AMBER Archive (2002) - By Author

Starting: Wed Jan 02 2002 - 16:22:14 CST
Ending: Tue Dec 31 2002 - 15:51:31 CST

• A. Ababou
  • MS program ... (Sat Mar 23 2002 - 10:21:15 CST)
• A. Hungie
  • How to generate PNA structure? (Mon Oct 07 2002 - 03:51:53 CDT)
  • dump coordinate into mdcrd (Fri Aug 30 2002 - 03:03:17 CDT)
  • force field name (Thu Aug 15 2002 - 08:50:48 CDT)
  • PTRAJ: radial distribution function (Wed Jul 17 2002 - 10:58:14 CDT)
  • propeller twist of ideal B-DNA (Wed Jun 19 2002 - 11:37:29 CDT)
  • vlimit exceeded (Wed Jun 12 2002 - 04:49:44 CDT)
  • benchmark for Amber7 (Fri Jun 07 2002 - 09:37:07 CDT)
  • Machine_file for Hitachi SR8000 (Wed Jun 05 2002 - 06:09:03 CDT)
  • compilation for Hitachi SR8000 (Sun May 26 2002 - 12:25:17 CDT)
  • PME & cutoff (Sat May 25 2002 - 08:12:48 CDT)
  • Re: NMR refinement (Thu May 16 2002 - 10:02:17 CDT)
• A.Madhumalar
  • err in specifying disulphide bridge using xleap! (Mon Dec 02 2002 - 10:25:30 CST)
  • Re: How to convert oldparmtop to newparmtop? (Thu Oct 17 2002 - 12:05:29 CDT)
  • How to convert oldparmtop to newparmtop? (Wed Oct 16 2002 - 12:18:35 CDT)
  • How to specify the counterion positions using xleap? (Wed Oct 16 2002 - 07:54:41 CDT)
  • parameters for sugars (Sun Sep 29 2002 - 11:30:36 CDT)
  • time scale to see the ion effect on DNA (Thu Jul 11 2002 - 01:40:52 CDT)
  • problem in compiling amber7 in IBMSP3 cluster (Thu Jul 04 2002 - 11:29:50 CDT)
  • Hydrogen bond energy using Anal (Tue Mar 26 2002 - 04:23:34 CST)
  • Re: redius of B-DNA duplex (Mon Feb 25 2002 - 11:41:42 CST)
  • pukering of DNA bases? (Sat Jan 12 2002 - 23:03:50 CST)
• ajakalian_at_lav.Boehringer-Ingelheim.com
  • RE: AM1-BCC sensitivity to AM1 charges (Tue Jul 30 2002 - 13:28:25 CDT)
• Alan Leo
  • Re: About the Memory allocation in MM_PBSA and SANDER (Fri Oct 04 2002 - 07:46:15 CDT)
  • Re: add DUMMY atom into coordinate file (Fri Aug 16 2002 - 14:51:35 CDT)
  • About the sander_classic calculation (Thu Apr 04 2002 - 15:32:34 CST)
• Albert Codony
  • Thanks to all (Sat May 04 2002 - 10:38:12 CDT)
  • max_rstack requested (Sun Apr 28 2002 - 17:39:58 CDT)
• Aldo Jongejan
  • CCl4 as solvent (Tue Nov 05 2002 - 07:44:02 CST)
  • FEP - ligand to nothing (or water)?? (Tue Oct 29 2002 - 03:50:54 CST)
  • Dummy torsions (Tue Oct 15 2002 - 08:33:02 CDT)
  • Computational alchemy (Tue Oct 15 2002 - 05:52:12 CDT)
• Alexander Issanin
  • IFTRES option in sander and gibbs (Tue Feb 12 2002 - 15:09:52 CST)
• Alicia Hopkins
  • Re: example 1 problems (Tue Sep 17 2002 - 07:03:53 CDT)
  • example 1 problems (Mon Sep 16 2002 - 10:57:23 CDT)
• Ambarish Nag
  • Question on 2 stage RESP fit (Thu Dec 12 2002 - 00:39:08 CST)
• amber mail account
  • Release of Amber, version 7 (fwd) (Sun Mar 03 2002 - 17:13:26 CST)
• amber_at_heimdal.compchem.ucsf.edu
  • Reflector problems (Tue Dec 03 2002 - 17:05:02 CST)
  • Energy decomposition with ANAL (fwd) (Tue Dec 03 2002 - 16:58:05 CST)
  • Amber Trajectories + VMD (fwd) (Tue Dec 03 2002 - 16:58:00 CST)
  • gB vs. explicit (fwd) (Tue Dec 03 2002 - 16:57:53 CST)
  • Constraints in Amber (fwd) (Tue Dec 03 2002 - 16:57:30 CST)
  • Re: CCL:freeware for RNA modeling on Linux (fwd) (Tue Dec 03 2002 - 16:57:21 CST)
  • freeware for RNA modeling on Linux (fwd) (Tue Dec 03 2002 - 16:57:10 CST)
  • Biphasic box (fwd) (Tue Dec 03 2002 - 16:13:10 CST)
  • Using GBSA for a DNA-PROTEIN complex (fwd) (Mon Aug 26 2002 - 16:52:06 CDT)
  • Re: "number of processors must be a power of two" (fwd) (Mon Aug 26 2002 - 16:52:01 CDT)
  • Scaling of Sander on Linux Clusters (fwd) (Mon Aug 26 2002 - 16:51:57 CDT)
  • Re: Extra points (fwd) (Mon Aug 26 2002 - 16:51:49 CDT)
  • leaprc file (fwd) (Mon Aug 26 2002 - 16:51:44 CDT)
  • a more general question (fwd) (Mon Aug 26 2002 - 16:51:41 CDT)
  • leaprc file (fwd) (Mon Aug 26 2002 - 16:51:29 CDT)
  • a more general question about ff (fwd) (Mon Aug 26 2002 - 16:51:25 CDT)
  • turning off ewald (fwd) (Mon Aug 26 2002 - 16:51:21 CDT)
  • Re: Etot drops after restarting MD in sander (fwd) (Mon Aug 26 2002 - 16:51:16 CDT)
  • Carnal RMSDs (fwd) (Mon Aug 26 2002 - 16:51:12 CDT)
  • How to make mpeg files from amber trajectories (fwd) (Mon Aug 26 2002 - 16:51:07 CDT)
  • Re: Can we get trajectories coordinates after FIT in Carnal? (fwd) (Mon Aug 26 2002 - 16:51:03 CDT)
  • why is mm_pbsa broken ? (fwd) (Mon Aug 26 2002 - 16:50:59 CDT)
  • regarding RESP run from gamess output (fwd) (Mon Aug 26 2002 - 16:50:55 CDT)
  • amber7, gaff and minimization (fwd) (Mon Aug 26 2002 - 16:50:50 CDT)
  • QUICK HELP! Parameters for neutral amino acids (fwd) (Mon Aug 26 2002 - 16:50:43 CDT)
  • Gibbs (FEP) (fwd) (Mon Aug 26 2002 - 16:50:36 CDT)
  • ambpdb problem (fwd) (Mon Aug 26 2002 - 16:50:32 CDT)
  • why is mm_pbsa broken ? (fwd) (Mon Aug 26 2002 - 16:50:27 CDT)
  • ewald bomb in md equilibration (fwd) (Mon Aug 26 2002 - 16:50:14 CDT)
  • adding_hydrogens_to_pdb (fwd) (Mon Aug 26 2002 - 16:50:07 CDT)
  • Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) (Mon Aug 26 2002 - 16:50:02 CDT)
  • RMSD by residue (fwd) (Mon Aug 26 2002 - 16:49:39 CDT)
• Amesh Patel
  • minimization probs (Tue Jun 11 2002 - 10:57:12 CDT)
  • xleap and carbohydrates and stuff (Wed Feb 27 2002 - 08:43:23 CST)
• amit kumar
  • assistance required (Mon Sep 16 2002 - 11:25:05 CDT)
• amutha ramaswamy
  • (no subject) (Thu Jan 10 2002 - 04:11:15 CST)
• Andrea Bernini
  • triNAG parameters?4 (Mon Jan 21 2002 - 09:13:26 CST)
• Andreas Kerzmann
  • example gibbs file for the methane tutorial (Fri Aug 30 2002 - 05:18:06 CDT)
  • What's this "interface" the tutorial talks about? (Wed Aug 28 2002 - 07:41:01 CDT)
  • Re: namelist error with sander (Mon Aug 12 2002 - 07:40:12 CDT)
  • namelist error with sander (Fri Aug 09 2002 - 03:47:53 CDT)
• Andreas Svrcek-Seiler
  • Re: default GB radii (Sat Dec 07 2002 - 06:02:09 CST)
  • Re: residue cross-correlation (Fri Nov 08 2002 - 14:16:59 CST)
  • Re: Reference for GB model 2 (Thu Oct 17 2002 - 15:34:40 CDT)
  • Re: error message (Wed Oct 16 2002 - 12:58:18 CDT)
  • Re: EGB = NaNQ (Fri Oct 04 2002 - 10:30:50 CDT)
  • Re: offset of temperature when running MD with CAP and no periodic conditions (Thu Sep 19 2002 - 12:11:31 CDT)
  • Re: Minimization in GB-SA-E-Spikes, LINMIN (Tue Jul 16 2002 - 11:00:55 CDT)
  • Re: van der Waals, hydrogen bond energy (Sat Jun 29 2002 - 07:29:38 CDT)
  • Re: help: nmode compile question!!! (Wed May 15 2002 - 06:30:12 CDT)
  • Re: topology file generation (Mon May 06 2002 - 07:11:54 CDT)
  • Re: your mail (Thu Apr 11 2002 - 09:33:22 CDT)
  • Re: convergence of MD simulations (Fri Apr 05 2002 - 04:12:11 CST)
  • Re: minimization problem (Tue Mar 19 2002 - 07:33:19 CST)
  • Re: removing rotational motion (Tue Feb 19 2002 - 06:27:18 CST)
  • Re: Latest parm + getting parm98 as default in LEaP (Mon Jan 21 2002 - 04:01:49 CST)
• Andrei Leitão
  • Molecular dynamic protocol... (Fri Dec 27 2002 - 12:40:26 CST)
  • About heating... (Wed Dec 18 2002 - 12:23:43 CST)
  • About counterions (Thu Dec 05 2002 - 13:10:30 CST)
  • Linmin question... (Thu Nov 14 2002 - 12:13:01 CST)
  • Linmin question... (Thu Nov 14 2002 - 12:10:21 CST)
  • Molecular Dynamic procedure... (Wed Oct 16 2002 - 10:48:10 CDT)
  • Problems with poly(A)-poly(T) tutorial... (Mon Sep 30 2002 - 14:55:53 CDT)
• Andrew Petersen
  • Protonated database (Tue Jun 11 2002 - 14:12:28 CDT)
• Andy Purkiss
  • Re: ramdomized start velocities (Fri Nov 08 2002 - 13:28:46 CST)
  • Re: carnal RST output format (Tue Mar 19 2002 - 14:45:00 CST)
  • NAD parameters (Thu Jan 17 2002 - 13:42:21 CST)
• Anke Eisenmann
  • off-to-mol2 (Wed Dec 18 2002 - 10:49:22 CST)
  • Re: how to make mpeg files from amber trajectories (Tue Aug 27 2002 - 09:41:01 CDT)
• Antonio J. Díaz Quintana
  • Fwd: NPT-MD (Fri May 31 2002 - 04:17:55 CDT)
• Apostoluk, Wlodzimierz K
  • divalent cations parameters (Mon Sep 30 2002 - 17:38:11 CDT)
  • (no subject) (Wed Sep 25 2002 - 14:09:53 CDT)
• arubin_at_unmc.edu
  • Re: Error running AMBER6 on Beowulf cluster (Fri Nov 22 2002 - 15:38:12 CST)
  • Error running AMBER6 on Beowulf cluster (Thu Nov 21 2002 - 17:10:39 CST)
• Arvid Soederhaell
  • timings? (Fri Dec 06 2002 - 02:51:10 CST)
  • .top files read into xLeap? (Mon Nov 11 2002 - 04:24:00 CST)
  • ramdomized start velocities (Fri Nov 08 2002 - 06:35:23 CST)
  • SDS forcefield? (Thu Oct 24 2002 - 04:25:58 CDT)
  • ambpdb? (Wed Sep 25 2002 - 02:38:34 CDT)
  • SHAKE... (Mon Jun 24 2002 - 06:25:05 CDT)
  • even more van der Waals explosion (Fri Jun 21 2002 - 04:23:17 CDT)
  • more van der Waals explosion (Fri Jun 21 2002 - 04:00:59 CDT)
  • van der Waals explosion (Fri Jun 21 2002 - 03:54:05 CDT)
  • Re: turning PME off in AMBER7 (Thu Jun 20 2002 - 08:45:25 CDT)
  • no mdcrd, no mden file (Fri Jun 07 2002 - 06:43:30 CDT)
  • Re: SHAKE troubles (Tue Jun 04 2002 - 03:22:40 CDT)
  • Re: SHAKE troubles (Fri May 31 2002 - 03:50:01 CDT)
  • SHAKE troubles (Wed May 29 2002 - 05:07:17 CDT)
  • order parameters? (Fri Apr 12 2002 - 07:55:33 CDT)
  • amber7, PME and anisotrop press. (Thu Apr 04 2002 - 03:46:58 CST)
• Asif Rahaman
  • running sander_classic for amber6 using different version of mpi (Mon Dec 09 2002 - 17:01:35 CST)
  • problem with gibbs !!!! (Mon Oct 21 2002 - 21:18:10 CDT)
  • Defining Restraints in Sander (Thu Jul 18 2002 - 15:21:59 CDT)
  • analysis of Gibbs 2D run (Thu Jun 06 2002 - 23:46:34 CDT)
  • Problem with Gibbs 2D run (Sun Jun 02 2002 - 22:29:38 CDT)
  • Problem with 2D Gibbs run (Wed May 22 2002 - 17:32:49 CDT)
  • this is a test for amber reflector - please ignore (Wed May 22 2002 - 17:17:29 CDT)
• Asim Okur
  • Re: cold belly run error (Mon Jun 10 2002 - 23:58:30 CDT)
• Bayly, Christopher
  • RE: antechamber best practices/charge equivalence w/ AM1-BCC (Tue Sep 24 2002 - 09:49:56 CDT)
• bdodson_at_scms.utmb.EDU
  • Running amber7 and nab on FreeBSD (Wed Jun 05 2002 - 15:31:24 CDT)
• Bernd Wellenzohn
  • MM-PGBSA Question!! (Tue Oct 22 2002 - 07:46:29 CDT)
  • Purine to Pyrimidine mutation (Thu Jul 25 2002 - 07:29:27 CDT)
  • Persistence length (Thu Feb 28 2002 - 09:39:11 CST)
  • Gibbs Question (Mon Feb 18 2002 - 14:47:15 CST)
• Bill Ross
  • Re: carnal (Fri Dec 06 2002 - 19:16:59 CST)
  • Re: ion distances (Mon Nov 25 2002 - 18:51:46 CST)
  • Re: more about averaging (Fri Nov 08 2002 - 15:21:39 CST)
  • Re: carnal output trajectory (Wed Oct 30 2002 - 10:37:00 CST)
  • Re: carnal output trajectory (Thu Oct 24 2002 - 16:26:15 CDT)
  • Re: How to define a sphere to minimize? (Mon Oct 21 2002 - 10:11:19 CDT)
  • Re: error message (Wed Oct 16 2002 - 14:22:44 CDT)
  • [Re: can carnal do the job as anal to break down the energy?] (Wed Aug 28 2002 - 15:35:40 CDT)
  • Re: Carnal RMSDs (Mon Aug 26 2002 - 18:56:50 CDT)
  • Re: Can we get trajectories coordinates after FIT in Carnal? (Mon Aug 26 2002 - 18:54:25 CDT)
  • Re: Questions about xleap ... (Tue Jul 23 2002 - 14:03:52 CDT)
  • Re: building general solvent boxes with leap (Thu Jul 18 2002 - 14:18:57 CDT)
  • Re: create new atom problem on xleap (Thu Jul 04 2002 - 15:58:59 CDT)
  • docking in xleap (Wed Jul 03 2002 - 23:25:50 CDT)
  • xmkmf: not found (Thu Jun 27 2002 - 17:29:08 CDT)
  • Re: transferring structures (Wed Jun 26 2002 - 14:47:02 CDT)
  • Re: SHAKE (actually: new atom types) (Mon Jun 24 2002 - 14:22:02 CDT)
  • Re: how to keep aromatic ring flat (Fri Jun 14 2002 - 18:34:42 CDT)
  • Re: Floating Invalid (Tue Jun 11 2002 - 00:36:16 CDT)
  • Re:xaLeap make fails on AIX (Mon Jun 10 2002 - 13:19:47 CDT)
  • Re: Suggestion to Bill and Case (Fri Jun 07 2002 - 15:16:30 CDT)
  • Re: About the box info read error (Fri May 17 2002 - 15:33:51 CDT)
  • Re: How can I get the correct residue number? (Thu May 02 2002 - 15:38:24 CDT)
  • Re: How can I get the correct residue number? (Thu May 02 2002 - 15:26:45 CDT)
  • Re: IFBOX=0 error in amber7 (Wed May 01 2002 - 00:15:05 CDT)
  • Re: install leap not working (Tue Apr 30 2002 - 14:21:01 CDT)
  • (no subject) (Tue Apr 23 2002 - 14:30:58 CDT)
  • leap bugfix (Sun Apr 21 2002 - 16:55:34 CDT)
  • RE: amber7 compilation on a beowulf cluster (Fri Apr 19 2002 - 17:26:19 CDT)
  • Re: PDB file with CONECT record (Fri Apr 12 2002 - 02:27:37 CDT)
  • Re: Save from LEaP to a PDBQ file ? (Fri Apr 12 2002 - 01:16:28 CDT)
  • Re: PDB file with CONECT record (Wed Apr 10 2002 - 01:09:36 CDT)
  • Re:PDB file with CONECT record (Mon Apr 08 2002 - 15:02:21 CDT)
  • Re: compiling error. (Mon Apr 01 2002 - 01:30:24 CST)
  • Re: Problem with atom type (Thu Mar 28 2002 - 18:14:16 CST)
  • Re: change topology (Thu Mar 28 2002 - 03:45:49 CST)
  • Re: creating a unit wth xleap (Tue Mar 19 2002 - 13:43:25 CST)
  • Re: carnal RST output format (Tue Mar 19 2002 - 13:32:36 CST)
  • Re: leap calculation (loadamberprep) (Wed Mar 06 2002 - 13:22:33 CST)
  • Re: a question about .in files (Wed Mar 06 2002 - 13:16:53 CST)
  • Re: Carnal coordinate averaging (Mon Feb 25 2002 - 16:44:17 CST)
  • Re: .OFF file format (Mon Feb 18 2002 - 14:26:16 CST)
  • Re: ImagingAtom (Thu Feb 07 2002 - 04:41:57 CST)
  • Re: "flags" in .lib files (Wed Jan 23 2002 - 13:39:45 CST)
  • Re:Latest parm + getting parm98 as default in LEaP (Tue Jan 22 2002 - 01:07:39 CST)
• Bimo Ario Tejo
  • limit of RMSD value (Tue Nov 19 2002 - 07:57:40 CST)
  • residue cross-correlation (Fri Nov 08 2002 - 12:57:48 CST)
  • residue cross-correlation (Fri Nov 08 2002 - 09:00:01 CST)
  • time correlation function (Fri Oct 25 2002 - 09:47:28 CDT)
  • once again: residue cross-correlation (Fri Oct 25 2002 - 09:39:40 CDT)
  • residue cross-correlation (Thu Oct 24 2002 - 16:15:50 CDT)
  • number of H-bonds (Sat Oct 19 2002 - 23:54:44 CDT)
  • NTX / IREST inconsistency (Fri Oct 04 2002 - 10:11:59 CDT)
  • atomicfluct (Thu Oct 03 2002 - 06:40:47 CDT)
  • creating a solvent box (Tue Aug 06 2002 - 12:23:13 CDT)
