ca binding site (Thu Aug 14 2003 - 12:07:26 CDT)
  • Re: AMBER: constant energy simulation (Tue Aug 12 2003 - 17:39:29 CDT)
  • Re: AMBER: constant energy simulation (Tue Aug 12 2003 - 14:51:24 CDT)
  • Re: AMBER: SHAKE Problem (Wed Aug 06 2003 - 15:26:05 CDT)
  • AMBER: N/C termini (Wed Jul 16 2003 - 17:24:19 CDT)
  • AMBER: neutral N- and C- termini ! (Wed Jul 16 2003 - 13:52:29 CDT)
• Xiang Mao
  • unsubscribe (Fri Feb 21 2003 - 09:29:28 CST)
• Xiang, Tian-Xiang
  • RE: charge determination for polariable ff02 force fields (Sun Feb 16 2003 - 12:19:39 CST)
  • charge determination for polariable ff02 force fields (Fri Feb 14 2003 - 14:27:51 CST)
  • RE: inter & intra-molecular interaction energies (Thu Feb 13 2003 - 17:47:54 CST)
  • RE: Periodic Box (Sat Feb 08 2003 - 10:52:49 CST)
  • some questions in gibbs calculation (Mon Feb 03 2003 - 07:46:39 CST)
  • gibbs calculation (Tue Jan 28 2003 - 13:03:44 CST)
  • gibbs run (Mon Jan 27 2003 - 11:05:06 CST)
  • RE: structure image (Mon Jan 27 2003 - 10:25:34 CST)
  • structure image (Mon Jan 27 2003 - 09:31:46 CST)
  • Zn2+ parameters (Fri Jan 24 2003 - 15:42:07 CST)
• Xiao Jian Tan
  • AMBER: PMF calculation with gibbs (Wed Aug 27 2003 - 17:34:16 CDT)
  • phi and psi angles analysis (Tue Apr 29 2003 - 18:27:17 CDT)
• xiaolin cheng
  • Re: AMBER: torsional restraints for groups of atoms (Wed Oct 22 2003 - 19:30:33 CDT)
  • Re: AMBER: Addles (Wed Oct 08 2003 - 10:56:18 CDT)
• Xiaoqin Huang
  • a question about simulation at high temperature (Thu Mar 20 2003 - 11:24:18 CST)
  • a question about simulation at high temperature (Thu Mar 20 2003 - 07:38:24 CST)
  • results of MD comparison (Wed Feb 26 2003 - 09:08:59 CST)
• XU Xingfu
  • angle violation in SANDER simulation (Wed Jun 04 2003 - 04:11:24 CDT)
• ya ya
  • Re: AMBER: improper (Wed Oct 01 2003 - 09:59:16 CDT)
• Yang, Mingfeng
  • quasih problem (Wed Jun 11 2003 - 09:10:30 CDT)
• yduan_at_udel.edu
  • Re: AMBER: MD problem!! (Thu Sep 18 2003 - 16:21:22 CDT)
• Ye Mei
  • Re: Re: AMBER: Compiling on Suse 9 Pro with ifc... (Fri Dec 05 2003 - 22:44:49 CST)
  • AMBER: a problem with memory size (Sun Nov 16 2003 - 09:45:39 CST)
  • Re: Re: Re: Re: AMBER: a problem with antechamber and leap (Thu Nov 13 2003 - 00:52:38 CST)
  • Re: Re: Re: AMBER: a problem with antechamber and leap (Wed Nov 12 2003 - 02:48:06 CST)
  • Re: AMBER: AM1-BCC in Amber7 (Mon Nov 10 2003 - 07:37:05 CST)
  • Re: Re: AMBER: a problem with antechamber and leap (Mon Nov 10 2003 - 03:15:06 CST)
  • AMBER: a problem with antechamber and leap (Sun Nov 09 2003 - 23:02:04 CST)
  • AMBER: how to mend the peptide with missing residues? (Tue Oct 21 2003 - 10:07:14 CDT)
  • Re: Re: AMBER: a problem with xleap (Wed Oct 15 2003 - 20:34:51 CDT)
  • AMBER: a problem with xleap (Wed Oct 15 2003 - 03:03:36 CDT)
  • about the dielectric (Wed May 28 2003 - 02:57:49 CDT)
  • about the dielectric (Wed May 28 2003 - 02:42:22 CDT)
  • a question about scale factor (Sat May 10 2003 - 21:53:45 CDT)
  • how to convert the amber force field files to any proper format that can be used by gaussian98 (Sat Mar 08 2003 - 21:06:10 CST)