  • problem with amber7 mpi (Thu Aug 01 2002 - 05:50:32 CDT)
  • creating a solvent box (Thu Jul 25 2002 - 07:32:17 CDT)
  • CCl4 solvent box (Wed Jul 24 2002 - 14:55:04 CDT)
  • CCL4 solvent box (Wed Jul 24 2002 - 10:40:10 CDT)
  • Re: Segmentation fault (Wed Jul 24 2002 - 04:42:26 CDT)
  • Segmentation fault (Tue Jul 23 2002 - 14:44:58 CDT)
  • CA-OS parameter (Tue Jul 23 2002 - 11:07:19 CDT)
  • Re: C sp2 connected to OS (Tue Jul 23 2002 - 03:23:03 CDT)
  • C sp2 connected to OS (Mon Jul 22 2002 - 12:37:27 CDT)
• Bjorn-Olav Brandsdal
  • Parameters for hexachloroethane (Wed Jun 05 2002 - 04:13:54 CDT)
• C. Klein
  • what are "end group interactions"? (Mon Oct 07 2002 - 03:43:00 CDT)
  • Re: old prmtop (Wed Sep 04 2002 - 11:21:18 CDT)
  • sander on NEC-SX5 (Thu Aug 15 2002 - 11:12:24 CDT)
  • Re: look for benchmark with myrinet vs. 100-BT (Sun Aug 04 2002 - 03:21:29 CDT)
  • Re: Origin300, Linux Cluster (Thu Jul 04 2002 - 12:41:31 CDT)
• Campbell, Matthew P
  • (no subject) (Tue Mar 05 2002 - 11:21:07 CST)
• Carles Ferrer
  • limit of written files with ptraj (Mon Mar 11 2002 - 14:54:16 CST)
• Carlos Andres Ramirez-Mondragon
  • prmtop file question. (Wed Jul 17 2002 - 16:15:59 CDT)
• Carlos P. Sosa
  • systems.Re: sander7: MPI_COMM_RANK problem (Mon Oct 21 2002 - 14:44:56 CDT)
  • Re: RESP gaussian job crashing (Thu Oct 03 2002 - 17:39:59 CDT)
  • Re: problems on IBM AIX (Fri Sep 13 2002 - 10:47:31 CDT)
• Carlos Simmerling
  • Re: water box, (Wed Dec 18 2002 - 07:18:18 CST)
  • Re: not compiled with -DHAS_10_12!! (Thu Dec 05 2002 - 11:03:08 CST)
  • Re: combinig two trajectory files. (Mon Dec 02 2002 - 06:49:21 CST)
  • Re: restrain a residue as center of mass (Wed Nov 27 2002 - 15:38:57 CST)
  • Re: Please help. Energy suddenly increase. Protein jump out (Wed Nov 27 2002 - 15:35:15 CST)
  • Re: restrain a residue as center of mass (Wed Nov 27 2002 - 15:34:00 CST)
  • Re: restrain a residue as center of mass (Tue Nov 26 2002 - 18:17:58 CST)
  • Re: Error running AMBER6 on Beowulf cluster (Fri Nov 22 2002 - 17:33:49 CST)
  • Re: restarting simulation (Fri Nov 22 2002 - 14:56:24 CST)
  • Re: targeted MD for more than 2 groups (Thu Nov 21 2002 - 17:54:53 CST)
  • Re: Targeted MD (Mon Oct 28 2002 - 17:09:19 CST)
  • Re: specification for memory requirement (Fri Oct 25 2002 - 20:55:42 CDT)
  • Re: targeted MD (Fri Oct 18 2002 - 10:45:33 CDT)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 11:49:15 CDT)
  • Re: groups in targeted md (Mon Sep 30 2002 - 09:04:26 CDT)
  • Re: Density during equilibration (sander) (Tue Sep 17 2002 - 20:44:13 CDT)
  • Re: large energy fluctration (Thu Sep 12 2002 - 13:50:09 CDT)
  • Re: sander.LES questions (Thu Sep 12 2002 - 12:24:25 CDT)
  • Re: Strange MD simulation results with GB solvation at high temp. (Wed Sep 11 2002 - 21:04:44 CDT)
  • Re: Strange MD simulation results with GB solvation at high temp. (Tue Sep 10 2002 - 07:07:58 CDT)
  • Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) (Thu Aug 29 2002 - 05:54:15 CDT)
  • Fw: amber problem (Wed Aug 28 2002 - 12:10:26 CDT)
  • Re: problem in MD (Tue Aug 27 2002 - 20:40:06 CDT)
  • Re: restraints in parm in amber7 (Tue Aug 27 2002 - 20:38:59 CDT)
  • Re: difference 94 99 force field (Tue Aug 27 2002 - 09:34:50 CDT)
  • Re: RMSD by residue (fwd) (Mon Aug 26 2002 - 20:10:41 CDT)
  • Re: problem with amber7 mpi (Thu Aug 01 2002 - 07:34:43 CDT)
  • Re: dielectric constant for partialy solvated MD (Wed Jul 31 2002 - 15:54:12 CDT)
  • Re: Error decoding variable (Wed Jul 31 2002 - 10:41:04 CDT)
  • Re: Error decoding variable (Wed Jul 31 2002 - 07:37:46 CDT)
  • Re: Trajectory files (Wed Jul 24 2002 - 10:52:29 CDT)
  • Re: "crd" file created with VMD (Tue Jul 23 2002 - 22:02:50 CDT)
  • Re: "crd" file created with VMD (Tue Jul 23 2002 - 20:42:15 CDT)
  • Re: (Tue Jul 23 2002 - 06:48:48 CDT)
  • Re: AMBER7 and Movie (Mon Jul 22 2002 - 11:56:52 CDT)
  • Re: Defining Restraints in Sander (Thu Jul 18 2002 - 16:29:22 CDT)
  • Re: van der Waals, hydrogen bond energy (Fri Jun 28 2002 - 18:41:11 CDT)
  • Re: box size & 1st equilibrium (Fri Jun 28 2002 - 06:56:09 CDT)
  • Re: partial charges (Mon Jun 24 2002 - 20:38:35 CDT)
  • Re: The atom number mismatch in coord and topology file. (Thu Jun 13 2002 - 17:27:38 CDT)
  • Re: vlimit exceeded (Wed Jun 12 2002 - 06:42:14 CDT)
  • Re: Reorder water in amber7 (Tue Jun 11 2002 - 06:36:04 CDT)
  • Re: glucose (Tue May 28 2002 - 10:50:59 CDT)
  • Re: topology file generation (Mon May 06 2002 - 07:27:06 CDT)
  • Re: Problems with AMBER7 and Multiple Processors on SGI servers (Fri Apr 26 2002 - 07:05:52 CDT)
  • Re: Recalculating energies (Wed Apr 17 2002 - 06:39:27 CDT)
  • Re: (Sat Apr 13 2002 - 07:06:29 CDT)
  • Re: input files (Wed Apr 03 2002 - 07:40:30 CST)
  • Re: compiling error. (Sun Mar 31 2002 - 09:24:19 CST)
  • Re: The link is out (Tue Feb 19 2002 - 14:53:45 CST)
  • Re: linux? (Fri Jan 04 2002 - 07:55:15 CST)
• Carsten Detering
  • antechamber (Wed Dec 18 2002 - 16:32:44 CST)
  • antechamber (Wed Dec 18 2002 - 13:38:16 CST)
• case
  • RE: bondbydistance (Fri Sep 06 2002 - 19:04:02 CDT)
  • RE: cut-off question (Fri Sep 06 2002 - 19:01:28 CDT)
  • RE: Escaping Atoms (Thu Sep 05 2002 - 17:04:06 CDT)
  • RE: minimization probs (Tue Jun 11 2002 - 12:36:57 CDT)
  • RE: entropy calculation (Tue Jun 11 2002 - 08:56:37 CDT)
  • RE: Reorder water in amber7 (Tue Jun 11 2002 - 08:53:59 CDT)
  • amber on MAC OSX (Thu Jun 06 2002 - 19:22:44 CDT)
  • Re: Intel Kernel Math Library (Thu Jun 06 2002 - 10:02:25 CDT)
• Cezary Czaplewski
  • amber 60 on Unicos Cray (Mon Mar 04 2002 - 11:56:36 CST)
• cfrenz_at_aecom.yu.edu
  • RESP (Thu Apr 18 2002 - 10:55:55 CDT)
• ch cureton
  • Torsion driving (Thu Sep 26 2002 - 11:00:34 CDT)
  • Escaping Atoms (Wed Sep 04 2002 - 05:43:03 CDT)
• CHAUMONT Alain
  • (no subject) (Mon Nov 25 2002 - 09:32:50 CST)
• Chen, Ya
  • Problems with tes.antechamber (Tue Oct 29 2002 - 19:21:59 CST)
• chernhoe
  • Re: amber on RH8 (Wed Nov 06 2002 - 22:43:41 CST)
  • amber on RH8 (Wed Nov 06 2002 - 01:23:18 CST)
• Chris Chipot
  • Announcement: Optimally Partitioned Electric Properties - OPEP (Wed Jul 10 2002 - 03:06:48 CDT)
• Chris Switzer
  • problem with amber7 compiling on SGI (Wed Aug 14 2002 - 20:26:54 CDT)
• Christian.Pilger_at_bc.boehringer-ingelheim.com
  • WG: (Tue Jun 18 2002 - 00:48:01 CDT)
  • (no subject) (Mon Jun 17 2002 - 05:09:11 CDT)
  • (no subject) (Fri Jun 14 2002 - 00:30:15 CDT)
• Christoph Brockmann
  • Carnal table output (Fri Oct 18 2002 - 03:48:37 CDT)
  • Re: nmr and positional restraint in input (Thu Oct 10 2002 - 04:12:49 CDT)
  • Re: groups in targeted md (Mon Sep 30 2002 - 09:48:16 CDT)
  • groups in targeted md (Mon Sep 30 2002 - 08:15:10 CDT)
• Christophe L M J Verlinde
  • counter-ions in FEP (Thu Jul 11 2002 - 11:37:41 CDT)
• Chuck Schneider
  • Re: MACHINE file for Tru64 ES45 (Tue Oct 08 2002 - 06:28:45 CDT)
  • Re: problem compiling roar (mop7mm) on alpha (Tue Jul 23 2002 - 12:09:37 CDT)
• Claire Edmonds
  • Information request - where to buy software (Mon Aug 05 2002 - 08:23:59 CDT)
• Computational Chemistry Job Market
  • Resending: Medicinal and Computational Chemistry Job Market (Mon Mar 25 2002 - 14:05:03 CST)
• Cozmuta
  • cut-off question (Fri Sep 06 2002 - 17:49:21 CDT)
  • protonation pH dependent (Thu Aug 08 2002 - 16:14:46 CDT)
  • Re: charges-again (Wed Aug 07 2002 - 20:47:14 CDT)
  • charges (Tue Aug 06 2002 - 18:24:14 CDT)
  • check-up question (Tue Aug 06 2002 - 14:13:31 CDT)
  • Re: Amber trajectory movies in Powerpoint (Tue Aug 06 2002 - 13:25:31 CDT)
  • PROTON_INFO (Fri Aug 02 2002 - 22:25:37 CDT)
  • water box-nonperiodic (Fri Aug 02 2002 - 22:14:35 CDT)
  • proton_info/PS (Thu Aug 01 2002 - 12:29:02 CDT)
  • file (Thu Aug 01 2002 - 12:24:13 CDT)
  • structure (Tue Jul 30 2002 - 22:34:44 CDT)
  • tests for amber (Tue Jul 30 2002 - 18:47:18 CDT)
  • building ss DNA/RNA (Tue Jul 30 2002 - 16:47:45 CDT)
• Craig A Bayse
  • periodic box (Mon Nov 04 2002 - 10:49:53 CST)
  • question (Tue Jun 18 2002 - 17:04:47 CDT)
• CUI, Guanglei
  • Re: corrupted trajectory (Tue Dec 03 2002 - 20:04:13 CST)
  • 2nd restart (Sun Oct 27 2002 - 11:02:30 CST)
  • Re: question on ouput of sander (Mon Oct 21 2002 - 13:43:40 CDT)
  • Re: Not able to use xleap ... (Mon Oct 21 2002 - 10:33:23 CDT)
  • Re: Not able to use xleap ... (Mon Oct 21 2002 - 08:43:51 CDT)
  • Re: Not able to use xleap ... (Fri Oct 18 2002 - 12:14:24 CDT)
  • Re: Not able to use xleap ... (Fri Oct 18 2002 - 11:26:47 CDT)
  • sander6 running and crashing at PSC? (Thu Oct 17 2002 - 12:17:40 CDT)
  • Re: a leap question (Thu Oct 17 2002 - 08:43:24 CDT)
  • Re: MACHINE file for Tru64 ES45 (Tue Oct 08 2002 - 08:47:16 CDT)
  • MACHINE file for Tru64 ES45 (Mon Oct 07 2002 - 14:20:19 CDT)
  • Re: a freeware to display RMSD matrices (Thu Sep 19 2002 - 08:42:29 CDT)
  • Re: protein minimization (Tue Sep 03 2002 - 08:19:39 CDT)
  • Re: GB in amber6 (Fri Aug 16 2002 - 08:25:52 CDT)
  • Re: GB in amber6 (Thu Aug 15 2002 - 21:33:27 CDT)
  • Re: distance restraint stuff (Thu Aug 01 2002 - 10:44:25 CDT)
  • Re: Potential Energy and RMS-Deviation Issues (Thu Aug 01 2002 - 10:38:36 CDT)
  • Re: creating a solvent box (Thu Jul 25 2002 - 08:33:01 CDT)
  • Re: your mail (Thu Jul 25 2002 - 08:30:30 CDT)
  • Re: combining trajectory file (Tue Mar 12 2002 - 10:24:44 CST)
  • Re: GB simulation (Mon Mar 04 2002 - 09:41:53 CST)
  • Re: frcmod file format (Mon Feb 11 2002 - 12:38:37 CST)
  • Re: quasih (Wed Feb 06 2002 - 09:53:55 CST)
• Daniel Flint
  • Stretching Constants (Thu Jan 17 2002 - 05:21:52 CST)
• Daniel Svozil
  • How Amber calculates electrostatic energy? (Wed Nov 27 2002 - 08:47:11 CST)
• darden
  • Re: water box, (Wed Dec 18 2002 - 18:45:55 CST)
  • Re: message during minimization (Wed Dec 18 2002 - 18:32:21 CST)
  • Re: water box, (Wed Dec 18 2002 - 10:33:07 CST)
  • Re: message during minimization (Wed Dec 18 2002 - 10:24:48 CST)
  • Re: external electric field/another try (Wed Nov 27 2002 - 17:27:32 CST)
  • Re: your mail (Sun Nov 24 2002 - 16:46:35 CST)
  • Re: belly and EWALD in amber7 (Sun Nov 10 2002 - 16:25:31 CST)
  • Re: vlimit and vmax (Fri Sep 20 2002 - 14:27:10 CDT)
  • Re: your mail (Wed Aug 07 2002 - 06:58:17 CDT)
  • Re: PME & cutoff (Sun May 26 2002 - 12:03:30 CDT)
  • Re: convergence of MD simulations (Mon Apr 08 2002 - 15:08:10 CDT)
  • Re: does PME function without charge neutralization? (Tue Apr 02 2002 - 16:23:02 CST)
  • Re: LIMIN Faliure/Energies per residue for B-DNA etc. (Thu Jan 31 2002 - 15:11:19 CST)
  • Re: box_size (Tue Jan 29 2002 - 09:38:55 CST)
• david
  • pseudoatoms and NMR restraints (Tue Nov 05 2002 - 03:46:42 CST)
  • *.top file: "PARM-F-UHOSED, try again" (Thu Oct 31 2002 - 11:17:18 CST)
• David A. Case
  • new on the Amber web pages... (Tue Dec 31 2002 - 15:51:31 CST)
  • Re: Molecular dynamic protocol... (Fri Dec 27 2002 - 13:25:51 CST)
  • Re: atomicfluct in ptraj (Thu Dec 19 2002 - 11:28:43 CST)
  • Re: ntwv saves v(t) or v(t+dt/2) ? (Thu Dec 19 2002 - 11:24:33 CST)
  • Re: message during minimization (Thu Dec 19 2002 - 10:05:00 CST)
  • Re: water box, (Wed Dec 18 2002 - 18:17:31 CST)
  • Re: About heating... (Wed Dec 18 2002 - 13:42:51 CST)
  • Re: off-to-mol2 (Wed Dec 18 2002 - 12:03:48 CST)
  • Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 21:28:21 CST)
  • Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 15:09:48 CST)
  • Re: a question about force field in AMBER (Mon Dec 16 2002 - 19:56:29 CST)
  • Re: Amber 7 MM-PBSA for Amber 6 trajectories (Sat Dec 14 2002 - 13:26:01 CST)
  • Re: ambpdb (Fri Dec 13 2002 - 22:46:12 CST)
  • Re: difference in energy in amber6 and amber7 (Wed Dec 11 2002 - 09:40:48 CST)
  • Re: default GB radii (Fri Dec 06 2002 - 15:11:13 CST)
  • Re: positional restraints (Fri Dec 06 2002 - 10:05:02 CST)
  • Re: timings? (Fri Dec 06 2002 - 09:46:27 CST)
  • Re: md failure: deep energetics problem (Thu Dec 05 2002 - 13:55:40 CST)
  • Re: About counterions (Thu Dec 05 2002 - 13:47:04 CST)
  • Re: bug fixes (Thu Dec 05 2002 - 10:41:02 CST)
  • Re: Energy decomposition with ANAL (fwd) (Wed Dec 04 2002 - 10:31:52 CST)
  • Re: gB vs. explicit (Wed Dec 04 2002 - 10:28:43 CST)
  • Re: Constraints in Amber (Tue Dec 03 2002 - 17:16:02 CST)
  • Re: freeware for RNA modeling on Linux (fwd) (Tue Dec 03 2002 - 17:11:48 CST)
  • Re: Biphasic box (Tue Dec 03 2002 - 17:09:50 CST)
  • Re: err in specifying disulphide bridge using xleap! (Mon Dec 02 2002 - 11:05:01 CST)
  • Re: solvateOct (Mon Dec 02 2002 - 09:40:02 CST)
  • Re: the tree name? (Wed Nov 27 2002 - 16:44:17 CST)
  • Re: esp.sh problem (Wed Nov 27 2002 - 13:12:54 CST)
  • Re: Please help. Energy suddenly increase. Protein jump out (Wed Nov 27 2002 - 10:26:55 CST)
  • Re: solvateOct (Tue Nov 26 2002 - 17:51:31 CST)
  • Re: GIBBS - ERROR: Restraint read error from RSTIN; Check format: (Tue Nov 26 2002 - 17:30:52 CST)
  • Re: using SHAKE for solvent only (Mon Nov 25 2002 - 12:17:54 CST)
  • Re: atom type not recognized by GB (Sun Nov 24 2002 - 19:50:01 CST)
  • Re: ntx=7, irest=0 (Fri Nov 22 2002 - 20:36:28 CST)
  • Re: solvateOct (Fri Nov 22 2002 - 20:31:03 CST)
  • Re: Restraint Ambiguities (Fri Nov 22 2002 - 10:33:34 CST)
  • Re: Restraint Ambiguities (Thu Nov 21 2002 - 20:08:04 CST)
  • Re: Error running AMBER6 on Beowulf cluster (Thu Nov 21 2002 - 19:31:47 CST)
  • Re: PARMSET (Thu Nov 21 2002 - 10:13:38 CST)
  • Re: intdiel & extdiel (Wed Nov 20 2002 - 09:51:44 CST)
  • Re: GIBBS - Error message. (Tue Nov 19 2002 - 11:09:09 CST)
  • Re: polarizabitlity (Mon Nov 18 2002 - 18:44:10 CST)
  • Re: simulating dna (Mon Nov 18 2002 - 18:29:22 CST)
  • Re: EWALD crash (Mon Nov 18 2002 - 18:27:37 CST)
  • Re: makeDIST_RST? (Mon Nov 18 2002 - 18:15:35 CST)
  • Re: question (Fri Nov 15 2002 - 20:45:34 CST)
  • Re: Linmin question... (Fri Nov 15 2002 - 02:12:20 CST)
  • Re: your mail (Thu Nov 14 2002 - 10:00:48 CST)
  • Re: input format for gibbs restraints (Wed Nov 13 2002 - 19:53:27 CST)
  • Re: help! Non bond list overflow! (Wed Nov 13 2002 - 18:51:07 CST)
  • Re: CMM method (Wed Nov 13 2002 - 18:42:26 CST)
  • Re: Ewald (Wed Nov 13 2002 - 10:09:08 CST)
  • Re: the removal of global motion (Tue Nov 12 2002 - 18:18:31 CST)
  • Re: NMR restraints on a 10-mer DNA in Sander (Tue Nov 12 2002 - 17:30:52 CST)
  • Re: the removal of global motion (Tue Nov 12 2002 - 17:25:09 CST)
  • Re: problem in PME (Tue Nov 12 2002 - 17:16:52 CST)
  • Re: problem in PME (Tue Nov 12 2002 - 08:06:47 CST)
  • Re: .top files read into xLeap? (Mon Nov 11 2002 - 20:20:41 CST)
  • Re: saveAmberParm of leap (Mon Nov 11 2002 - 18:05:15 CST)
  • Re: Forwarded mail.... (Sun Nov 10 2002 - 16:40:19 CST)
  • Re: belly and ivcap conflict in gibbs (Sun Nov 10 2002 - 16:35:16 CST)
  • Re: ramdomized start velocities (Fri Nov 08 2002 - 13:20:54 CST)
  • Re: procheck (Tue Nov 05 2002 - 10:31:31 CST)
  • Re: torsion restraints in GIBBS (Tue Nov 05 2002 - 10:20:57 CST)
  • Re: equilibrium problem about cut and belly (Tue Nov 05 2002 - 10:14:51 CST)
  • Re: pseudoatoms and NMR restraints (Tue Nov 05 2002 - 10:06:07 CST)
  • Re: restart (Mon Nov 04 2002 - 15:59:15 CST)
  • Re: Visualizing AMBER coordinates trajectory in VMD (Mon Nov 04 2002 - 15:57:10 CST)
  • Re: periodic box (Mon Nov 04 2002 - 12:32:11 CST)
  • Re: flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 (Fri Nov 01 2002 - 07:51:26 CST)
  • Re: molsurf reference (Fri Nov 01 2002 - 07:46:21 CST)
  • Re: *.top file: "PARM-F-UHOSED, try again" (Thu Oct 31 2002 - 11:19:06 CST)
  • Re: time correlation function (Thu Oct 31 2002 - 09:21:28 CST)
  • Re: FEP - ligand to nothing (or water)?? (Tue Oct 29 2002 - 08:24:47 CST)
  • Re: 64-bit Compilation SUN's forte compiler (Mon Oct 28 2002 - 21:41:15 CST)
  • Re: leap - sander information flow (Mon Oct 28 2002 - 15:44:28 CST)
  • Re: min output (Wed Oct 23 2002 - 18:51:06 CDT)
  • Re: Dummy atoms... (Wed Oct 23 2002 - 11:35:31 CDT)
• David A. Case
  • Re: replacing fft routines (Tue Oct 22 2002 - 17:58:34 CDT)
  • Re: MM-PGBSA Question!! (Tue Oct 22 2002 - 09:45:20 CDT)
  • Re: question on ouput of sander (Mon Oct 21 2002 - 13:59:27 CDT)
  • Re: reg: MAC OS (Mon Oct 21 2002 - 11:11:56 CDT)
  • Re: Not able to use xleap ... (Fri Oct 18 2002 - 11:38:23 CDT)
  • Re: targeted MD (Fri Oct 18 2002 - 10:32:14 CDT)
  • cutoffs in GB (Thu Oct 17 2002 - 16:08:16 CDT)
  • Re: dummy torsional parameters again. (Thu Oct 17 2002 - 12:58:38 CDT)
  • Re: a leap question (Thu Oct 17 2002 - 10:35:01 CDT)
  • Re: syntax (Wed Oct 16 2002 - 13:57:44 CDT)
  • Re: IGB =4 with GAFF and bugfix24 incomplete? (Wed Oct 16 2002 - 13:55:24 CDT)
  • Re: confusing error messages (Wed Oct 16 2002 - 13:42:15 CDT)
  • Re: How to convert oldparmtop to newparmtop? (Wed Oct 16 2002 - 13:04:59 CDT)
  • Re: Can I use belly and ntr at the same time? (Wed Oct 16 2002 - 10:45:49 CDT)
  • Re: Bug in reading binary restart file with BOX parameters (Wed Oct 16 2002 - 10:27:51 CDT)
  • Re: How to specify the counterion positions using xleap? (Wed Oct 16 2002 - 10:09:21 CDT)
  • Re: Error in Antechamber program in ammber7 (Wed Oct 16 2002 - 10:04:40 CDT)
  • Re: Error in Antechamber program in ammber7 (Tue Oct 15 2002 - 10:33:09 CDT)
  • Re: Dummy torsions (Tue Oct 15 2002 - 10:25:41 CDT)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 13:10:50 CDT)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 11:04:30 CDT)
  • Re: problem in sander (Fri Oct 11 2002 - 10:00:53 CDT)
  • Re: about dummy parameter of multiplicity (Thu Oct 10 2002 - 13:37:40 CDT)
  • Re: Dielectric constant for interior of proteins (Thu Oct 10 2002 - 13:33:19 CDT)
  • Re: LINMIN FAILURE (Tue Oct 08 2002 - 20:33:07 CDT)
  • Re: crdgrow (Tue Oct 08 2002 - 20:17:45 CDT)
  • Re: xleap on a SGI Fuel (Mon Oct 07 2002 - 21:50:33 CDT)
  • Re: Different numbers on different architectures. (Fri Oct 04 2002 - 11:26:07 CDT)
  • Re: NTX / IREST inconsistency (Fri Oct 04 2002 - 10:35:07 CDT)
  • Re: compiling SGI/mpi (Fri Oct 04 2002 - 10:07:23 CDT)
  • Re: compiling SGI/mpi (Thu Oct 03 2002 - 20:50:11 CDT)
  • Re: MM-GBSA and counterions (Thu Oct 03 2002 - 15:43:35 CDT)
  • Re: regarding resp-doubts (Thu Oct 03 2002 - 11:10:48 CDT)
  • Re: Questions on crosslinking residues (Thu Oct 03 2002 - 10:04:18 CDT)
  • Re: xleap XENVIRONMENT (Wed Oct 02 2002 - 18:55:31 CDT)
  • Re: Questions on crosslinking residues (Wed Oct 02 2002 - 18:34:47 CDT)
  • Re: tutorial on plastocyanin (Wed Oct 02 2002 - 09:48:27 CDT)
  • Re: antechamber web page (Tue Oct 01 2002 - 18:00:33 CDT)
  • Re: NON-BONDED INTERACTION (Tue Oct 01 2002 - 10:28:00 CDT)
  • Re: Image charges with the solvate cap command (Mon Sep 30 2002 - 19:34:28 CDT)
  • Re: your mail (Mon Sep 30 2002 - 11:35:06 CDT)
  • Re: Request for help with Antechamber (Fri Sep 27 2002 - 19:54:21 CDT)
  • Re: nmanal help request (Fri Sep 27 2002 - 10:38:23 CDT)
  • Re: Constant pressure equilibration in a system with a solvent cap (Fri Sep 27 2002 - 10:26:09 CDT)
  • Re: mm_pbsa and statistic program (Thu Sep 26 2002 - 10:37:15 CDT)
  • Re: GB tutorial (Thu Sep 26 2002 - 10:31:19 CDT)
  • Re: Question about Antechamber (Thu Sep 26 2002 - 10:28:51 CDT)
  • Re: expression of V(lambda) in GIBBS (Tue Sep 24 2002 - 09:14:01 CDT)
  • Re: mm_pbsa (Mon Sep 23 2002 - 08:25:02 CDT)
  • Re: mol2 file format in the future of amber (Sun Sep 22 2002 - 10:10:42 CDT)
  • Re: Parameters for AMBER (Fri Sep 20 2002 - 08:53:18 CDT)
  • Re: BLOWUP after 100 ns??? (Thu Sep 19 2002 - 19:29:58 CDT)
  • Re: image (Thu Sep 19 2002 - 12:43:32 CDT)
  • Re: bug in New2oldparm (Thu Sep 19 2002 - 10:28:30 CDT)
  • Re: Density during equilibration (sander) (Tue Sep 17 2002 - 14:21:49 CDT)
  • Re: SETVEL, incorrect number of arguments? (Tue Sep 17 2002 - 14:18:38 CDT)
  • Re: example 1 problems (Tue Sep 17 2002 - 09:45:31 CDT)
  • Re: question about nmode again. (Tue Sep 17 2002 - 09:40:00 CDT)
  • Re: amber question (Mon Sep 16 2002 - 11:47:03 CDT)
  • Re: example 1 problems (Mon Sep 16 2002 - 11:25:54 CDT)
  • Re: problems on IBM AIX (Fri Sep 13 2002 - 09:42:14 CDT)
  • Re: Distace dependent dielectric constant (Thu Sep 12 2002 - 17:39:35 CDT)
  • Re: Strange MD simulation results with GB solvation at high temp. (Wed Sep 11 2002 - 20:20:17 CDT)
  • Re: mm_pbsa positive binding energies (Mon Sep 02 2002 - 12:50:30 CDT)
  • Re: ewald bomb (Fri Aug 30 2002 - 14:13:14 CDT)
  • Re: NTX value (Fri Aug 30 2002 - 14:07:44 CDT)
  • Re: Interface and Amber 7.0 (Tue Aug 27 2002 - 06:53:45 CDT)
  • Re: amber7, gaff and minimization (fwd) (Mon Aug 26 2002 - 20:35:26 CDT)
  • Re: QUICK HELP! Parameters for neutral amino acids (fwd) (Mon Aug 26 2002 - 20:32:50 CDT)
  • Re: Gibbs (FEP) (fwd) (Mon Aug 26 2002 - 20:30:28 CDT)
  • Re: ambpdb problem (fwd) (Mon Aug 26 2002 - 20:27:08 CDT)
  • Re: ewald bomb in md equilibration (fwd) (Mon Aug 26 2002 - 20:23:52 CDT)
  • Re: Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) (Mon Aug 26 2002 - 20:21:06 CDT)
  • Re: turning off ewald (fwd) (Mon Aug 26 2002 - 20:12:29 CDT)
  • Re: leaprc file (fwd) (Mon Aug 26 2002 - 20:09:22 CDT)
  • Re: adding_hydrogens_to_pdb (fwd) (Mon Aug 26 2002 - 19:34:36 CDT)
  • Re: Im lost (Tue Aug 20 2002 - 10:15:29 CDT)
  • Re: Antibody residue numbering (Mon Aug 19 2002 - 16:15:45 CDT)
  • Re: antechamber's prepc option (Fri Aug 16 2002 - 15:10:55 CDT)
  • Re: PMF with sander module (Fri Aug 16 2002 - 14:23:16 CDT)
  • Re: Extra points (Thu Aug 15 2002 - 18:01:21 CDT)
  • Re: trajectory file limit??? (Thu Aug 15 2002 - 12:26:34 CDT)
  • Re: E going up and down??? (Wed Aug 14 2002 - 17:16:05 CDT)
  • Re: Q: waters in NPT & periodic boundary condition (Wed Aug 14 2002 - 11:45:46 CDT)
  • Re: GB in Amber7 (Wed Aug 14 2002 - 10:33:57 CDT)
  • Re: minimization in amber7 for nonperiodic systems (Wed Aug 14 2002 - 10:28:21 CDT)
  • Re: Format of prep input files (Tue Aug 13 2002 - 13:13:47 CDT)
  • Re: Memory and swap in sander (Mon Aug 12 2002 - 10:55:55 CDT)
  • Re: Constant pressure MD problems (sander) (Mon Aug 12 2002 - 10:47:10 CDT)
  • Re: literature for NVE (Mon Aug 12 2002 - 10:38:45 CDT)
  • Re: LINMIN failure during minimization (Fri Aug 09 2002 - 11:09:09 CDT)
  • Re: namelist error with sander (Fri Aug 09 2002 - 10:50:27 CDT)
  • Re: protonation pH dependent (Thu Aug 08 2002 - 17:05:25 CDT)
  • using belly with GB (Wed Aug 07 2002 - 20:36:18 CDT)
  • Re: charges (Wed Aug 07 2002 - 20:35:07 CDT)
  • Re: check-up question (Tue Aug 06 2002 - 16:14:56 CDT)
  • Re: Leap error: PDB file with more than 10000 residues (Tue Aug 06 2002 - 16:13:30 CDT)
  • Re: am1-bcc charges (Tue Aug 06 2002 - 14:32:12 CDT)
  • Re: creating a solvent box (Tue Aug 06 2002 - 13:53:50 CDT)
  • Re: "number of processors must be a power of two" (Tue Aug 06 2002 - 11:40:33 CDT)
  • Re: Generalized Born and OPLS potential (Mon Aug 05 2002 - 10:51:30 CDT)
  • Re: reorder water with nmropt (Fri Aug 02 2002 - 11:01:22 CDT)
  • Re: file (Thu Aug 01 2002 - 15:46:52 CDT)
  • Re: Potential Energy and RMS-Deviation Issues (Thu Aug 01 2002 - 11:25:57 CDT)
  • Re: building ss DNA/RNA (Tue Jul 30 2002 - 17:29:19 CDT)
  • Re: SANDER documentation for nmropt (Mon Jul 29 2002 - 19:27:52 CDT)
  • Re: ptraj (Fri Jul 26 2002 - 14:08:54 CDT)
  • Re: mol2 with antechamber (Fri Jul 26 2002 - 10:54:08 CDT)
  • Re: Gibbs tutorial problem (Thu Jul 25 2002 - 14:03:17 CDT)
  • Re: Umbrella sampling in AMBER (Wed Jul 24 2002 - 16:44:35 CDT)
  • Re: increase lastist (Wed Jul 24 2002 - 16:41:48 CDT)
  • Re: SS bond (Wed Jul 24 2002 - 15:00:44 CDT)
  • Re: am1-bcc charges, antechamber (Wed Jul 24 2002 - 14:58:25 CDT)
  • Re: Trajectory files (Wed Jul 24 2002 - 10:15:55 CDT)
  • Re: gaff and parm99 (Wed Jul 24 2002 - 10:13:48 CDT)
  • Re: several questions (Tue Jul 23 2002 - 19:08:10 CDT)
  • Re: Segmentation fault (Tue Jul 23 2002 - 17:44:02 CDT)
  • Re: Questions about xleap and mm_pbsa(cont.) (Tue Jul 23 2002 - 12:18:44 CDT)
  • Re: Questions about xleap and mm_pbsa] (Fri Jul 19 2002 - 13:59:24 CDT)
  • Re: electrostatics truncation in AMBER (Fri Jul 19 2002 - 10:26:20 CDT)
  • Re: GENERALIZED BORN model on a protein with Fe (Thu Jul 18 2002 - 12:41:53 CDT)
  • Re: Minimization in GB-SA-E-Spikes, LINMIN (Wed Jul 17 2002 - 19:43:57 CDT)
  • Re: prmtop file question. (Wed Jul 17 2002 - 19:08:28 CDT)
  • Re: building general solvent boxes with leap (Wed Jul 17 2002 - 15:14:40 CDT)
  • Re: amber on sp3 (Wed Jul 17 2002 - 14:14:44 CDT)
  • Re: water molecules diffuse during equilibration (Tue Jul 16 2002 - 20:31:12 CDT)
  • Re: Problem with LEAP (Tue Jul 16 2002 - 10:19:24 CDT)
  • LEaP gives "no sp2 improper torsion term" warnings (Fri Jul 12 2002 - 15:25:35 CDT)
  • are there inconsistencies in anal? (Fri Jul 12 2002 - 13:58:02 CDT)
  • Re: counter-ions in FEP (Fri Jul 12 2002 - 11:00:11 CDT)
  • Re: Question about error message about "lastist" and "virtual box" (Fri Jul 12 2002 - 10:55:51 CDT)
  • Re: Net Charge is Different In The Sander Output!! (Tue Jul 09 2002 - 22:53:47 CDT)
  • Re: eedmeth variable in AMBER7 (Tue Jul 09 2002 - 10:31:59 CDT)
  • Re: md equilibration in chloroform (Mon Jul 08 2002 - 10:42:24 CDT)
  • Re: How to decrease the solvated system in Amber6? (Tue Jul 02 2002 - 06:38:50 CDT)
  • Re: mopac (Thu Jun 27 2002 - 13:34:34 CDT)
  • Re: problems compiling Amber 7 (Thu Jun 27 2002 - 13:27:09 CDT)
  • Re: dummy torsional parameters (Thu Jun 27 2002 - 10:38:49 CDT)
  • Re: xleap problem (Thu Jun 27 2002 - 10:33:16 CDT)
  • Re: partial charges (Mon Jun 24 2002 - 20:52:47 CDT)
  • Re: taupt: time constant for heat bath coupling for the SOLUTE (Fri Jun 21 2002 - 19:28:38 CDT)
  • Re: van der Waals explosion (Fri Jun 21 2002 - 09:55:26 CDT)
  • Re: j3 coupling (Fri Jun 21 2002 - 09:49:40 CDT)
  • Re: turning PME off in AMBER7 (Thu Jun 20 2002 - 08:49:33 CDT)
• David Bevan
  • MacOS X (Tue Jan 29 2002 - 10:15:12 CST)
• David Case
  • Re: CCL:Amber7 and partial charges (Wed Dec 11 2002 - 12:07:10 CST)
  • Re: your mail (Fri Nov 29 2002 - 14:07:19 CST)
  • Re: Problem (Fri Nov 29 2002 - 13:49:20 CST)
  • Re: ntx=7, irest=0, redux (Sat Nov 23 2002 - 00:53:37 CST)
  • Re: Conterions (Sat Nov 16 2002 - 13:45:01 CST)
  • Re: your mail (Sat Nov 16 2002 - 09:43:29 CST)
  • Re: Problem in run (Sat Nov 09 2002 - 01:33:27 CST)
  • Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) (Sat Nov 09 2002 - 01:17:18 CST)
  • Re: Compiler & Hardware requirement of AMBER7 ? (Tue Oct 15 2002 - 00:51:43 CDT)
  • Re: GBSA with IGB=2, setting the PBradii bondi (Sat Aug 31 2002 - 12:58:35 CDT)
  • Re: GB in amber6 (Fri Aug 16 2002 - 00:23:23 CDT)
  • minimization in amber7 for nonperiodic systems (Wed Aug 14 2002 - 00:47:43 CDT)
  • Re: Nanotubes with AMBER (Sun Aug 11 2002 - 23:13:23 CDT)
  • Re: mpich, I/O, Master node, filesystem (Thu Aug 08 2002 - 00:14:25 CDT)
  • Re: MD in alcohol (Mon Aug 05 2002 - 00:31:40 CDT)
  • Re: Import of CHARMM force field and GB potential parameters into Amber7 (Mon Aug 05 2002 - 00:25:28 CDT)
  • problems with parallel sander on linux clusters? (Sun Aug 04 2002 - 13:34:20 CDT)
  • Re: Please give me a hand on understanding AMBER/MPI and locmem. (Sat Aug 03 2002 - 15:02:42 CDT)
  • Re: water box-nonperiodic (Sat Aug 03 2002 - 00:16:18 CDT)
  • Re: structure (Wed Jul 31 2002 - 00:43:50 CDT)
  • Re: a water jumps (Tue Jul 30 2002 - 00:13:16 CDT)
  • Re: trajectory problem? (Thu Jul 25 2002 - 00:22:57 CDT)
  • Re: "crd" file created with VMD (Wed Jul 24 2002 - 02:04:02 CDT)
  • Re: Running TIP5P with PBC (Wed Jul 03 2002 - 14:49:28 CDT)
  • Re: Problem in amber (Thu Jun 27 2002 - 09:38:30 CDT)
  • Re: mm_pbsa in parallel system (Mon Jun 03 2002 - 09:49:08 CDT)