• Yichen Cao
  • AMBER: GB/SA (Tue Nov 11 2003 - 13:02:41 CST)
  • AMBER: PARMSET problem (Wed Aug 20 2003 - 12:07:29 CDT)
  • Amber6 on RH 9 (Thu Jun 26 2003 - 10:37:09 CDT)
• Ying-Chieh Sun
  • compiling amber: Machine file for new 64 bit HP-Itanium II CPU (Tue Jan 14 2003 - 19:40:40 CST)
• Yogesh Sabnis
  • AMBER: Problem generating .tpp and .rst files for a complex (Fri Aug 01 2003 - 05:57:07 CDT)
• Yong Duan
  • RE: AMBER: mpich problem (Sun Nov 09 2003 - 18:13:13 CST)
  • RE: AMBER: infinitely long DNA (to Yong Duan) (Fri Nov 07 2003 - 16:24:41 CST)
  • RE: AMBER: shake constraint on all bonds (Wed Nov 05 2003 - 22:08:44 CST)
  • RE: AMBER: surface code in Amber (Tue Oct 28 2003 - 11:01:33 CST)
  • RE: AMBER: aminoacid mutation (Mon Oct 27 2003 - 20:09:02 CST)
  • RE: AMBER: RMSD and Radius of Gyration (Sat Oct 25 2003 - 20:40:07 CDT)
  • RE: AMBER: prmtop file format (Fri Oct 24 2003 - 14:19:16 CDT)
  • RE: AMBER: prmtop file format (Fri Oct 24 2003 - 10:05:35 CDT)
  • RE: AMBER: Simulation of small protein (Thu Oct 23 2003 - 20:51:12 CDT)
  • RE: AMBER: Simulation of small protein (Thu Oct 23 2003 - 20:11:02 CDT)
  • RE: AMBER: how to mend the peptide with missing residues? (Tue Oct 21 2003 - 10:15:53 CDT)
  • AMBER: ECC vs non-ECC (non-amber issue) (Mon Oct 20 2003 - 21:04:37 CDT)
  • RE: AMBER: carnal (Sun Oct 19 2003 - 15:00:11 CDT)
  • RE: AMBER: Implicit precision in sander vs architecture (Fri Oct 17 2003 - 11:30:31 CDT)
  • RE: AMBER: tru64 alpha (Fri Oct 17 2003 - 06:53:39 CDT)
  • RE: AMBER: tru64 alpha (Thu Oct 16 2003 - 21:00:04 CDT)
  • RE: AMBER: infinitely long DNA & moil-view? (Tue Oct 14 2003 - 15:15:29 CDT)
  • RE: AMBER: output frequency (Mon Oct 06 2003 - 09:08:21 CDT)
  • RE: AMBER: constant pressure in GB (Wed Oct 01 2003 - 20:45:04 CDT)
  • RE: AMBER: AMBER Carnal files (Sun Sep 21 2003 - 21:02:40 CDT)
  • RE: AMBER: AMBER Carnal files (Sat Sep 20 2003 - 17:44:44 CDT)
  • RE: AMBER: Suggestion regarding long simulation. (Thu Sep 18 2003 - 19:33:30 CDT)
  • RE: AMBER: re: MD problem!! (Thu Sep 18 2003 - 14:32:49 CDT)
  • RE: AMBER: 'ho' vDW parameters (Mon Sep 08 2003 - 15:27:48 CDT)
  • RE: AMBER: minimization error (Thu Aug 14 2003 - 15:56:54 CDT)
  • RE: AMBER: Insight pdb file in xleap (Thu Aug 07 2003 - 18:35:03 CDT)
  • RE: a bug? Re: AMBER: one more line about the npscal, box size changes and rms (Thu Aug 07 2003 - 13:49:39 CDT)
  • AMBER: RE: Restrain of dihedral angle! (Fri Aug 01 2003 - 08:27:04 CDT)
  • RE: AMBER: Amber parallelisation (Fri Aug 01 2003 - 07:28:31 CDT)
  • RE: AMBER: parallelisation (Fri Aug 01 2003 - 07:21:36 CDT)
  • RE: AMBER: frequency analysis (Wed Jul 30 2003 - 18:04:00 CDT)
  • RE: AMBER: H-O-H angle in TIP3P water model during minimization (Mon Jul 28 2003 - 19:54:28 CDT)
  • RE: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 13:51:30 CDT)
  • RE: AMBER: variable not in namelist for Sander input (Mon Jul 21 2003 - 09:49:07 CDT)
  • RE: AMBER: question on LJ parameters for molecules (Mon Jul 14 2003 - 22:52:27 CDT)
  • RE: Valdiation of Latest Amber parameters (Thu Jul 10 2003 - 00:25:33 CDT)
  • RE: Valdiation of Latest Amber parameters (Tue Jul 08 2003 - 22:12:27 CDT)
  • RE: Valdiation of Latest Amber parameters (Mon Jul 07 2003 - 18:28:41 CDT)
  • RE: How to do a rigid solvent model? (Sun Jul 06 2003 - 14:59:23 CDT)
  • RE: How to do a rigid solvent model? (Sat Jul 05 2003 - 13:48:01 CDT)
  • RE: AMBER7 on linux cluster (Fri Jun 20 2003 - 20:35:04 CDT)
  • RE: debug sander (Thu Jun 19 2003 - 04:21:27 CDT)
  • RE: May I get you help from new user of amber? (Mon Jun 09 2003 - 10:12:41 CDT)
  • RE: MD problem (Thu May 29 2003 - 19:58:21 CDT)
  • RE: about the dielectric (Wed May 28 2003 - 04:24:58 CDT)
  • RE: EWALD BOMB (Mon May 26 2003 - 18:51:22 CDT)
  • RE: non-periodic system (Wed May 21 2003 - 22:24:01 CDT)
  • RE: non-periodic system (Wed May 21 2003 - 22:17:03 CDT)
  • RE: off-diagonal VDW term (Tue May 20 2003 - 02:24:25 CDT)
  • RE: Etot is not constant in NVE ensemble (Fri May 09 2003 - 09:58:25 CDT)
  • RE: diffusion coefficients (Sun Apr 13 2003 - 22:50:48 CDT)
  • RE: Tleap-metalloprotein (Thu Apr 10 2003 - 21:42:53 CDT)
  • RE: Trying to understand parm99.dat (Tue Apr 08 2003 - 20:48:48 CDT)
  • RE: doubts (Fri Mar 21 2003 - 08:30:59 CST)
  • RE: GB vs. explicit solvent calculations (Thu Mar 20 2003 - 08:48:30 CST)
  • RE: leap remove command (Mon Mar 17 2003 - 06:32:21 CST)
  • RE: Why the NMA discrepancies? (Sun Mar 16 2003 - 21:46:57 CST)
  • RE: leap remove command (Sun Mar 16 2003 - 21:31:12 CST)
  • RE: how to convert the amber force field files to any proper format that can be used by gaussian98 (Sun Mar 09 2003 - 22:17:33 CST)
  • RE: failure of minimization (Mon Feb 24 2003 - 19:42:14 CST)
  • RE: failure of minimization (Fri Feb 21 2003 - 20:34:04 CST)
  • RE: question on EWALD (Mon Feb 17 2003 - 16:54:14 CST)
  • RE: question on EWALD (Mon Feb 17 2003 - 15:08:17 CST)
  • RE: Velocity (Mon Feb 17 2003 - 15:00:01 CST)
  • RE: energy calculation (Sun Feb 09 2003 - 10:36:28 CST)
• Yong Wang
  • AMBER: about the mopac7 installation. (Fri Sep 26 2003 - 02:07:16 CDT)
• Yong-Liang Zhu
  • AMBER: Water as part of protein in mm_pbsa calculation (Sat Oct 11 2003 - 22:20:12 CDT)
  • AMBER: Added water and mm_pbsa (Wed Oct 01 2003 - 12:29:37 CDT)
  • AMBER: How to add new atom type. (Thu Aug 14 2003 - 14:49:49 CDT)
  • RE: AMBER: Atom type in prepin file - new problem (Wed Aug 13 2003 - 18:05:01 CDT)
  • AMBER: Atom type in prepin file (Wed Aug 13 2003 - 17:21:28 CDT)
• Yongmei Wang
  • surface accesible area (Fri Mar 07 2003 - 17:22:22 CST)
  • probelms with antechamber (Thu Feb 20 2003 - 14:09:44 CST)
  • mm_pbsa (Tue Feb 18 2003 - 17:14:01 CST)
• Yongxing Liu
  • Re: essential dynamics (Fri Feb 07 2003 - 12:13:09 CST)
• Youyi Peng
  • AMBER: RESP charge redistribution (Mon Dec 22 2003 - 15:27:13 CST)
  • Re: AMBER: RESP charges (Thu Dec 18 2003 - 17:31:51 CST)
  • Re: AMBER: RESP charges (Thu Dec 18 2003 - 09:20:43 CST)
  • Re: AMBER: RESP charges (Thu Dec 11 2003 - 10:41:45 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 16:50:46 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 16:48:05 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 14:57:56 CST)