  • Re: Fwd: NPT-MD (Fri May 31 2002 - 09:56:43 CDT)
  • Re: Intel ifc Compiler (Fri May 31 2002 - 09:51:21 CDT)
  • Re: TIP4P (Fri May 31 2002 - 09:44:19 CDT)
  • Re: sander_classic, erratic on IBM (Thu May 30 2002 - 09:13:44 CDT)
  • Re: Intel ifc Compiler (Thu May 30 2002 - 09:00:55 CDT)
  • Re: helix analysis (fwd) (Thu May 23 2002 - 16:41:00 CDT)
  • Re: charges (Thu May 23 2002 - 15:54:38 CDT)
  • Re: ambpdb in AMBER7 (Wed May 22 2002 - 16:09:32 CDT)
  • Protonate doesn-t recognize by pdb input file (Wed May 22 2002 - 11:20:20 CDT)
  • Re: again about sander_classic Amber 6.0 (Wed May 22 2002 - 10:15:06 CDT)
  • Re: Junmei et al. 1999 (Wed May 22 2002 - 10:05:23 CDT)
  • Re: antechamber (Wed May 22 2002 - 10:03:50 CDT)
  • Re: Anal in AMBER7 (Sun May 19 2002 - 20:44:38 CDT)
  • Re: Energy problem during dynamics with amber 7 (Wed May 15 2002 - 12:29:55 CDT)
  • Re: NMR refinement (Wed May 15 2002 - 12:09:27 CDT)
  • Re: Topology file format in AMBER 7 (Tue May 14 2002 - 16:33:15 CDT)
  • Re: "Unit 5 Error" with a Linux/MPICH Amber7 (Mon May 06 2002 - 11:18:24 CDT)
  • Re: Amber7 nmode (Wed May 01 2002 - 12:55:07 CDT)
  • Re: about ew_legal.h (Wed May 01 2002 - 11:10:36 CDT)
  • Re: heterochirical peptides ? (Tue Apr 30 2002 - 13:21:38 CDT)
  • Re: NTT=5? (Tue Apr 30 2002 - 13:16:04 CDT)
  • Re: Problems with AMBER7 and Multiple Processors on SGI servers (Tue Apr 30 2002 - 11:02:30 CDT)
  • Re: NTT=5? (Tue Apr 30 2002 - 00:32:20 CDT)
  • Re: TIP4P parameters (Tue Apr 30 2002 - 00:17:49 CDT)
  • Re: parmjoin (Mon Apr 29 2002 - 13:26:26 CDT)
  • Re: amber7 and tip5p (Wed Apr 24 2002 - 16:04:05 CDT)
  • Re: generating left-handed A-DNA (Wed Apr 24 2002 - 11:09:07 CDT)
  • Re: sander & prmtop file generated from antechamber input ? (Wed Apr 24 2002 - 10:59:14 CDT)
  • Re: RESP tutorial (Tue Apr 23 2002 - 19:41:49 CDT)
  • Re: your mail (Sat Apr 20 2002 - 11:06:32 CDT)
  • Re: amber7 compilation on a beowulf cluster (Fri Apr 19 2002 - 20:56:50 CDT)
  • Re: Help! Sander run error: Bus error (Tue Apr 16 2002 - 00:32:16 CDT)
  • Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error (Fri Apr 12 2002 - 19:37:01 CDT)
  • Re: DNA structure get distorted (Fri Apr 12 2002 - 11:27:10 CDT)
  • Re: PDB file with CONECT record (fwd) (Tue Apr 09 2002 - 22:30:38 CDT)
  • Initial Amber 7 benchmark timings (Wed Apr 03 2002 - 20:33:14 CST)
  • Re: a little bit confused with leap-frog algorithm... (Thu Mar 28 2002 - 19:52:38 CST)
  • Re: Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) (Thu Mar 28 2002 - 12:40:16 CST)
  • Re: What is the atoms limit for Amber 7? (Wed Mar 27 2002 - 17:45:44 CST)
  • Re: GB model and belly (Tue Mar 26 2002 - 17:07:33 CST)
  • Re: MM-PBSA philosophy (Wed Mar 20 2002 - 10:10:05 CST)
  • Re: scaleCharges (Mon Mar 11 2002 - 11:37:51 CST)
  • Re: vlimit exceed (Sun Feb 24 2002 - 00:03:24 CST)
  • Re: The link is out (Wed Feb 20 2002 - 11:20:00 CST)
  • Re: AMBER logo citation (Wed Feb 20 2002 - 11:11:41 CST)
  • Re: problem in running MM-PBSA script (Thu Feb 14 2002 - 10:42:52 CST)
  • Re: question regarding ntwv. (Fri Feb 01 2002 - 00:43:51 CST)
  • Re: Latest parm + getting parm98 as default in LEaP (Tue Jan 22 2002 - 10:14:55 CST)
  • Re: nmode memory requirements (Fri Jan 18 2002 - 11:50:29 CST)
  • Re: Amino acid unit "NHE" problem ? (Thu Jan 17 2002 - 10:37:55 CST)
  • Re: how to neutralise the system? (Mon Jan 14 2002 - 13:35:00 CST)
  • Re: inquiry regarding AMBER (Thu Jan 10 2002 - 16:51:54 CST)
• David Keller
  • several questions (Tue Jul 23 2002 - 17:24:04 CDT)
• David Pearlman
  • Re: What's this "interface" the tutorial talks about? (Wed Aug 28 2002 - 14:49:57 CDT)
  • Re: Interface and Amber 7.0 (Tue Aug 27 2002 - 11:35:19 CDT)
  • Re: PMF calculations (Thu Apr 25 2002 - 13:36:41 CDT)
  • Re: PMF calculations (Thu Apr 25 2002 - 13:30:24 CDT)
  • Re: INTPRT and PMF (Tue Apr 23 2002 - 15:05:12 CDT)
  • Re: recursively calling sander? (Mon Feb 25 2002 - 21:10:22 CST)
• David Smith
  • Re: esp.sh problem (Wed Nov 27 2002 - 12:13:09 CST)
  • Re: How to define a sphere to minimize? (Mon Oct 21 2002 - 06:00:03 CDT)
  • Different numbers on different architectures. (Fri Oct 04 2002 - 08:33:24 CDT)
  • Re: RESP gaussian job crashing (Fri Oct 04 2002 - 07:08:53 CDT)
  • Re: Constant pressure equilibration in a system with a solvent cap (Fri Sep 27 2002 - 11:11:19 CDT)
  • Re: PME box ? (Wed Jun 05 2002 - 09:15:44 CDT)
  • Re: PMF calculations (Thu Apr 25 2002 - 10:13:23 CDT)
  • Re: Number of WATBOX (Thu Apr 25 2002 - 08:25:40 CDT)
• David.Rilett_at_astrazeneca.com
  • mopac (Thu Jun 27 2002 - 12:50:41 CDT)
• deepak rangaswamy
  • (no subject) (Wed Jul 24 2002 - 22:57:14 CDT)
  • (no subject) (Tue Jul 23 2002 - 02:01:41 CDT)
  • Re: your mail (Tue Apr 30 2002 - 07:06:06 CDT)
  • (no subject) (Sat Apr 20 2002 - 00:22:54 CDT)
  • (no subject) (Tue Apr 02 2002 - 22:52:55 CST)
  • (no subject) (Fri Mar 01 2002 - 05:00:51 CST)
  • (no subject) (Tue Feb 26 2002 - 05:28:18 CST)
• DeLano, Warren
  • Periodicity Question (Fri Sep 20 2002 - 19:29:49 CDT)
  • Dual Processor AMD vs. Single Processor (Wed Sep 11 2002 - 19:34:47 CDT)
  • RE: PyMOL + AMBER Trajectories (Tue Sep 03 2002 - 12:51:57 CDT)
  • PyMOL + AMBER Trajectories (Thu Aug 29 2002 - 13:27:01 CDT)
• Demchuk, Eugene
  • RE: Dual AMD motherboards (Mon Mar 18 2002 - 18:52:55 CST)
• dianah_at_unm.edu
  • Constant pressure equilibration in a system with a solvent cap (Thu Sep 26 2002 - 20:04:38 CDT)
  • Format of prep input files (Tue Aug 13 2002 - 12:42:11 CDT)
  • Using the new2oldparm command (Thu Aug 01 2002 - 15:18:32 CDT)
• dkeller_at_unm.edu
  • Image charges with the solvate cap command (Mon Sep 30 2002 - 10:52:11 CDT)
• dkon_at_email.arizona.edu
  • More GB/Belly (Tue Mar 26 2002 - 16:00:23 CST)
  • GB model and belly (Tue Mar 26 2002 - 15:46:40 CST)
  • rms and watershell (in ptraj) (Wed Feb 20 2002 - 18:54:58 CST)
• Dmitry Pavlov
  • H-bond (Fri May 31 2002 - 03:01:42 CDT)
• Donald Thomas
  • xLeap problem (Wed May 29 2002 - 23:42:04 CDT)
• Douglas Kojetin
  • RE: Vanderbilt Biomolecular Modeling Symposium (Fri Aug 30 2002 - 14:22:19 CDT)
• Dov Barak
  • Compilation ov Amber 7 (Fri Jun 21 2002 - 11:40:58 CDT)
• Dow Hurst
  • Re: Origin300, Linux Cluster (Mon Jul 08 2002 - 09:40:34 CDT)
• Dr Jan Rosenzweig
  • .OFF file format (Mon Feb 18 2002 - 12:14:27 CST)
• DTphonehome33_at_aol.com
  • AMBER Machine Questions (Tue Jul 30 2002 - 12:00:33 CDT)
• dynamic group
  • beginners question (Sun Dec 22 2002 - 23:17:52 CST)
• Elizabeth K. White
  • acetyl groups on protein fragments (Thu Jul 25 2002 - 13:55:04 CDT)
  • group input in ANAL (Fri Jan 25 2002 - 16:11:13 CST)
• Elsa de Sousa Henriques
  • Re: rdparm (Tue Oct 08 2002 - 21:40:58 CDT)
  • Re: parameters for sugars (Mon Sep 30 2002 - 11:42:24 CDT)
  • Re: Amber trajectory movies in Powerpoint (Tue Aug 06 2002 - 20:58:15 CDT)
  • Re: building general solvent boxes with leap (Thu Jul 18 2002 - 22:41:25 CDT)
  • Re: average position of water (Tue Jan 08 2002 - 16:15:44 CST)
• Emma.Sigfridsson_at_astrazeneca.com
  • MM-PBSA and Insight's version of Delphi (Mon Oct 14 2002 - 02:47:21 CDT)
  • igb problem in sander (Wed Jun 12 2002 - 04:11:20 CDT)
  • Amber protein-ion problem (Tue Jun 11 2002 - 06:41:29 CDT)
• Eric ARNOULT
  • CH2Cl2 box (Mon Oct 14 2002 - 12:51:21 CDT)
  • ImagingAtom (Wed Feb 06 2002 - 10:07:04 CST)
• eric hu
  • targeted MD sample (Thu Dec 26 2002 - 14:25:36 CST)
  • bad protein structure (Tue Dec 10 2002 - 19:30:52 CST)
  • md failure: deep energetics problem (Thu Dec 05 2002 - 12:42:42 CST)
  • Re: restrain a residue as center of mass (Wed Nov 27 2002 - 12:42:36 CST)
  • restrain a residue as center of mass (Tue Nov 26 2002 - 17:36:19 CST)
  • Re: atom type not recognized by GB (Sun Nov 24 2002 - 20:30:17 CST)
  • atom type not recognized by GB (Sun Nov 24 2002 - 19:05:59 CST)
  • Re: large energy fluctration (Fri Sep 20 2002 - 13:00:17 CDT)
  • large energy fluctration (Thu Sep 12 2002 - 13:05:10 CDT)
  • bondbydistance (Thu Sep 05 2002 - 18:20:43 CDT)
  • Re: water box size (Thu Jul 25 2002 - 14:21:24 CDT)
  • water box size (Fri Jul 19 2002 - 17:09:25 CDT)
  • Re: sander parallel (Thu Jun 13 2002 - 17:05:13 CDT)
  • sander parallel (Wed Jun 12 2002 - 16:11:24 CDT)
  • Re: cold belly run error (Tue Jun 11 2002 - 14:42:19 CDT)
  • Re: cold belly run error (Tue Jun 11 2002 - 12:41:47 CDT)
  • cold belly run error (Sun Jun 09 2002 - 17:55:47 CDT)
  • Re: cap water (Fri Jun 07 2002 - 13:39:22 CDT)
  • cap water (Wed Jun 05 2002 - 19:14:10 CDT)
• Esther Kellenberger
  • BR parameters in AMBER (Wed Jul 03 2002 - 09:24:26 CDT)
• Etienne ENGLER
  • MPI (parallel) version of GIBBS (Mon Jan 07 2002 - 06:13:45 CST)
• Eva Darian
  • IFBOX=0 error in amber7 (Tue Apr 30 2002 - 23:43:31 CDT)
• Fabrice Yerly
  • Amber PGF77 comilation error + MPICH problem (Wed Jun 05 2002 - 03:31:26 CDT)
  • MPich error (Wed May 29 2002 - 07:46:29 CDT)
  • Linux Parallel compilation Linux Mpich PGI (Mon May 27 2002 - 07:31:09 CDT)
  • Re Europium force field parms (Mon Mar 11 2002 - 01:32:59 CST)
• Fabrizio Giordanetto
  • torsional fit (Fri Jan 25 2002 - 04:34:55 CST)
• Felipe Pineda
  • Re: MM-PBSA philosophy (Wed Mar 20 2002 - 08:25:05 CST)
  • Re: AMBER 99 (Fri Mar 01 2002 - 02:25:27 CST)
• Fernando Martin
  • RE: 64-bit Compilation SUN's forte compiler (Mon Oct 28 2002 - 18:24:21 CST)
  • 64-bit Compilation SUN's forte compiler (Mon Oct 28 2002 - 17:15:52 CST)
• Filip Lankas
  • bug fixes (Thu Dec 05 2002 - 08:48:00 CST)
• Filip Ryjacek
  • DNA shifts during MD; C.O.M. removing and ptraj doesn't help... (Thu Apr 18 2002 - 10:17:12 CDT)
  • (no subject) (Wed Apr 17 2002 - 11:01:48 CDT)
• Florence CASSET
  • Energy problem during dynamics with amber 7 (Wed May 15 2002 - 04:48:23 CDT)
• Florian Barth
  • replacing fft routines (Tue Oct 22 2002 - 15:08:14 CDT)
  • Re: compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 17:13:31 CDT)
• Francesca Mocci
  • Re: help on VMD movie (Wed Nov 13 2002 - 08:28:06 CST)
  • Re: carnal output trajectory (Fri Nov 01 2002 - 10:53:31 CST)
• franck chevalier
  • adiabatic map (Wed Jan 09 2002 - 06:41:57 CST)
• Francois Dupradeau
  • Follow distances during MD (Thu Apr 11 2002 - 05:19:02 CDT)
• Fredrick Robin Devadoss
  • Error in Equilibration (Tue Nov 26 2002 - 04:14:12 CST)
  • Equilibration output Amber7 (Fri Nov 22 2002 - 03:42:32 CST)
  • Re: intdiel & extdiel (Wed Nov 20 2002 - 22:28:35 CST)
  • intdiel & extdiel (Wed Nov 20 2002 - 05:23:59 CST)
• FyD
  • Re: esp.sh problem (Thu Nov 28 2002 - 02:03:33 CST)
  • esp.sh problem (Wed Nov 27 2002 - 11:17:40 CST)
  • MEP g98_option (Sat Nov 09 2002 - 00:35:22 CST)
  • xleap problem (Thu Jun 27 2002 - 03:20:53 CDT)
  • plep question (Wed Jun 26 2002 - 02:28:23 CDT)
  • Thanks (Fri Apr 12 2002 - 02:04:53 CDT)
  • dG of wild type/mutant (Thu Mar 07 2002 - 05:26:31 CST)
  • AMBER logo citation (Wed Feb 20 2002 - 01:53:18 CST)
• Ge Zhou
  • TIP4P parameters (Mon Apr 29 2002 - 21:03:54 CDT)
• Gemma Kinsella
  • Re: Biphasic box (Wed Dec 04 2002 - 02:15:53 CST)
• Genefax
  • China International Biology Projects Fair (Fri Jul 12 2002 - 00:40:19 CDT)
• Giovanni Fossati
  • write problem on IBM-AIX (Mon Sep 30 2002 - 10:51:54 CDT)
  • SETVEL, incorrect number of arguments? (Mon Sep 16 2002 - 17:43:30 CDT)
  • problems on IBM AIX (Thu Sep 12 2002 - 20:43:52 CDT)
  • Re: sander_classic, erratic on IBM (Thu May 30 2002 - 12:05:22 CDT)
  • sander_classic, erratic on IBM (Thu May 30 2002 - 01:17:07 CDT)
• giudice
  • Truncated Octahedron Box (Thu Oct 17 2002 - 08:06:28 CDT)
  • Re: NTX value (Mon Sep 02 2002 - 02:05:45 CDT)
  • NTX value (Fri Aug 30 2002 - 05:31:19 CDT)
• Giulio Rastelli
  • P.3 in antechamber (Thu Nov 21 2002 - 05:02:16 CST)
  • carnal7 produces memory fault and a core (Sat Nov 09 2002 - 10:21:10 CST)
  • molsurf reference (Fri Nov 01 2002 - 06:17:35 CST)
  • Targeted MD (Mon Oct 28 2002 - 15:44:05 CST)
  • total energies during MM-PBSA (Sun Oct 27 2002 - 12:20:19 CST)
  • targeted MD (Fri Oct 18 2002 - 09:28:48 CDT)
  • MM-PBSA tutorial (Thu Oct 10 2002 - 09:22:59 CDT)
  • reaction field energy of a ligand in MM-PBSA (Wed Oct 09 2002 - 13:04:10 CDT)
  • xleap on a SGI Fuel (Mon Oct 07 2002 - 09:50:39 CDT)
  • memory allocation in mm_pbsa (Wed Sep 11 2002 - 05:41:04 CDT)
  • dihedral parameter for conjugated double bonds in GAFF (Fri Aug 16 2002 - 11:37:03 CDT)
  • Re: minimization in amber7 for nonperiodic systems (Wed Aug 14 2002 - 10:03:11 CDT)
  • dihedral parameter for conjugated double bonds in GAFF (Wed Aug 14 2002 - 03:37:50 CDT)
  • LINMIN failure during minimization (Fri Aug 09 2002 - 03:46:18 CDT)
  • (no subject) (Wed Aug 07 2002 - 04:07:21 CDT)
  • mol2 with antechamber (Fri Jul 26 2002 - 05:57:22 CDT)
  • Re: am1-bcc charges, antechamber (Thu Jul 25 2002 - 05:53:46 CDT)
  • dummy torsional parameters (Thu Jun 27 2002 - 05:31:50 CDT)
  • antechamber (Wed May 22 2002 - 05:56:25 CDT)
  • GB simulation (Mon Mar 04 2002 - 10:32:28 CST)
  • MD with simulated annealing (Fri Feb 22 2002 - 12:39:56 CST)
• giulio_at_unimo.it
  • entropy calcs in mm_pbsa (Tue Nov 05 2002 - 14:21:00 CST)
• Greaves, Greg (Contractor-SIMTECH)
  • RE: Dual AMD motherboards (Fri Jul 12 2002 - 10:33:54 CDT)
• Guanglei Cui
  • Re: amber trajectory (Wed Dec 18 2002 - 09:02:05 CST)
  • MXVAR (Thu Dec 12 2002 - 10:34:17 CST)
  • Re: bad protein structure (Tue Dec 10 2002 - 23:07:20 CST)
  • corrupted trajectory (Tue Dec 03 2002 - 17:07:46 CST)
  • Re: restarting simulation (Fri Nov 22 2002 - 14:50:05 CST)
  • Re: Equilibration output Amber7 (Fri Nov 22 2002 - 08:42:02 CST)
  • Re: error in rMD (Fri Jun 28 2002 - 08:22:35 CDT)
  • Re: pairlist limit (Fri Jan 04 2002 - 22:56:39 CST)
• Guillermo Mulliert Carlín