  • Re: AMBER: RESP charges (Wed Dec 10 2003 - 11:28:40 CST)
  • AMBER: RESP charges (Wed Dec 10 2003 - 08:34:58 CST)
  • AMBER: RESP charge (Mon Nov 17 2003 - 08:46:32 CST)
  • AMBER: water prep file needed (Thu Nov 13 2003 - 15:37:36 CST)
  • no MD output (Mon May 12 2003 - 14:01:47 CDT)
  • RMSD fluctuation too much (Thu May 08 2003 - 10:02:43 CDT)
  • initial velocity (Fri May 02 2003 - 09:22:52 CDT)
  • Re: problem about virtual box? (Thu May 01 2003 - 12:42:47 CDT)
  • problem about virtual box? (Thu May 01 2003 - 10:49:00 CDT)
  • Re: job stopped (Thu Apr 24 2003 - 15:33:37 CDT)
  • Re: job stopped (Thu Apr 24 2003 - 13:49:47 CDT)
  • job stopped (Thu Apr 24 2003 - 12:52:12 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 14:28:14 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 13:55:51 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 13:33:26 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 12:36:35 CDT)
  • Re: MD went crazy (Fri Apr 18 2003 - 11:17:24 CDT)
  • MD went crazy (Fri Apr 18 2003 - 10:20:25 CDT)
  • makeDIST_RST (Wed Apr 16 2003 - 21:24:19 CDT)
  • CYS and HIS (Wed Apr 16 2003 - 09:20:40 CDT)
  • ambpdb (Tue Apr 15 2003 - 20:32:22 CDT)
  • ibelly and ntr (Tue Apr 15 2003 - 16:59:59 CDT)
• yu275197_at_yorku.ca
  • AMBER: amber on mac cluster (Mon Nov 17 2003 - 19:58:34 CST)
• yuan bo
  • RMSF problem (Sat May 10 2003 - 04:31:27 CDT)
  • leap problem (Wed Apr 23 2003 - 22:49:36 CDT)
  • diffusion coefficients (Sun Apr 13 2003 - 21:34:25 CDT)
  • hydration site (Tue Mar 25 2003 - 20:33:31 CST)
  • problem of mass center (Wed Mar 12 2003 - 21:06:32 CST)
  • How do NTC=2 recognize hydrogen atom? (Wed Feb 19 2003 - 04:24:55 CST)
  • RE:RE: TAUP and density problem (Mon Feb 17 2003 - 03:50:08 CST)
  • TAUP and density problem (Sun Feb 16 2003 - 03:29:34 CST)
  • MAXINT problem (Fri Feb 14 2003 - 23:51:13 CST)
  • NTC=3 for organic solvent and NTC=2 for solute? (Wed Feb 12 2003 - 03:57:42 CST)
  • NTC=3 for organic solvent and NTC=2 for soluter? (Wed Feb 12 2003 - 03:57:21 CST)
  • Shake problem in organic solvent (Fri Jan 24 2003 - 06:03:48 CST)
• yuann
  • AMBER: RESP fitting limit? (Tue Nov 04 2003 - 22:46:10 CST)
  • AMBER: density equilibrium & harmonic restrain (Mon Sep 29 2003 - 21:59:50 CDT)
  • AMBER: derive corresponding torsional parameters (Fri Aug 08 2003 - 05:25:31 CDT)
  • 1-4 vdw term in Glycam2000 (Sun Jun 22 2003 - 23:24:16 CDT)
  • Re: LEAP compiling problem (Tue Jun 17 2003 - 20:17:56 CDT)
  • LEAP compiling problem (Tue Jun 17 2003 - 05:14:23 CDT)
  • difference between iwrap and image? (Sun May 11 2003 - 00:47:23 CDT)
  • A problem in Sander production dynamics (Mon Apr 14 2003 - 03:37:50 CDT)
  • Problem of Hbond in CARNAL (Tue Apr 01 2003 - 06:08:59 CST)
  • improper torsion for X -CB-CB-X (Mon Mar 24 2003 - 21:23:33 CST)
  • question about partial charge (Mon Feb 17 2003 - 20:43:48 CST)
  • naphthalene, anthracene force field (Wed Jan 29 2003 - 08:58:47 CST)