  • How to define a sphere to minimize? (Mon Oct 21 2002 - 01:46:57 CDT)
• Hagedorn, Dan N
  • FW: Compiling on HP-UX 11.00 (Fri Aug 09 2002 - 13:45:00 CDT)
• hagop demirdjian
  • ntwv saves v(t) or v(t+dt/2) ? (Thu Dec 19 2002 - 10:04:55 CST)
  • using SHAKE for solvent only (Mon Nov 25 2002 - 09:42:57 CST)
  • error in reading .crd file with GIBBS (Thu Nov 14 2002 - 09:40:32 CST)
  • do I need to mutate H1 atoms to HC in a "not really" perturbed part of a molecule ? (Tue Oct 08 2002 - 09:51:50 CDT)
  • expression of V(lambda) in GIBBS (Tue Sep 24 2002 - 07:44:02 CDT)
  • problem compiling roar (mop7mm) on alpha (Tue Jul 23 2002 - 10:35:11 CDT)
• Haizhen Zhong
  • can carnal do the job as anal to break down the energy? (Wed Aug 28 2002 - 13:02:48 CDT)
  • Re: nmode segmentation fault (Fri Aug 09 2002 - 08:46:19 CDT)
• hathaimard pongkasem
  • Amber 6.0 purchasing!! (Wed Jan 16 2002 - 02:15:03 CST)
  • Amber 6.0 purchasing!! (Wed Jan 16 2002 - 02:14:48 CST)
• Heather A Carlson
  • Re: several questions (Tue Jul 23 2002 - 22:17:35 CDT)
• Holger Gohlke
  • Re: ambpdb (Thu Dec 12 2002 - 18:44:44 CST)
  • Re: MM-PBSA: .crg file for Delphi (Wed Dec 11 2002 - 12:31:07 CST)
  • Re: Amber 7 bugfix 27 !! urgent (Wed Dec 04 2002 - 15:18:48 CST)
  • Re: intdiel & extdiel (Thu Nov 21 2002 - 09:55:15 CST)
  • Re: nonpeoridic boundary + mm/gbsa (Mon Nov 11 2002 - 10:59:27 CST)
  • Re: average and runningaverage in ptraj (Wed Nov 06 2002 - 10:56:23 CST)
  • Re: entropy calcs in mm_pbsa (Tue Nov 05 2002 - 15:27:39 CST)
  • Re: xleap and modified sugar residues (Thu Oct 31 2002 - 13:54:23 CST)
  • Re: IDECOMP (Wed Oct 30 2002 - 14:11:13 CST)
  • Re: Carnal table output (Fri Oct 18 2002 - 10:20:57 CDT)
  • Re: error message (Wed Oct 16 2002 - 12:38:34 CDT)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 10:51:01 CDT)
  • Re: MM-PBSA tutorial (Thu Oct 10 2002 - 13:57:41 CDT)
  • [Fwd: Re: trouble with snapshots GC option of MM_PBSA] (Thu Oct 10 2002 - 11:15:39 CDT)
  • Re: MM-PBSA basics (Sun Sep 29 2002 - 21:44:52 CDT)
  • Re: mm_pbsa output error (Mon Sep 23 2002 - 23:21:30 CDT)
  • Re: mm_pbsa (Sun Sep 22 2002 - 16:01:22 CDT)
  • Re: betaP,SURFOFF inconsistency (Sun Sep 22 2002 - 15:20:03 CDT)
  • Re: Do I have to rerun 1ns MD?? (Sun Sep 22 2002 - 14:30:40 CDT)
  • Re: memory allocation in mm_pbsa (Wed Sep 11 2002 - 10:55:07 CDT)
  • Re: why are the results so large difference calculating by mm_pbsa and mm_gbsa? (Tue Sep 10 2002 - 11:26:07 CDT)
  • Re: nmode compile question? (Tue Sep 10 2002 - 11:17:24 CDT)
  • Re: who to address this to?... (Mon Sep 09 2002 - 11:25:00 CDT)
  • Re: DNA Tutorial Script (Wed Sep 04 2002 - 22:29:23 CDT)
  • Re: old prmtop (Wed Sep 04 2002 - 11:21:32 CDT)
  • Re: carnal averaging (Mon Sep 02 2002 - 15:43:52 CDT)
  • Re: Tutorial Error Message (Thu Aug 29 2002 - 10:22:25 CDT)
  • [Re: can carnal do the job as anal to break down the energy?] (Wed Aug 28 2002 - 13:36:51 CDT)
  • Re: why is mm_pbsa broken ? (fwd) (Tue Aug 27 2002 - 12:12:17 CDT)
  • Re: RMSD by residue (fwd) (Mon Aug 26 2002 - 20:08:35 CDT)
  • Re: Help needed about mm_pbsa (Thu Aug 15 2002 - 12:04:03 CDT)
  • Re: Can we get trajectories coordinates after FIT in Carnal? (Wed Aug 14 2002 - 16:29:41 CDT)
  • Re: nmode segmentation fault (Thu Aug 08 2002 - 13:16:11 CDT)
  • Re: Using the new2oldparm command (Thu Aug 01 2002 - 15:52:23 CDT)
• Holger Sondermann
  • parameter file for MgGTP (Tue Jul 02 2002 - 20:34:24 CDT)
• hung_at_atc.atccu.chula.ac.th
  • procheck (Tue Nov 05 2002 - 00:53:56 CST)
  • RUNMIN (Mon Nov 04 2002 - 19:04:23 CST)
  • LINMIN FAILURE (Tue Oct 08 2002 - 19:41:00 CDT)
• Hungie Hungie
  • pentane minimization...again (Thu Apr 18 2002 - 11:30:15 CDT)
  • pentane minimization (Thu Apr 18 2002 - 04:16:46 CDT)
  • pentane minimization (Thu Apr 18 2002 - 04:15:33 CDT)
  • again...Minimization of pentane holding a plane of carbon atoms (Wed Apr 17 2002 - 13:03:23 CDT)
  • Minimization of pentane holding a plane of carbon atoms (Wed Apr 17 2002 - 12:32:28 CDT)
  • redius of B-DNA duplex (Mon Feb 25 2002 - 10:49:26 CST)
  • average position of water (Tue Jan 08 2002 - 06:28:00 CST)
• Ian bates
  • Re: Problems with AMBER7 and Multiple Processors on SGI servers (Fri Apr 26 2002 - 10:17:52 CDT)
  • (no subject) (Wed Feb 27 2002 - 15:23:17 CST)
• Ian R Bates
  • does PME function without charge neutralization? (Tue Apr 02 2002 - 12:30:41 CST)
  • secondary structure (Tue Mar 26 2002 - 13:49:48 CST)
  • mdcrd to arc (Sat Mar 23 2002 - 10:46:21 CST)
• Ioana Cozmuta
  • cap option (Sun Dec 22 2002 - 19:21:01 CST)
  • selection of residues (Fri Dec 20 2002 - 18:51:52 CST)
  • Re: water/nonTIP3P (Wed Dec 18 2002 - 20:17:24 CST)
  • Re: message during minimization (Wed Dec 18 2002 - 20:02:26 CST)
  • water/nonTIP3P (Wed Dec 18 2002 - 19:33:23 CST)
  • Re: SUMMARY: solvating a protein with large cavity (Wed Dec 18 2002 - 19:21:23 CST)
  • Re: water box, (Wed Dec 18 2002 - 17:37:41 CST)
  • Re: message during minimization (Wed Dec 18 2002 - 17:09:05 CST)
  • message during minimization (Tue Dec 17 2002 - 23:31:52 CST)
  • amber trajectory (Tue Dec 17 2002 - 23:16:14 CST)
  • water box, (Tue Dec 17 2002 - 17:18:31 CST)
  • Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 15:07:24 CST)
  • plotting electrostatic potential surface (Fri Dec 13 2002 - 17:18:17 CST)
  • carnal (Fri Dec 06 2002 - 17:47:56 CST)
  • increasing the number of processors (fwd) (Tue Dec 03 2002 - 18:19:24 CST)
  • increasing the number of processors (Tue Dec 03 2002 - 18:17:58 CST)
  • external electric field/another try (Wed Nov 27 2002 - 16:13:08 CST)
  • a second question (Mon Nov 25 2002 - 18:20:52 CST)
  • external electric field (Mon Nov 25 2002 - 17:18:38 CST)
  • Re: pdb file (Fri Nov 22 2002 - 19:44:22 CST)
  • pdb file (Fri Nov 22 2002 - 18:41:01 CST)
  • Re: question (Fri Nov 15 2002 - 21:22:13 CST)
  • CMM method (Wed Nov 13 2002 - 16:57:10 CST)
  • Re: the removal of global motion (Tue Nov 12 2002 - 17:52:41 CST)
  • surface (Thu Nov 07 2002 - 15:03:56 CST)
  • nbflag (Wed Nov 06 2002 - 21:45:02 CST)
  • nbflag (Wed Nov 06 2002 - 21:19:26 CST)
  • Re: RUNMIN (Mon Nov 04 2002 - 19:37:08 CST)
  • restart (Mon Nov 04 2002 - 14:57:16 CST)
  • carnal (Thu Oct 31 2002 - 12:30:35 CST)
  • Re: 64-bit Compilation SUN's forte compiler (Mon Oct 28 2002 - 17:33:49 CST)
  • Re: HIS residues (Thu Oct 24 2002 - 16:51:40 CDT)
  • min output (Wed Oct 23 2002 - 18:26:44 CDT)
  • Re: allocation memory error (Tue Oct 22 2002 - 16:52:56 CDT)
  • allocation memory error (Fri Oct 18 2002 - 14:50:22 CDT)
  • Re: restraining atoms (Thu Oct 17 2002 - 12:54:37 CDT)
  • syntax (Wed Oct 16 2002 - 13:14:54 CDT)
  • restraining atoms (Wed Oct 16 2002 - 12:56:10 CDT)
  • Re: How to specify the counterion positions using xleap? (Wed Oct 16 2002 - 12:45:06 CDT)
  • problem in sander (Thu Oct 10 2002 - 21:11:06 CDT)
  • Re: Some error message on Leap (Thu Oct 10 2002 - 17:22:51 CDT)
  • question about antibodies (Thu Oct 10 2002 - 15:05:25 CDT)
  • rdparm (Tue Oct 08 2002 - 12:33:41 CDT)
  • crdgrow (Tue Oct 08 2002 - 12:19:23 CDT)
  • (no subject) (Fri Oct 04 2002 - 19:12:44 CDT)
  • Re: compiling SGI/mpi (Thu Oct 03 2002 - 22:09:02 CDT)
  • compiling SGI/mpi (Thu Oct 03 2002 - 20:16:38 CDT)
  • tutorial on plastocyanin (Wed Oct 02 2002 - 01:04:37 CDT)
  • antechamber web page (Tue Oct 01 2002 - 17:33:36 CDT)
  • Re: Is H-bonding really there? (Tue Oct 01 2002 - 16:44:55 CDT)
  • Re: Is H-bonding really there? (Fri Sep 27 2002 - 17:04:37 CDT)
  • cut-off question (Wed Sep 04 2002 - 14:43:38 CDT)
  • question (Tue Sep 03 2002 - 12:46:04 CDT)
  • additional info (Sun Sep 01 2002 - 13:44:32 CDT)
  • mpirun (Sun Sep 01 2002 - 13:32:08 CDT)
• Ishita sharma
  • (no subject) (Mon Jun 03 2002 - 06:07:38 CDT)
• Itziar Maestre Asenjo
  • building bcyd with tleap (Wed Mar 20 2002 - 04:51:47 CST)
  • leap calculation (Wed Mar 06 2002 - 11:43:44 CST)
• Ivan Beà
  • unsuscribe (Wed Jan 16 2002 - 09:25:38 CST)
• Jake Isaacs
  • time-averaged restraint developer (Wed Nov 06 2002 - 16:20:11 CST)
  • time averaged restraint parameters (Thu Oct 17 2002 - 15:09:59 CDT)
  • Re: How to make mpeg files from amber trajectories (fwd) (Tue Aug 27 2002 - 08:48:24 CDT)
  • solvated time-averaged restraint refinement of DNA (Wed Jun 19 2002 - 11:52:35 CDT)
  • Re: still having ptraj problems (Wed May 22 2002 - 10:50:11 CDT)
  • still having ptraj problems (Wed May 22 2002 - 10:19:06 CDT)
  • ptraj problem (Tue May 21 2002 - 16:20:02 CDT)
  • NMR refinement (Tue May 14 2002 - 14:16:37 CDT)
  • Re: NTT=5? (Wed May 01 2002 - 14:47:09 CDT)
  • statistical analysis of MD trajectories (Thu Mar 07 2002 - 11:24:03 CST)
  • residual dipolar coupling restraints (Thu Feb 14 2002 - 13:37:42 CST)
  • timescale of deoxyribose ring repuckering (Tue Jan 22 2002 - 10:43:40 CST)
• James Caldwell
  • Re: Sander rfree error (Mon Dec 30 2002 - 18:36:45 CST)
  • Re: Nmode (Thu Dec 19 2002 - 15:17:31 CST)
• James W. Caldwell
  • Re: freeware for RNA modeling on Linux (fwd) (Tue Dec 17 2002 - 13:09:37 CST)
  • Re: Cap-atom-pointer in GIBBS (Thu Dec 05 2002 - 13:23:45 CST)
  • Re: Biphasic box (fwd) (Tue Dec 03 2002 - 17:15:50 CST)
  • Re: LEAP - Introducing dummy atoms (Mon Dec 02 2002 - 13:11:27 CST)
  • Re: err in specifying disulphide bridge using xleap! (Mon Dec 02 2002 - 13:07:07 CST)
  • Re: external electric field/another try (Wed Nov 27 2002 - 17:31:24 CST)
  • Amber7/CYGWIN compiling (Tue Nov 12 2002 - 15:09:33 CST)
  • Re: ramdomized start velocities (Fri Nov 08 2002 - 14:35:39 CST)
  • Re: LEaP: The parm and coord files disagree on the number of atoms (Tue Oct 29 2002 - 09:50:26 CST)
  • Re: min output (Thu Oct 24 2002 - 11:01:15 CDT)
  • Re: Antechamber generating bad charges w/ gaussian 98. (Wed Oct 23 2002 - 18:16:05 CDT)
  • Re: problem with gibbs !!!! (Tue Oct 22 2002 - 09:34:23 CDT)
  • Re: How to specify the counterion positions using xleap? (Wed Oct 16 2002 - 10:28:06 CDT)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 12:28:15 CDT)
  • Re: regarding resp-doubts (Thu Oct 03 2002 - 11:35:26 CDT)
  • Re: RESP gaussian job crashing (Thu Oct 03 2002 - 09:04:59 CDT)
  • Partial charge generation RESP/antechamber (Mon Sep 30 2002 - 17:27:37 CDT)
  • Re: Amber 7 and 6 topology files. (Mon Sep 30 2002 - 10:41:25 CDT)
  • Re: Request for help with Antechamber (Sat Sep 28 2002 - 00:54:24 CDT)
  • Re: Constant pressure equilibration in a system with a solvent cap (Fri Sep 27 2002 - 08:54:46 CDT)
  • Amber Reflector (Thu Sep 26 2002 - 12:47:58 CDT)
  • Re: compiling amber 7 with Intel Fortran Compiler 6.0 (Wed Sep 25 2002 - 15:58:04 CDT)
  • Re: compiling amber 7 with Intel Fortran Compiler 6.0 (Wed Sep 25 2002 - 15:16:48 CDT)
  • Mopac509mn/linux (Tue Sep 24 2002 - 10:00:20 CDT)
  • Re: example 1 problems (Tue Sep 17 2002 - 09:24:30 CDT)
  • Re: amber question (Mon Sep 16 2002 - 12:24:20 CDT)
  • Re: D-tryptophan (Sat Sep 14 2002 - 10:21:42 CDT)
  • Re: Qustion about calculation of pressure (Thu Sep 12 2002 - 11:43:25 CDT)
  • Re: memory allocation in mm_pbsa (Wed Sep 11 2002 - 10:26:19 CDT)
  • Re: loadpdb error messages (Tue Sep 10 2002 - 18:49:48 CDT)
  • Re: nmode compile question? (Tue Sep 10 2002 - 13:04:07 CDT)
  • Re: compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 19:56:42 CDT)
  • Re: NTX value (Fri Aug 30 2002 - 13:35:30 CDT)
  • Re: NTX value (Fri Aug 30 2002 - 11:10:10 CDT)
  • Re: ES40 hangs amber7 jobs. (Fri Aug 30 2002 - 11:07:11 CDT)
  • Re: iwrap and image (Wed Aug 28 2002 - 09:35:50 CDT)
  • mail reflector (Mon Aug 26 2002 - 17:35:53 CDT)
  • test (Mon Aug 26 2002 - 17:04:35 CDT)
• Jarrod Smith
  • Vanderbilt Biomolecular Modeling Symposium (Fri Aug 30 2002 - 13:00:40 CDT)
• Jean-Christophe Ducom
  • Re: P4_GLOBMEMSIZE problem (Tue Nov 05 2002 - 11:53:11 CST)
  • P4_GLOBMEMSIZE problem (Mon Nov 04 2002 - 11:33:19 CST)
• Jeff Ames
  • recursively calling sander? (Mon Feb 25 2002 - 10:32:54 CST)
• jeff dyason
  • Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. (Wed Aug 07 2002 - 23:45:49 CDT)
  • Charge export from Leap is rounded off (Sun May 26 2002 - 19:06:36 CDT)
  • sander & prmtop file generated from antechamber input ? (Tue Apr 23 2002 - 22:33:58 CDT)
  • Save from LEaP to a PDBQ file ? (Thu Apr 11 2002 - 22:50:32 CDT)
  • sulfate and sulfamate parameters (Wed Mar 27 2002 - 22:28:55 CST)
• Jennifer Hawkings
  • (no subject) (Sat Dec 07 2002 - 16:48:46 CST)
• Jerry Matthew Parks
  • Nitro parameters (Wed Aug 21 2002 - 16:28:48 CDT)
• Jerry wu
  • concentrated system (Mon Mar 04 2002 - 02:36:21 CST)
  • temperature control (Mon Jan 14 2002 - 21:55:16 CST)
• Jessica Swanson
  • who to address this to?... (Sun Sep 08 2002 - 17:59:23 CDT)
• Jian Zhang
  • Re: help! Non bond list overflow! (Wed Nov 13 2002 - 20:32:01 CST)
• Jianhui Wu
  • Reference, GB 2, Amber7 (Thu Oct 17 2002 - 14:34:12 CDT)
  • Reference for GB model 2 (Thu Oct 17 2002 - 14:26:18 CDT)
  • compile Moil-View, GL header files (Tue Sep 03 2002 - 10:20:09 CDT)
  • Binding site volume/Sander MD (Fri Aug 30 2002 - 16:20:09 CDT)
  • Amber/Gentoo linux (Fri Aug 09 2002 - 14:53:16 CDT)
  • Gentoo vs. Redhat Linux, shared/distributed filesystem (Thu Aug 08 2002 - 14:44:53 CDT)
  • mpich, I/O, Master node, filesystem (Wed Aug 07 2002 - 23:24:13 CDT)
  • Amber+Mosix (Wed Aug 07 2002 - 15:40:15 CDT)
  • look for benchmark with myrinet vs. 100-BT (Fri Aug 02 2002 - 12:15:29 CDT)
  • Summary: make_crd_hp, mm_pbsa (Mon Jul 22 2002 - 16:45:32 CDT)
  • problem with make_crd_hg, mm_pbsa (Mon Jul 22 2002 - 13:28:29 CDT)
  • Origin300, Linux Cluster (Thu Jul 04 2002 - 11:04:07 CDT)
  • Amber7, sander, restart, blast up (Wed Jun 05 2002 - 12:07:51 CDT)
  • Re: mm_pbsa in parallel system (fwd) (Mon Jun 03 2002 - 11:03:12 CDT)
  • igb=2,gbsa=1,antechamber,bad atom type (Fri May 17 2002 - 14:20:14 CDT)
  • Sander, Setup for Parallel SMP Linux Cluster (Wed May 15 2002 - 14:02:27 CDT)
• Jianxin Guo
  • Re: removing rotational motion (Fri Feb 22 2002 - 16:32:48 CST)
• Jim
  • Re: "number of processors must be a power of two" (Tue Aug 06 2002 - 12:29:48 CDT)
  • "number of processors must be a power of two" (Tue Aug 06 2002 - 09:50:53 CDT)
  • Amber 7 timings? (Mon Aug 05 2002 - 09:53:25 CDT)
• Jim Caldwell
  • test mail (Tue Dec 03 2002 - 16:48:07 CST)
  • mail host switchover (Mon Aug 19 2002 - 16:58:11 CDT)
  • Re: Extra points (Thu Aug 15 2002 - 16:54:21 CDT)
  • Re: trajectory file limit??? (Thu Aug 15 2002 - 14:26:13 CDT)
  • Re: nmode segmentation fault (Thu Aug 08 2002 - 13:21:03 CDT)
  • Re: Leap error: PDB file with more than 10000 residues (Tue Aug 06 2002 - 16:57:34 CDT)
  • Re: Error decoding variable (Wed Jul 31 2002 - 09:43:56 CDT)
  • Re: tests for amber (Tue Jul 30 2002 - 19:57:49 CDT)
  • Re: parallel jobs die with no error message from sander (Mon Jul 29 2002 - 15:08:50 CDT)
  • "amber mail" (Thu Jul 25 2002 - 11:11:01 CDT)
  • Re: Pressure probs in MD (Thu Jul 25 2002 - 10:55:57 CDT)
  • Re: increase lastist (Wed Jul 24 2002 - 17:45:43 CDT)
  • Re: van der Waals, hydrogen bond energy (Fri Jun 28 2002 - 19:24:21 CDT)
  • Re: question (Tue Jun 18 2002 - 17:52:19 CDT)
  • Re: Floating Invalid (Tue Jun 11 2002 - 09:43:49 CDT)
  • Re: compilation of sander on Alpha/Linux clusters (Fri May 24 2002 - 16:41:00 CDT)
  • Re: TIP4P water with AMBER6 (Wed May 22 2002 - 15:25:00 CDT)
  • Re: RESP (Mon Apr 22 2002 - 10:04:25 CDT)
  • Re: RESP charges (Wed Apr 17 2002 - 09:22:04 CDT)
  • Dual AMD ASUS A7M266-D Solved (Mon Mar 18 2002 - 20:37:19 CST)
  • RE: Dual AMD motherboards (Mon Mar 18 2002 - 20:04:24 CST)
  • Dual AMD motherboards (Mon Mar 18 2002 - 17:47:12 CST)
  • Re: box_size (Tue Jan 29 2002 - 09:56:23 CST)
  • Re: your mail (Mon Jan 14 2002 - 13:01:44 CST)
  • Re: Amber on Tru64 (Tue Jan 08 2002 - 13:51:06 CST)
• Jithesh
  • Re: Running amber7 on Param10000 (Thu Aug 15 2002 - 02:35:46 CDT)
  • GB in Amber7 (Wed Aug 14 2002 - 03:37:54 CDT)
  • MAX_RSTACK (Wed Jul 10 2002 - 01:24:42 CDT)
• Jiyoung Heo
  • E going up and down??? (Wed Aug 14 2002 - 16:13:44 CDT)
  • periodic box (Fri Jul 26 2002 - 17:00:28 CDT)
  • model molecules for getting charges of DNA (Sat Jun 08 2002 - 19:20:10 CDT)
• Jo.Vinje_at_kj.uib.no
  • NMR restraints on a 10-mer DNA in Sander (Tue Nov 12 2002 - 11:34:55 CST)
• Joachim Reichelt
  • Re: Intel ifc Compiler (Mon Jun 03 2002 - 01:51:54 CDT)
  • Intel ifc Compiler (Thu May 30 2002 - 04:23:21 CDT)
  • Open position: Postdoctoral Scientist (Wed Jan 16 2002 - 09:57:07 CST)
• Joe Fernandez
  • TI using sander on cluster (Mon May 06 2002 - 09:52:50 CDT)
  • TI integration (Sat May 04 2002 - 08:59:57 CDT)
• Joel Konkle-Parker
  • Sander segmentation fault (Thu Oct 17 2002 - 14:28:48 CDT)
  • DNA Tutorial: min_ntr.in (Fri Oct 11 2002 - 17:28:47 CDT)
  • MD Primers (Fri Sep 27 2002 - 14:54:03 CDT)
  • Changing MAXINT (Thu Sep 12 2002 - 18:21:13 CDT)
  • loadpdb error messages (Tue Sep 10 2002 - 17:58:07 CDT)
  • DNA Tutorial Script (Wed Sep 04 2002 - 18:18:16 CDT)
  • Tutorial Error Message (Wed Aug 28 2002 - 18:19:48 CDT)
• Joerg-Gerald Siebers
  • Re: freeware for RNA modeling on Linux (fwd) (Mon Dec 16 2002 - 20:43:05 CST)
• Joffre Heredia
  • Overwrite files (Thu Dec 05 2002 - 14:25:33 CST)
  • rdparm (Tue Sep 10 2002 - 13:07:26 CDT)
  • Re: parallel jobs die with no error message from sander (Tue Jul 30 2002 - 12:46:37 CDT)
  • Re: parallel jobs die with no error message from sander (Mon Jul 29 2002 - 23:06:33 CDT)
  • Re: MAX_RSTACK (Wed Jul 10 2002 - 12:12:15 CDT)
  • Re: Amber 7 Installation (Wed Jul 10 2002 - 01:17:45 CDT)
  • Re: sander parallel (Thu Jun 13 2002 - 12:39:55 CDT)
  • Intel Kernel Math Library (Thu Jun 06 2002 - 14:46:32 CDT)
  • Re: Sander, Setup for Parallel SMP Linux Cluster (Thu May 16 2002 - 13:01:16 CDT)
  • Topology file format in AMBER 7 (Tue May 14 2002 - 16:14:55 CDT)
• John Bushnell
  • Re: PARMSET (Thu Nov 21 2002 - 16:32:25 CST)
  • compiling amber 7 with Intel Fortran Compiler 6.0 (fwd) (Wed Sep 25 2002 - 15:10:50 CDT)
  • Re: Changing MAXINT (Fri Sep 13 2002 - 17:38:52 CDT)
  • Re: compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 18:43:12 CDT)
  • sander minimizations failing (Tue Aug 13 2002 - 19:03:12 CDT)
  • Re: Defining Restraints in Sander (Thu Jul 18 2002 - 19:44:16 CDT)
  • Re: xLeap problem (Thu May 30 2002 - 00:53:05 CDT)
  • Re: How to run the leap module (Tue Apr 30 2002 - 12:46:35 CDT)
  • RE: a problem (Wed Apr 24 2002 - 16:02:31 CDT)
  • RE: amber7 compilation on a beowulf cluster (Fri Apr 19 2002 - 16:48:00 CDT)
  • RE: RESP-ivary (Fri Apr 19 2002 - 13:16:40 CDT)
  • Re: About the sander_classic calculation (Thu Apr 04 2002 - 16:31:11 CST)
• John Finke
  • Recalculating energies (Tue Apr 16 2002 - 19:45:23 CDT)
  • problems using Link (Tue Mar 26 2002 - 14:39:59 CST)
  • AMBER 99 (Thu Feb 28 2002 - 18:22:55 CST)
  • removing rotational motion (Tue Feb 19 2002 - 03:44:08 CST)
• John Pritchard
  • Studying in Australia (Tue Dec 17 2002 - 22:36:07 CST)
• Jones de Andrade
  • C=C=C bending parameters (Sun Jun 09 2002 - 15:55:33 CDT)
• Jose Ramon Blas
  • Cap-atom-pointer in GIBBS (Thu Dec 05 2002 - 13:50:45 CST)
  • input format for gibbs restraints (Wed Nov 13 2002 - 20:59:43 CST)
  • torsion restraints in GIBBS (Tue Nov 05 2002 - 18:35:44 CST)
• Joseph Nachman
  • RE: ptraj (Fri Jul 26 2002 - 15:14:53 CDT)
  • ptraj (Fri Jul 26 2002 - 14:43:36 CDT)
• Jung-Hsing Lin
  • Re: NTT=5? (Tue Apr 30 2002 - 15:36:45 CDT)
  • Re: NTT=5? (Tue Apr 30 2002 - 11:10:46 CDT)
  • NTT=5? (Mon Apr 29 2002 - 18:10:30 CDT)
• jzhou
  • a question about force field in AMBER (Sat Dec 14 2002 - 19:55:15 CST)
• K.Seshadri
  • amber7 compilation on irix6.4 mp (Mon Sep 09 2002 - 12:44:13 CDT)
  • sander crash (Mon Jul 29 2002 - 03:40:57 CDT)
• K.Veluraja
  • amber (Mon Sep 16 2002 - 00:14:04 CDT)
• Kang, Jonghoon
  • question (Wed Jan 02 2002 - 16:22:14 CST)
• Karen Haskell
  • RE: sander (CAP) chokes on efc (Itanium2/Linux) (Tue Dec 17 2002 - 16:05:31 CST)
  • RE: sander on NEC-SX5 (Thu Aug 15 2002 - 11:38:57 CDT)
  • RE: Using the new2oldparm command (Thu Aug 01 2002 - 15:55:28 CDT)
  • tleap error for systems with 64-bit pointers (Fri Jun 14 2002 - 14:55:16 CDT)
  • Amber 6 on IA64 (Wed Jan 09 2002 - 15:35:02 CST)
• Katherine W. Abold
  • DME and Carnal with AMBER6 (Tue Apr 23 2002 - 09:48:04 CDT)
• kbyun_at_wesleyan.edu
  • (no subject) (Tue Oct 08 2002 - 13:10:53 CDT)
• Khatcharin Siriwong
  • Re: literature for NVE (Mon Aug 12 2002 - 11:19:03 CDT)
  • literature for NVE (Mon Aug 12 2002 - 04:07:05 CDT)
  • amber6 with parallel (Mon Apr 22 2002 - 07:48:24 CDT)
• Kidley N J
  • Sander-Gibbs (Mon Apr 08 2002 - 10:34:49 CDT)
• kiyean.nam_at_pharma.novartis.com
  • Interaction table from minimization (Fri Jun 28 2002 - 16:40:59 CDT)
• Krishna Bisetty
  • Power Point slides (Mon Feb 18 2002 - 01:11:22 CST)
• Kristina Furse
  • RE: atomicfluct in ptraj (Thu Dec 19 2002 - 13:28:16 CST)
  • atomicfluct in ptraj (Wed Dec 18 2002 - 17:16:29 CST)
  • RE: solvateOct (Sun Dec 01 2002 - 15:57:13 CST)
  • RE: solvateOct (Tue Nov 26 2002 - 16:51:52 CST)
  • solvateOct (Fri Nov 22 2002 - 15:36:33 CST)
  • Frictional forces in gB (Tue Nov 19 2002 - 17:41:32 CST)
  • RE: problem in PME (Tue Nov 12 2002 - 10:43:03 CST)
  • RE: How to check whether the trajectory file matches the coordinates file or not? (Mon Sep 09 2002 - 14:32:27 CDT)
  • FWD: RE: Including explicit waters in GB dynamics (Fri Aug 02 2002 - 15:32:52 CDT)
  • RE: ptraj (Fri Jul 26 2002 - 13:32:38 CDT)
  • Including explicit waters in GB dynamics (Sat Jul 20 2002 - 19:30:43 CDT)
• kxg2248_at_njit.edu
  • Sander rfree error (Mon Dec 30 2002 - 16:58:19 CST)
• Laila Abou Zeid
  • pairlist limit (Fri Jan 04 2002 - 08:32:57 CST)
• lamon_at_lav.Boehringer-Ingelheim.com
  • RE: sander mpirun hangs with 4 CPU, but not with 2 (Tue Jul 30 2002 - 12:06:05 CDT)
  • parallel jobs die with no error message from sander (Mon Jul 29 2002 - 12:48:20 CDT)
  • turning PME off in AMBER7 (Thu Jun 20 2002 - 08:28:30 CDT)
  • re: parameters for zn2+ bond to cys- (Thu Jun 20 2002 - 08:17:38 CDT)
• Laurent Chiche
  • Re: acetyl groups on protein fragments (Fri Jul 26 2002 - 02:43:03 CDT)
  • Re: creating a solvent box (Thu Jul 25 2002 - 09:46:47 CDT)
  • Re: am1-bcc charges, antechamber (Thu Jul 25 2002 - 04:17:58 CDT)
  • Re: Trajectory files (Wed Jul 24 2002 - 10:26:36 CDT)
• Layi Adekoya
  • restart mm_pbsa (Thu Nov 14 2002 - 07:02:51 CST)
  • Snapshot stuff (Tue Nov 05 2002 - 08:32:11 CST)
  • distance restraint stuff (Thu Aug 01 2002 - 10:24:50 CDT)
• Lepsa
  • Fw: Valine to alanine Gibbs tutorial (Mon Dec 16 2002 - 07:20:26 CST)
  • Fw: Fw: Charges derivation question! (Thu Dec 12 2002 - 03:55:17 CST)
  • Fw: Charges derivation question! (Wed Dec 11 2002 - 10:21:23 CST)
  • Re: FEP/Gibbs question (Tue Dec 10 2002 - 09:59:39 CST)
  • Re: restart mm_pbsa (Thu Nov 14 2002 - 07:52:22 CST)
  • Re: total energies during MM-PBSA (Fri Nov 01 2002 - 11:29:33 CST)
  • Fw: Re:SURFTEN for GB (Fri Oct 25 2002 - 08:55:12 CDT)
  • Re:SURFTEN for GB (Fri Oct 25 2002 - 08:51:30 CDT)
  • Re: Patching AMBER7 with #24 (Wed Oct 23 2002 - 10:23:14 CDT)
  • Re: Patching AMBER7 with #24 (Wed Oct 23 2002 - 02:49:07 CDT)
  • Re: restraining atoms (Thu Oct 17 2002 - 01:56:17 CDT)
  • Re: Error in Antechamber program in ammber7 (Tue Oct 15 2002 - 10:07:57 CDT)
  • Re: MM-PBSA tutorial (Mon Oct 14 2002 - 02:14:47 CDT)
  • Re: reaction field energy of a ligand in MM-PBSA (Wed Oct 09 2002 - 08:19:56 CDT)
  • Re: xleap XENVIRONMENT (Thu Oct 03 2002 - 02:47:39 CDT)
  • Re: MM-PBSA basics (Mon Sep 30 2002 - 02:13:16 CDT)
  • Re: ambpdb? (Wed Sep 25 2002 - 03:29:25 CDT)
  • Fw: Do I have to rerun 1ns MD?? (Mon Sep 23 2002 - 10:50:26 CDT)
  • Re: leap and topology file (Fri Sep 13 2002 - 09:39:45 CDT)
  • Re: protein minimization (Tue Sep 03 2002 - 01:13:54 CDT)
  • Re: SHAKE troubles (Wed May 29 2002 - 09:02:15 CDT)
  • Fw: mm_pbsa (Fri May 24 2002 - 09:27:21 CDT)
  • Re: Junmei et al. 1999 (Wed May 22 2002 - 03:58:41 CDT)
  • Re: (Wed Apr 17 2002 - 09:38:47 CDT)
  • Re: RESP charges (Wed Apr 17 2002 - 07:26:27 CDT)
  • Re: polarizabilities (Tue Mar 26 2002 - 03:12:09 CST)
  • Fw: parameter estimation (Fri Mar 08 2002 - 03:52:50 CST)
  • Re: AMBER logo citation (Wed Feb 20 2002 - 03:02:15 CST)
  • Re: frcmod file format (Tue Feb 12 2002 - 01:05:54 CST)
  • Re: Latest parm + getting parm98 as default in LEaP (Tue Jan 22 2002 - 00:39:59 CST)
• Lich Nguyen
  • Please help. Energy suddenly increase. Protein jump out (Wed Nov 27 2002 - 01:42:29 CST)
  • Re: Protein jump out, please help (Thu Oct 24 2002 - 22:21:40 CDT)
  • Protein jump out, please help (Thu Oct 24 2002 - 04:45:45 CDT)
• lifang xu
  • RE: Floating Invalid (Wed Jun 12 2002 - 22:02:21 CDT)
• Lifeng Tian
  • Anal Error : Group (Fri Sep 27 2002 - 17:35:23 CDT)
• Ling Zhang
  • How to check whether the trajectory file matches the coordinates file or not? (Mon Sep 09 2002 - 13:31:13 CDT)
  • Decrease the solvated system by removing the outside crystal water (Mon Jul 15 2002 - 11:58:34 CDT)
  • Re: How to decrease the solvated system in Amber6? (Tue Jul 02 2002 - 10:30:19 CDT)
  • How to decrease the solvated system in Amber6? (Mon Jul 01 2002 - 11:28:51 CDT)
  • The crystal water is solute or solvent during solvation (Fri Jun 28 2002 - 13:58:08 CDT)
  • iwrap set in sander of Amber6 (Thu Jun 27 2002 - 15:43:41 CDT)
  • Using a trucated octahedral box in Amber6 (Wed Jun 26 2002 - 20:28:46 CDT)
  • The atom number mismatch in coord and topology file in AMBER6. (Fri Jun 14 2002 - 09:58:45 CDT)
  • The atom number mismatch in coord and topology file. (Thu Jun 13 2002 - 16:41:08 CDT)
  • How to set the dielctric constant equals 1, when running MD simulations in real solvent water? (Thu Jun 13 2002 - 15:54:53 CDT)
• Long Hai
  • Re: Overwrite files (Thu Dec 05 2002 - 15:33:53 CST)
  • Re: PME box ? (Wed Jun 05 2002 - 11:07:29 CDT)
• Lorenzo Gontrani
  • Distace dependent dielectric constant (Mon Sep 09 2002 - 03:33:43 CDT)
  • This is a test for amber reflector - please ignore (Thu May 23 2002 - 03:34:38 CDT)
• Luis Gracia
  • Re: solvatebox (Wed Dec 18 2002 - 09:58:47 CST)
  • solvatebox (Tue Dec 17 2002 - 18:52:07 CST)
  • Re: Chains, LEaP and ambpdb (Tue Dec 17 2002 - 15:23:55 CST)
  • Chains, LEaP and ambpdb (Tue Dec 17 2002 - 13:47:59 CST)
  • Nz-Acetyllysine parameters (Tue Nov 19 2002 - 18:08:13 CST)
  • Re: Amber Perl module (Thu Nov 14 2002 - 15:55:25 CST)
• Luo Liu
  • Hydrophobic protein in water (Sun Nov 24 2002 - 16:52:20 CST)
  • 2D RMSd (Tue Oct 08 2002 - 03:32:34 CDT)
• M. L. Dodson
  • roar-cp problems (Wed Dec 18 2002 - 15:00:37 CST)
  • Re: solvating a protein with large cavity (Sat Dec 14 2002 - 10:23:15 CST)
  • Re: Question on 2 stage RESP fit (Thu Dec 12 2002 - 07:05:15 CST)
  • Re: Calculating atomic charges for AMBER with Gaussian98W (Sat Nov 23 2002 - 09:36:27 CST)
  • Roar capabilities (Fri Nov 08 2002 - 11:37:48 CST)
  • Re: How to specify the counterion positions using xleap? (Wed Oct 16 2002 - 19:10:22 CDT)
  • perturbation of gln to glu (Sun Oct 13 2002 - 19:02:00 CDT)
  • Re: Questions on crosslinking residues (Thu Oct 03 2002 - 07:42:08 CDT)
  • Re: mol2 file format in the future of amber (Sun Sep 22 2002 - 10:34:06 CDT)
  • mol2 file format in the future of amber (Fri Sep 20 2002 - 09:41:02 CDT)
  • Re: am1-bcc charges, antechamber (Thu Jul 25 2002 - 07:32:05 CDT)
  • Re: am1-bcc charges, antechamber (Wed Jul 24 2002 - 15:24:23 CDT)
• m.elizabeth sophia
  • protein minimization (Tue Sep 03 2002 - 11:01:35 CDT)
• Mahadevan Seetharaman
  • CHARMm NPT input files (Sat Dec 07 2002 - 17:39:07 CST)