  • Re: nmanal & quasih question (Thu Jan 09 2003 - 10:13:30 CST)
  • nmanal & quasih question (Wed Jan 08 2003 - 01:16:56 CST)
  • looking for 'pdb_to_mass' (Tue Jan 07 2003 - 00:54:32 CST)
• Yuguang Mu
  • AMBER: secondary structure (Wed Aug 13 2003 - 07:37:08 CDT)
  • Re: helix movement (Wed Jun 11 2003 - 07:47:34 CDT)
  • PME (Wed Jun 11 2003 - 03:33:29 CDT)
  • PME (Tue Jun 10 2003 - 07:04:08 CDT)
  • Re: helix movement (Tue Jun 10 2003 - 05:47:42 CDT)
  • unit of output velocity (Fri Jun 06 2003 - 10:33:01 CDT)
  • Re: EWALD (Mon Mar 10 2003 - 01:13:31 CST)
  • EWALD (Sun Mar 09 2003 - 10:46:16 CST)
• Yuhui Cheng
  • AMBER: Amber charge problem (Mon Oct 13 2003 - 19:25:58 CDT)
  • AMBER: RESP calculation (Wed Aug 27 2003 - 21:04:57 CDT)
  • AMBER: Antechamber Problem (Wed Aug 27 2003 - 11:31:43 CDT)
  • Sander problem (Tue Jun 24 2003 - 21:31:28 CDT)
  • Sander error (Tue Jun 17 2003 - 13:37:21 CDT)
  • A weird antechamber error (Tue Apr 01 2003 - 22:21:46 CST)
  • How to do with two MG2+ ions? (Wed Mar 26 2003 - 22:29:49 CST)
  • How to do the image using ptraj? (Tue Feb 04 2003 - 20:35:53 CST)
• yuming chen
  • Re: A question about AMBER, leaprc.ff02EP (Wed May 14 2003 - 05:45:11 CDT)
  • A question about AMBER, leaprc.ff02EP (Wed May 14 2003 - 00:17:47 CDT)
• Yunfeng Hu
  • id_torus(): Could not find torus for atoms 1878 and 1894 (Mon Apr 14 2003 - 17:26:18 CDT)
• Yuqin Cai
  • AMBER: Why I get the same TSTRA for different strucutures from Nmode calculation? (Fri Nov 21 2003 - 14:54:54 CST)
  • AMBER: Nmode Problem (Thu Nov 13 2003 - 10:26:25 CST)
• Yuuki Komata
  • atom position restraints (Tue Apr 29 2003 - 20:34:06 CDT)
  • atom position restraints (Tue Apr 29 2003 - 07:44:25 CDT)
• zhaoxc_at_puccini.che.pitt.edu
  • AMBER: how to measure the minor groove widths of a DNA? (Tue Oct 28 2003 - 11:16:06 CST)
  • AMBER: what is the unit for the energy calculated from MM_PBSA? (Mon Oct 20 2003 - 20:08:51 CDT)
  • AMBER: is there a good program to quantitatively analyze hydration effect? (Fri Oct 10 2003 - 07:36:08 CDT)
  • Re: AMBER: Freezing the residues (Fri Oct 10 2003 - 07:30:38 CDT)
  • Re: AMBER: performance vs number of processors (Mon Sep 15 2003 - 14:41:20 CDT)
  • AMBER: mpprun: exec of '/usr/local/bin/sander7.0' failed: Not enough space (Tue Aug 26 2003 - 18:17:00 CDT)
  • Re: effect of forcing neutrality (Mon Jul 14 2003 - 11:17:24 CDT)
  • effect of forcing neutrality (Thu Jul 10 2003 - 14:56:00 CDT)
  • memory problem (Wed Jul 09 2003 - 08:34:09 CDT)
  • how to set up a carbon nanotube pdb file (Mon May 05 2003 - 16:24:10 CDT)
• Zheng Suxin
  • AMBER: Can use mm_pbsa_statistics.pl to calculate each snapshot's Delta Delta G, then give the SD (Thu Nov 06 2003 - 21:41:12 CST)
  • AMBER: How to estimate SD of the delta delta G between two mm_pbsa runs (Wed Nov 05 2003 - 07:41:34 CST)
• Zhi Qiang ZHOU
  • about the read error (Tue Jul 01 2003 - 21:35:41 CDT)
• Zhijun Li
  • RE: May I get your help? (Fri Jul 11 2003 - 10:22:30 CDT)
• zsx
  • vlimit exceeded when sander calculate free energies using TI (Wed Jun 11 2003 - 06:51:09 CDT)