  • penalty function in NMR refinement (Mon Dec 02 2002 - 11:09:05 CST)
  • ISTAR2 - oops, just found the answer... (Wed Sep 25 2002 - 14:55:46 CDT)
  • sander_classic: Recompile without ISTAR2 (Wed Sep 25 2002 - 14:53:59 CDT)
  • Re: mm_pbsa (Sun Sep 22 2002 - 21:07:27 CDT)
  • MD on cytochrome (Thu Aug 01 2002 - 16:15:52 CDT)
  • 'triangular' bond or angle (Tue Jul 30 2002 - 15:53:20 CDT)
  • GENERALIZED BORN model on a protein with Fe (Thu Jul 18 2002 - 09:55:01 CDT)
• Mako Furukawa
  • Re: AMBER6 on cluster (Mon Oct 07 2002 - 19:43:31 CDT)
  • AMBER6 on cluster (Mon Oct 07 2002 - 19:12:28 CDT)
• Mao Xiang
  • perturbed type DH not found (Wed Jun 12 2002 - 05:47:19 CDT)
• Marc Baaden
  • Re Europium force field parms (Mon Mar 11 2002 - 05:52:40 CST)
• Marc Dobler
  • Re: Density during equilibration (sander) (Wed Sep 18 2002 - 02:11:21 CDT)
  • Re: Density during equilibration (sander) (Tue Sep 17 2002 - 19:29:22 CDT)
  • Re: MD in alcohol (Mon Aug 05 2002 - 03:46:17 CDT)
  • MD in alcohol (Sun Aug 04 2002 - 21:33:52 CDT)
• Marcela Madrid
  • NMR restrains (Mon Dec 09 2002 - 14:33:31 CST)
  • ntx=7, irest=0 (Fri Nov 22 2002 - 17:56:00 CST)
  • Re: restarting simulation (Fri Nov 22 2002 - 16:07:47 CST)
  • restarting simulation (Fri Nov 22 2002 - 14:06:42 CST)
  • problem in restrt (Fri Nov 22 2002 - 10:37:53 CST)
  • ion distances (Thu Nov 21 2002 - 14:59:12 CST)
  • restrt format problem (Wed Nov 06 2002 - 16:48:02 CST)
  • scaling of amber with number of atoms (Mon Oct 21 2002 - 14:23:59 CDT)
  • leap and topology file (Thu Sep 12 2002 - 11:12:20 CDT)
  • increase lastist (Wed Jul 24 2002 - 15:41:45 CDT)
  • torsion angle constrains (Tue Jul 02 2002 - 16:22:09 CDT)
  • charges for peptides (Fri Jun 07 2002 - 10:14:59 CDT)
  • reference (Wed Jun 05 2002 - 10:48:55 CDT)
  • xleap (Tue May 28 2002 - 16:21:39 CDT)
  • subdomain moving as a rigid unit during MD (Fri May 24 2002 - 10:59:40 CDT)
  • charges (Thu May 23 2002 - 15:25:43 CDT)
  • this is a test of the amber reflector. Please ignore. Marcela (Wed May 22 2002 - 08:59:24 CDT)
  • generating left-handed A-DNA (Tue Apr 23 2002 - 19:41:08 CDT)
  • creating a unit wth xleap (Tue Mar 19 2002 - 13:07:30 CST)
• Marcelo Roitburd
  • Re: Fwd: Re: probelms in install of amber (fwd) (Thu Jun 27 2002 - 17:47:41 CDT)
  • Re: Fwd: Re: probelms in install of amber (fwd) (Thu Jun 27 2002 - 17:23:29 CDT)
  • Re: Fwd: Re: probelms in install of amber (fwd) (Thu Jun 27 2002 - 15:59:35 CDT)
• Marco Aurélio Correia Preto
  • Charges derivation question! (Wed Oct 30 2002 - 10:39:24 CST)
  • Resp Multiconformational charge fitting! (Wed Oct 30 2002 - 05:50:52 CST)
• Marco Preto
  • Re: RESP-group constraint (Wed Oct 30 2002 - 10:50:21 CST)
• Margaret Cheung
  • Re: carnal output trajectory (Thu Oct 24 2002 - 15:57:50 CDT)
  • Re: error message (Wed Oct 16 2002 - 12:56:50 CDT)
  • Re: geometry optimization/turning off Elec and Vdw terms (Mon Oct 07 2002 - 17:26:01 CDT)
  • Re: question about using 10-12 in amber7/sander. (Sat Sep 28 2002 - 15:35:48 CDT)
  • question about using 10-12 in amber7/sander. (Sat Sep 28 2002 - 14:53:56 CDT)
  • RE: Amber/Gentoo linux (Sun Aug 11 2002 - 18:31:02 CDT)
  • Re: Please give me a hand on understanding AMBER/MPI and locmem. (Sat Aug 03 2002 - 17:23:50 CDT)
  • Please give me a hand on understanding AMBER/MPI and locmem. (Sat Aug 03 2002 - 01:49:46 CDT)
  • Re: look for benchmark with myrinet vs. 100-BT (Fri Aug 02 2002 - 13:20:22 CDT)
  • Re: compiling error. (Sun Mar 31 2002 - 22:44:07 CST)
  • compiling error. (Sun Mar 31 2002 - 01:26:53 CST)
  • Re: a little bit confused with leap-frog algorithm... (Sat Mar 30 2002 - 21:35:36 CST)
  • a little bit confused with leap-frog algorithm... (Thu Mar 28 2002 - 15:08:40 CST)
  • flying monomers... (Fri Feb 15 2002 - 17:58:39 CST)
  • question regarding ntwv. (Thu Jan 31 2002 - 19:55:58 CST)
• Mark Beardsell
  • AMBER 7 - more problems with leap (Wed May 01 2002 - 07:17:46 CDT)
  • (no subject) (Thu Apr 11 2002 - 08:36:29 CDT)
• Mark C. Ballew
  • Re: xleap XENVIRONMENT (Thu Oct 03 2002 - 16:09:25 CDT)
  • xleap XENVIRONMENT (Wed Oct 02 2002 - 17:34:09 CDT)
• Mark Hsieh
  • IDECOMP (Wed Oct 30 2002 - 12:11:02 CST)
  • RE: Antibody residue numbering (Tue Aug 20 2002 - 11:52:24 CDT)
  • RE: Antibody residue numbering (Mon Aug 19 2002 - 20:00:03 CDT)
  • Antibody residue numbering (Mon Aug 19 2002 - 15:56:00 CDT)
  • missing residues (Sun May 05 2002 - 02:15:31 CDT)
  • RE: sander mpich hangs (Fri Apr 26 2002 - 14:08:48 CDT)
  • sander mpich hangs (Thu Apr 25 2002 - 17:01:26 CDT)
  • RE: parallel sander? (Tue Apr 23 2002 - 14:35:44 CDT)
  • parallel sander? (Tue Apr 23 2002 - 14:31:55 CDT)
  • mm_pbsa for uhbd (Fri Apr 19 2002 - 20:56:18 CDT)
  • MPICH and AMBER 7 (Thu Apr 18 2002 - 18:12:58 CDT)
  • mm pbsa: generate snapshots (Wed Apr 17 2002 - 16:52:41 CDT)
  • (no subject) (Wed Apr 10 2002 - 15:31:50 CDT)
• Markus Drumm
  • Question about Counterions (Thu Sep 19 2002 - 12:38:24 CDT)
• Marta Murcia
  • Parameters (Wed Jan 16 2002 - 09:59:26 CST)
• Martina Roeselova
  • question: velocity units (Wed Jan 09 2002 - 11:46:00 CST)
• Masaki Tomimoto
  • Question about Antechamber (Wed Sep 25 2002 - 16:37:55 CDT)
  • RE: Order of a protein, bound waters and ligand in saveamberparm (Thu Aug 15 2002 - 17:04:18 CDT)
  • Order of a protein, bound waters and ligand in saveamberparm (Thu Aug 15 2002 - 15:25:45 CDT)
  • Q: waters in NPT & periodic boundary condition (Wed Aug 14 2002 - 11:06:15 CDT)
  • a water jumps (Mon Jul 29 2002 - 22:47:21 CDT)
  • RE: Water molecule numbering (Thu Jul 25 2002 - 19:32:19 CDT)
  • RE: Water molecule numbering (Thu Jul 25 2002 - 19:04:01 CDT)
  • Water molecule numbering (Thu Jul 25 2002 - 17:28:25 CDT)
  • SS bond (Wed Jul 24 2002 - 14:04:21 CDT)
  • Format in a trajectory files is suddenly changed (Mon Jul 22 2002 - 11:54:44 CDT)
  • Question about error message about "lastist" and "virtual box" (Fri Jul 12 2002 - 10:19:12 CDT)
• Masamichi Fujinami 4029
  • question (Wed May 15 2002 - 00:49:03 CDT)
• Mathy Froeyen
  • mm_pbsa positive binding energies (Mon Sep 02 2002 - 04:11:34 CDT)
  • Re: mm pbsa: generate snapshots (Thu Apr 18 2002 - 02:19:35 CDT)
• Matt Hartings
  • Re: transferring structures (Wed Jun 26 2002 - 15:58:11 CDT)
  • transferring structures (Wed Jun 26 2002 - 12:24:23 CDT)
• Matteo Dal Peraro
  • sander7: MPI_COMM_RANK problem (Mon Oct 21 2002 - 14:17:14 CDT)
• Matthew Lee
  • a couple missing gaff angle terms (Fri Aug 16 2002 - 16:55:44 CDT)
  • antechamber's prepc option (Fri Aug 16 2002 - 14:20:59 CDT)
  • AM1-BCC sensitivity to AM1 charges (Tue Jul 30 2002 - 12:31:43 CDT)
  • ambpdb in AMBER7 (Wed May 22 2002 - 15:42:34 CDT)
• Matthew Randolph Lee, Ph.D.
  • Re: a missing variable (Wed Aug 28 2002 - 17:27:12 CDT)
  • follow-up post on missing gaff terms (Tue Aug 20 2002 - 12:21:50 CDT)
  • mol2_to_off (Fri Aug 16 2002 - 17:15:41 CDT)
• McAteer, Kathleen
  • makeDIP_RST.dna (Wed Jul 24 2002 - 14:24:42 CDT)
• mdk7p_at_cms.mail.virginia.edu
  • Amber trajectory movies in Powerpoint (Tue Aug 06 2002 - 10:53:39 CDT)
  • Potential Energy and RMS-Deviation Issues (Thu Aug 01 2002 - 10:01:07 CDT)
  • Zn/Mg Counterion placement around DNA (Fri Jun 28 2002 - 14:46:11 CDT)
• medicinal and Compuatational Chemistry Resumes and Jobs
  • 4 Medicinal and Computational Chemistry Candidates (Tue Apr 16 2002 - 16:55:48 CDT)
• meiselba
  • FEP/Gibbs question to valine alanine tutorial (Sat Dec 14 2002 - 10:58:12 CST)
  • Question to perturbation charge (Tue Dec 10 2002 - 07:35:38 CST)
  • FEP/Gibbs question (Tue Nov 19 2002 - 09:29:07 CST)
• Mengjuei Hsieh
  • Re: reg: MAC OS (Mon Oct 21 2002 - 13:13:35 CDT)
• mer_at_chem.wayne.edu
  • average of LES copies (Sun Aug 18 2002 - 20:00:22 CDT)
  • Analysis of LES simulation (Sun Jun 30 2002 - 17:40:39 CDT)
• mer_at_gordon.chem.wayne.edu
  • PMF with sander module (Wed Aug 14 2002 - 18:23:25 CDT)
• Mercury
  • NAV detected a virus in a document YOU sent to webmaster@nctimes.com. (Thu Oct 31 2002 - 21:12:51 CST)
• Michael Crowley
  • Re: who to address this to?... (Mon Sep 09 2002 - 12:41:16 CDT)
  • Re: "number of processors must be a power of two" (Tue Aug 06 2002 - 12:31:50 CDT)
  • Re: correction about solvateOct (Fri Jul 19 2002 - 11:37:10 CDT)
  • Re: problem in compiling amber7 in IBMSP3 cluster (Fri Jul 05 2002 - 13:11:55 CDT)
• Michael Ford
  • Re: chirality.c failure - diagnosis, but no cure... (Thu Dec 19 2002 - 17:25:21 CST)
  • chirality.c failure - diagnosis, but no cure... (Thu Dec 19 2002 - 12:07:07 CST)
  • Re: mm_pbsa error message! (Wed Dec 18 2002 - 11:37:57 CST)
  • dual H-bonding of bridging waters - CARNAL (Tue Dec 10 2002 - 18:16:24 CST)
  • Re: Amber Perl module (Thu Nov 14 2002 - 17:26:24 CST)
  • xleap and modified sugar residues (Thu Oct 31 2002 - 13:22:17 CST)
  • Re: *.top file: "PARM-F-UHOSED, try again" (Thu Oct 31 2002 - 11:43:10 CST)
  • mm_pbsa error message (warning?) (Tue Oct 29 2002 - 16:47:02 CST)
  • mm_pbsa curious output of coordinates and resulting errors... (Tue Oct 29 2002 - 16:01:43 CST)
  • Re: Solvent exposed surface area over a trajectory (Thu Oct 17 2002 - 14:09:17 CDT)
  • Re: How to convert oldparmtop to newparmtop? (Wed Oct 16 2002 - 14:47:57 CDT)
  • Re: Some error message on Leap (Thu Oct 10 2002 - 16:27:03 CDT)
  • Re: trouble with snapshots GC option of MM_PBSA - Now no output for lig and rec (Thu Oct 10 2002 - 10:10:35 CDT)
  • Re: trouble with snapshots GC option of MM_PBSA (Thu Oct 10 2002 - 09:31:05 CDT)
  • trouble with snapshots GC option of MM_PBSA (Thu Oct 10 2002 - 09:23:24 CDT)
  • MM-GBSA and counterions (Thu Oct 03 2002 - 14:27:27 CDT)
  • MM-PBSA basics (Fri Sep 27 2002 - 14:53:01 CDT)
  • Re: triNAG parameters?4 (Tue Jan 22 2002 - 11:19:21 CST)
• Michael G Cooney
  • Re: NMR restraints on a 10-mer DNA in Sander (Tue Nov 12 2002 - 14:16:32 CST)
  • Re: Protein jump out, please help (Thu Oct 24 2002 - 13:51:52 CDT)
  • misdirected message (Mon Aug 12 2002 - 14:35:35 CDT)
  • chesey@panther.gsu.edu (Mon Aug 12 2002 - 14:03:37 CDT)
  • RESP tutorial (Tue Apr 23 2002 - 12:15:51 CDT)
  • Carnal coordinate averaging (Mon Feb 25 2002 - 16:01:26 CST)
  • Re: temperature control (Tue Feb 05 2002 - 13:15:58 CST)
  • Re: restart md simulation (Tue Jan 29 2002 - 10:44:03 CST)
  • Re: minimising WATBOX216 (Tue Jan 15 2002 - 15:38:58 CST)
  • ptraj and compressed files (Mon Jan 14 2002 - 10:48:40 CST)
  • ptraj cannot use compressed files? (Mon Jan 14 2002 - 10:17:03 CST)
  • removing rotational motion in MD (Wed Jan 09 2002 - 11:41:26 CST)
• Michael Jakusch
  • Re: IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) (Thu Aug 29 2002 - 06:56:12 CDT)
  • IMIN=5 ? (Was: Re: [Re: can carnal do the job as anal ...) (Thu Aug 29 2002 - 02:36:57 CDT)
  • sulfonic group generated with antechamber (Thu Jul 25 2002 - 07:23:30 CDT)
  • Re: correction about solvateOct (Fri Jul 19 2002 - 04:49:48 CDT)
  • EWALD BOMB (The system has extended beyond ...) (Fri Jun 28 2002 - 04:17:20 CDT)
  • antechamber charges don't sum up to zero (Mon Jun 24 2002 - 14:38:15 CDT)
  • nmode memory requirements (Fri Jan 18 2002 - 10:15:52 CST)
  • Re: Amino acid unit "NHE" problem ? (Thu Jan 17 2002 - 08:32:28 CST)
• Michael Murray
  • mm_pbsa output error (Mon Sep 23 2002 - 12:26:11 CDT)
• Michael Petersen
  • Re: problem reading rstrnt file with pgf77 (Fri Aug 16 2002 - 08:23:48 CDT)
  • problem reading rstrnt file with pgf77 compiled sander (Wed Aug 14 2002 - 05:13:24 CDT)
• Michael Sattler
  • AMBER7 (Thu May 30 2002 - 07:59:11 CDT)
• Michael Trieb
  • watershell in ptraj (Tue Sep 24 2002 - 04:03:49 CDT)
• Michal Otyepka
  • restart without velocities (Wed Oct 02 2002 - 02:39:02 CDT)
  • Re: binding site volume (Fri Sep 13 2002 - 02:13:08 CDT)
  • Polarizability, a general question (Wed Sep 11 2002 - 03:56:32 CDT)
  • Re: How to make mpeg files from amber trajectories (fwd) (Wed Aug 28 2002 - 02:22:54 CDT)
  • Re: Junmei et al. 1999 (Wed May 22 2002 - 02:57:11 CDT)
  • change topology (Thu Mar 28 2002 - 02:44:38 CST)
  • Polarizabilities, charge scaling and ions (Wed Mar 27 2002 - 03:42:29 CST)
  • MM-PBSA philosophy (Wed Mar 20 2002 - 06:34:24 CST)
  • B-factor (Thu Jan 31 2002 - 04:45:50 CST)
• Miguel Angel
  • Re: PDB file with CONECT record (Fri Apr 12 2002 - 05:03:09 CDT)
• Miguel Angel Rodriguez Carvajal
  • Linking to its own image (Thu Feb 14 2002 - 08:15:52 CST)
• Miguel de Federico
  • GIBBS - Routine TORCON (internal constraints) failed (Tue Dec 17 2002 - 09:29:04 CST)
  • GIBBS - end-of-file during read (Fri Dec 13 2002 - 04:12:48 CST)
  • LEAP - Introducing dummy atoms (Mon Dec 02 2002 - 10:42:49 CST)
  • GIBBS - ERROR: Restraint read error from RSTIN; Check format: (Tue Nov 26 2002 - 03:14:19 CST)
  • GIBBS - Error message. (Tue Nov 19 2002 - 10:00:25 CST)
  • LEaP: The parm and coord files disagree on the number of atoms (Tue Oct 29 2002 - 02:24:58 CST)
  • Dummy atoms... (Wed Oct 23 2002 - 02:44:34 CDT)
  • Re: regarding resp-doubts (Thu Oct 03 2002 - 11:01:23 CDT)
  • Amber 7 and 6 topology files. (Mon Sep 30 2002 - 10:08:36 CDT)
  • Trajectory files (Wed Jul 24 2002 - 07:10:51 CDT)
  • Problem with LEAP (Tue Jul 16 2002 - 05:53:37 CDT)
  • RESP Multiconformer Fitting (Thu Jun 20 2002 - 18:05:11 CDT)
• Miguel de Federico de la Rúa
  • Sander: check COM velocity, temp: 0.000000 0.00(Removed) (Fri Nov 08 2002 - 08:08:38 CST)
• Mihaly Mezei
  • Re: amber-request@cgl.ucsf.edu (Mon Jul 29 2002 - 13:42:22 CDT)
  • Re: The 216 water box (Thu Jul 18 2002 - 17:48:12 CDT)
• Mike Keller
  • Magnesium as a DNA counterion in AMBER 6.0 (Thu Mar 28 2002 - 09:31:29 CST)
  • RESP Crash (Thu Feb 14 2002 - 09:24:51 CST)
• Mirjam Lerch
  • seperate_solute_output (Fri Jan 11 2002 - 03:02:31 CST)
• Mite51
  • Re: group input in ANAL (Sat Jan 26 2002 - 15:09:46 CST)
• Miyashita, Osamu
  • dielectric constant for partialy solvated MD (Wed Jul 31 2002 - 13:55:58 CDT)
• Monica
  • error in rMD (Fri Jun 28 2002 - 08:35:34 CDT)
• Monica
  • Problem (Fri Nov 29 2002 - 00:35:19 CST)
  • Conterions (Sat Nov 16 2002 - 02:10:15 CST)
  • (no subject) (Thu Nov 14 2002 - 00:26:57 CST)
  • Ewald (Wed Nov 13 2002 - 09:20:23 CST)
  • problem in PME (Tue Nov 12 2002 - 07:42:21 CST)
  • Problem in run (Fri Nov 08 2002 - 22:41:52 CST)
  • Problem in amber (Thu Jun 27 2002 - 00:28:21 CDT)
  • New Residue (Mon Jun 24 2002 - 10:01:42 CDT)
  • Application of Amber (Wed Jun 12 2002 - 10:24:49 CDT)
  • noesy intensity input in DNA (Thu Apr 11 2002 - 03:03:50 CDT)
  • DNA structure get distorted (Thu Apr 11 2002 - 03:00:48 CDT)
  • input files (Wed Apr 03 2002 - 07:00:42 CST)
  • AMBER 5 (Wed Mar 27 2002 - 22:29:12 CST)
• Monica Jain
  • Re: Problem in run (Sat Nov 09 2002 - 00:52:46 CST)
• Mr. Daniel Osondu
  • Business Cooperation (Inheritance Claim) (Fri Dec 13 2002 - 01:50:38 CST)
  • Business Cooperation (Inheritance Claim) (Thu Dec 12 2002 - 10:10:29 CST)
• Narang Manpreet Kaur
  • NATOM mismatch in coord and topology files. (Mon Nov 18 2002 - 00:49:46 CST)
  • (no subject) (Sat Nov 16 2002 - 04:17:02 CST)
  • Forwarded mail.... (Sat Nov 09 2002 - 03:56:37 CST)
  • Error in Antechamber program in ammber7 (Tue Oct 15 2002 - 09:49:52 CDT)
• Narang Manpreet Kaur
  • (no subject) (Fri Nov 29 2002 - 04:54:03 CST)
  • (no subject) (Sat Nov 23 2002 - 04:40:12 CST)
  • Re: Error in Antechamber program in ammber7 (Wed Oct 16 2002 - 00:01:45 CDT)
  • (no subject) (Wed Jul 03 2002 - 10:08:40 CDT)
• Natasja Brooijmans
  • Re: RESTARTED DUE TO LINMIN FAILURE (Thu Dec 19 2002 - 15:16:44 CST)
  • Re: disulfide bond link between two chains (Mon Dec 16 2002 - 07:49:46 CST)
  • Re: Energy decomposition with ANAL (Fri Dec 06 2002 - 11:24:21 CST)
  • Re: HIS residues (Thu Oct 24 2002 - 18:09:55 CDT)
  • Re: Amber Crd format (Tue Oct 22 2002 - 14:04:43 CDT)
  • Re: Solvent exposed surface area over a trajectory (Thu Oct 17 2002 - 14:35:34 CDT)
  • Re: error message (Wed Oct 16 2002 - 12:48:41 CDT)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 11:46:54 CDT)
  • Re: example 1 problems (Mon Sep 16 2002 - 11:40:38 CDT)
  • Re: Trajectory files (Wed Jul 24 2002 - 09:34:28 CDT)
  • Re: parallel sander on T3E (Sat May 25 2002 - 10:44:34 CDT)
  • vanadium (Sun May 19 2002 - 21:35:27 CDT)
  • Re: combining trajectory file (Tue Mar 12 2002 - 10:00:38 CST)
• Nathan A. Baker
  • Re: MPI_BCAST error (Wed Dec 18 2002 - 19:31:47 CST)
  • MPI_BCAST error (Wed Dec 18 2002 - 09:51:02 CST)
• navjot_at_bioinfo.ernet.in
  • Mn parameters!!! (Mon Jun 17 2002 - 04:19:12 CDT)
• Neema Salimi
  • Re: Restraint Ambiguities (Thu Nov 21 2002 - 22:37:13 CST)
  • Restraint Ambiguities (Thu Nov 21 2002 - 16:56:44 CST)
• nepenthes_at_vplaces.net
  • install leap not working (Tue Apr 30 2002 - 02:52:07 CDT)
  • choosing a forcefield (Thu Mar 07 2002 - 21:51:25 CST)
• Nicholson, James D Mr ARO
  • RE: Amber Trajectories + VMD (fwd) (Tue Dec 03 2002 - 17:35:09 CST)
  • Are posters to the Amber list being spammed? (Sun Nov 17 2002 - 19:48:15 CST)
  • RE: Antechamber generating bad charges w/ gaussian 98. (Wed Oct 23 2002 - 21:12:32 CDT)
  • RE: Antechamber generating bad charges w/ gaussian 98. (Wed Oct 23 2002 - 21:00:47 CDT)
  • Antechamber generating bad charges w/ gaussian 98. (Wed Oct 23 2002 - 16:50:56 CDT)
  • RE: RESP gaussian job crashing (Thu Oct 03 2002 - 16:57:46 CDT)
  • RESP gaussian job crashing (Wed Oct 02 2002 - 20:22:59 CDT)
  • RE: Questions on crosslinking residues (Wed Oct 02 2002 - 20:03:47 CDT)
  • Questions on crosslinking residues (Tue Oct 01 2002 - 16:59:19 CDT)
  • RE: Request for help with Antechamber (Fri Sep 27 2002 - 20:00:37 CDT)
  • Request for help with Antechamber (Fri Sep 27 2002 - 18:58:58 CDT)
  • Question on Antechamber paper (Thu Sep 26 2002 - 12:18:17 CDT)
  • Help using moilview to make animations of trajectories (Fri Sep 13 2002 - 17:15:33 CDT)
  • RE: bondbydistance (Sat Sep 07 2002 - 19:16:28 CDT)
  • Solvated DNA using Amber 7 (Thu Aug 01 2002 - 16:32:13 CDT)
• Nicolas Le Novere
  • loss of disulfide bonds (Mon Oct 14 2002 - 10:31:23 CDT)
• Nicolas Grima
  • Re: write problem on IBM-AIX (Tue Oct 01 2002 - 04:40:07 CDT)
• nicolescholiz1_at_web.de
  • Pictausch?? (Mon Jul 08 2002 - 18:14:10 CDT)
• Nigel D Priestley
  • Interface and Amber 7.0 (Mon Aug 26 2002 - 21:45:55 CDT)
• Nikolai Smolin
  • Qustion about calculation of pressure (Thu Sep 12 2002 - 05:01:44 CDT)
  • correction about solvateOct (Fri Jul 19 2002 - 04:09:58 CDT)
  • about solvateOct (Fri Jul 19 2002 - 03:22:20 CDT)
  • minimum image cut-off (Wed Jun 26 2002 - 06:05:08 CDT)
  • again about sander_classic Amber 6.0 (Wed May 22 2002 - 06:42:50 CDT)
  • about sander_classic AMBER6.0 (Mon May 20 2002 - 08:08:14 CDT)
• Nitin Kumar Singh
  • Query regarding Gamess (Tue Jun 25 2002 - 10:23:09 CDT)
• Noriaki Okimoto
  • TIP4P water with AMBER6 (Wed May 22 2002 - 13:01:35 CDT)
• Numan Oezguen
  • Re: Energy decomposition with ANAL (Mon Dec 16 2002 - 09:49:08 CST)
  • Re: Energy decomposition with ANAL (Fri Dec 06 2002 - 11:08:20 CST)
  • Break down energy contributions (Fri Nov 29 2002 - 15:06:36 CST)
• Osvaldo Santos-Filho
  • partial charges (Mon Jun 24 2002 - 19:33:15 CDT)
• param_at_ibab.ac.in
  • How to run the leap module (Tue Apr 30 2002 - 04:34:32 CDT)
• Pascal Bonnet
  • Re: Resp Multiconformational charge fitting! (Wed Dec 18 2002 - 04:21:46 CST)
  • Re: combinig two trajectory files. (Mon Dec 02 2002 - 06:50:26 CST)
  • Re: C60 parameter (Thu Nov 28 2002 - 06:12:19 CST)
  • Re: restart mm_pbsa (Thu Nov 14 2002 - 09:13:06 CST)
  • Re: MEP g98_option (Mon Nov 11 2002 - 05:05:55 CST)
  • flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 (Fri Nov 01 2002 - 03:08:20 CST)
  • mm_pbsa and statistic program (Thu Sep 26 2002 - 05:50:52 CDT)
  • new2oldparm format (2) (Thu Sep 19 2002 - 05:43:39 CDT)
  • bug in New2oldparm (Thu Sep 19 2002 - 05:35:46 CDT)
  • Re: Using the new2oldparm command (Fri Aug 02 2002 - 03:17:54 CDT)
  • Re: gaff and parm99 (Wed Jul 24 2002 - 10:51:30 CDT)
  • gaff and parm99 (Wed Jul 24 2002 - 08:11:36 CDT)
  • Re: AMBER7 and Movie (Mon Jul 22 2002 - 03:36:50 CDT)
  • Re: mopac (Fri Jun 28 2002 - 03:49:11 CDT)
  • carnal RST output format (Tue Mar 19 2002 - 08:12:31 CST)
  • carnal and union: solution (Mon Mar 04 2002 - 06:33:17 CST)
  • carnal and union (Mon Mar 04 2002 - 03:00:20 CST)
  • Re: AMBER logo citation (Wed Feb 20 2002 - 02:17:39 CST)
  • Re: question: velocity units (Wed Jan 09 2002 - 11:57:58 CST)
• Perdita Barran
  • D-tryptophan (Sat Sep 14 2002 - 09:16:45 CDT)
• Peter Fojan
  • nmanal help request (Fri Sep 27 2002 - 08:59:11 CDT)
  • Question about obtaining amber! (Thu Mar 21 2002 - 07:19:59 CST)
• Peter Gannett
  • Re: MD Primers (Fri Sep 27 2002 - 18:34:40 CDT)
  • Beowulf killing jobs (Fri Sep 13 2002 - 16:03:19 CDT)
  • Re: old prmtop (Wed Sep 04 2002 - 13:10:56 CDT)
  • Re: Scaling of Sander on Linux Clusters (fwd) (Mon Aug 26 2002 - 19:56:06 CDT)
  • RE: force field name (Thu Aug 15 2002 - 18:03:52 CDT)
  • Energies/coordinate files from mm_pbsa problem (Tue Jul 30 2002 - 13:25:29 CDT)
  • Re: periodic box (Sat Jul 27 2002 - 09:41:50 CDT)
  • parallel sander on T3E (Sat May 25 2002 - 09:46:37 CDT)
  • NaCl concentration (Tue Apr 30 2002 - 14:34:38 CDT)
  • Re: amber7 compilation on a beowulf cluster (Sat Apr 20 2002 - 07:14:01 CDT)
  • amber7 compilation on a beowulf cluster (Fri Apr 19 2002 - 14:59:56 CDT)
  • Amber in a distributed environment (Wed Apr 17 2002 - 07:07:56 CDT)
  • Re: Compiling Amber7 on a Beowulf Cluster - Compiling Error (Sat Apr 13 2002 - 08:59:29 CDT)
  • Compiling Amber7 on a Beowulf Cluster - Compiling Error (Fri Apr 12 2002 - 18:59:38 CDT)
  • Europium force field parms (Sun Mar 10 2002 - 14:07:44 CST)
  • DOCK (Thu Jan 24 2002 - 08:48:52 CST)
• Peter VARNAI
  • Re: targeted MD (Sat Oct 19 2002 - 09:26:30 CDT)
  • solved: nmr and positional restraint in input (Thu Oct 10 2002 - 10:26:27 CDT)
  • nmr and positional restraint in input (Wed Oct 09 2002 - 12:44:03 CDT)
  • ptraj-6.4/LES (Mon Sep 23 2002 - 04:18:25 CDT)
  • sander.LES questions (Thu Sep 12 2002 - 11:27:12 CDT)
  • sander7 on IBM 7040-681 under AIX 5.1 (Fri Aug 30 2002 - 08:01:07 CDT)
  • reorder water with nmropt (Fri Aug 02 2002 - 07:24:59 CDT)
  • Re: remove COM velocity in Amber7 (Thu Jun 20 2002 - 07:03:07 CDT)
  • remove COM velocity in Amber7 (Mon Jun 17 2002 - 07:16:27 CDT)
  • Re: Reorder water in amber7 (Tue Jun 11 2002 - 12:16:00 CDT)
  • Reorder water in amber7 (Tue Jun 11 2002 - 03:38:32 CDT)
• Philippe Aplincourt
  • Amber on PC-Linux (Thu Nov 14 2002 - 09:22:20 CST)
• Pierre Mignon
  • dummy parameters (Wed Oct 16 2002 - 02:10:46 CDT)
• Pietro Amodeo
  • Re: Dual AMD motherboards (Mon Jul 15 2002 - 03:36:34 CDT)
• postmaster_at_96com.com
  • MDaemon Warning - Virus Found (Fri Sep 13 2002 - 08:13:22 CDT)
  • MDaemon Warning - Virus Found (Fri Sep 13 2002 - 08:10:40 CDT)
  • MDaemon Warning - Virus Found (Tue Sep 10 2002 - 10:57:00 CDT)
  • MDaemon Warning - Virus Found (Mon Sep 09 2002 - 06:04:45 CDT)
  • MDaemon Warning - Virus Found (Fri Sep 06 2002 - 06:13:47 CDT)
  • MDaemon Warning - Virus Found (Wed Sep 04 2002 - 05:40:26 CDT)
  • MDaemon Warning - Virus Found (Tue Sep 03 2002 - 06:57:12 CDT)
  • MDaemon Warning - Virus Found (Mon Sep 02 2002 - 06:25:18 CDT)
  • MDaemon Warning - Virus Found (Mon Sep 02 2002 - 05:12:42 CDT)
  • MDaemon Warning - Virus Found (Fri Aug 30 2002 - 05:59:25 CDT)
  • MDaemon Warning - Virus Found (Fri Aug 30 2002 - 05:08:15 CDT)
  • MDaemon Warning - Virus Found (Thu Aug 29 2002 - 12:02:23 CDT)
  • MDaemon Warning - Virus Found (Thu Aug 29 2002 - 07:20:52 CDT)
  • MDaemon Warning - Virus Found (Thu Aug 29 2002 - 05:14:06 CDT)
• postmaster_at_bydnet.com.pl
  • MDaemon Warning - Virus Found (Wed Dec 04 2002 - 21:49:28 CST)
• pposton
  • Bulk Email Sending & Bullet Proof Web Hosting (Wed Nov 20 2002 - 16:25:53 CST)
• Prabal Maiti
  • difference in energy in amber6 and amber7 (Mon Dec 09 2002 - 20:07:15 CST)
  • ptraj rdf output (Fri Sep 20 2002 - 18:24:35 CDT)
  • GB in amber6 (Thu Aug 15 2002 - 19:26:22 CDT)
  • This one with anal in amber6 (Fri Jul 12 2002 - 13:09:39 CDT)
  • anal in AMBER7 gives inconsistent results with itself (fwd) (Fri Jul 12 2002 - 12:38:19 CDT)
  • Re: anal in AMBER7 gives inconsistent results with itself (Mon Jul 08 2002 - 00:46:31 CDT)
  • anal in AMBER7 gives inconsistent results with itself (Fri Jul 05 2002 - 18:00:55 CDT)
  • helix analysis (fwd) (Thu May 23 2002 - 16:30:33 CDT)
  • Re: ptraj problem (Tue May 21 2002 - 18:51:22 CDT)
  • helix analysis (Mon May 20 2002 - 14:20:45 CDT)
  • Re: PDB file with CONECT record (Tue Apr 16 2002 - 00:48:00 CDT)
  • Re: PDB file with CONECT record (Fri Apr 12 2002 - 01:27:15 CDT)
  • PDB file with CONECT record (fwd) (Tue Apr 09 2002 - 20:04:50 CDT)
  • PDB file with CONECT record (Mon Apr 08 2002 - 14:06:21 CDT)
  • anal input (Fri Feb 22 2002 - 18:31:58 CST)
  • vlimit exceed (Thu Feb 21 2002 - 21:23:39 CST)
  • belly input (Tue Feb 12 2002 - 16:26:21 CST)
  • LIMIN Faliure/Energies per residue for B-DNA etc. (Thu Jan 31 2002 - 13:49:00 CST)
  • xleap and PDB file (Tue Jan 29 2002 - 01:28:23 CST)
• Pradipta Bandyopadhyay
  • correlated motions in a protein! (Wed Feb 27 2002 - 17:52:55 CST)
  • visualizaion program for NMODE! (Wed Feb 27 2002 - 16:48:30 CST)
• Pratul Agarwal
  • Nmode (Thu Dec 19 2002 - 15:07:47 CST)
  • Visualizing AMBER coordinates trajectory in VMD (Mon Nov 04 2002 - 14:54:57 CST)
  • quasih (Mon Oct 28 2002 - 16:25:02 CST)
  • Re: Dielectric constant for interior of proteins (Thu Oct 10 2002 - 14:25:51 CDT)
  • Dielectric constant for interior of proteins (Thu Oct 10 2002 - 12:53:59 CDT)
  • Re: SHAKE problem (Wed Oct 09 2002 - 08:39:55 CDT)
  • Re: EGB = NaNQ (Fri Oct 04 2002 - 15:26:47 CDT)
  • EGB = NaNQ (Thu Oct 03 2002 - 16:05:55 CDT)
  • Re: Is H-bonding really there? (Fri Sep 27 2002 - 15:58:25 CDT)
  • Re: Density during equilibration (sander) (Thu Sep 26 2002 - 09:09:02 CDT)
  • RMSD for heavy atoms only (Wed Sep 25 2002 - 15:54:45 CDT)
  • Re: Density during equilibration (sander) (Tue Sep 17 2002 - 19:22:22 CDT)
  • Density during equilibration (sander) (Tue Sep 17 2002 - 11:56:10 CDT)
  • Re: non-bonded metal ion in complex (Tue Sep 17 2002 - 08:59:14 CDT)
  • Re: Problems during equilibration (Wed Sep 11 2002 - 21:40:05 CDT)
  • Re: Problems during equilibration (Wed Sep 11 2002 - 15:14:05 CDT)
  • Problems during equilibration (Wed Sep 11 2002 - 14:38:36 CDT)
  • atoms coming too close during MD (with SHAKE on) (Mon Sep 02 2002 - 20:01:18 CDT)
  • Re: sorry!!!!maybe another stupid question (Wed Aug 28 2002 - 20:45:28 CDT)
  • Re: Scaling of Sander on Linux Clusters (fwd) (Mon Aug 26 2002 - 19:32:24 CDT)
  • Torsion restraint between center of mass groups (Mon Aug 26 2002 - 16:51:33 CDT)
  • Etot drops after restarting MD in sander (Fri Aug 16 2002 - 13:18:58 CDT)
  • Re: trajectory file limit??? (Thu Aug 15 2002 - 16:12:35 CDT)
  • Re: PMF with sander module (Wed Aug 14 2002 - 22:49:34 CDT)
  • Constant pressure MD problems (sander) (Mon Aug 12 2002 - 09:45:15 CDT)
  • Re: Leap error: PDB file with more than 10000 residues (Tue Aug 06 2002 - 16:47:00 CDT)
  • Leap error: PDB file with more than 10000 residues (Tue Aug 06 2002 - 14:50:04 CDT)
  • Umbrella sampling in AMBER (Wed Jul 24 2002 - 15:53:54 CDT)
• Prem Raj
  • Re: reg: MAC OS (Mon Oct 21 2002 - 13:19:40 CDT)
  • vlimit and vmax (Fri Sep 20 2002 - 12:27:07 CDT)
  • (no subject) (Fri Sep 20 2002 - 11:42:14 CDT)
  • npairs (Thu Sep 19 2002 - 17:22:42 CDT)
  • compiling without ISTAR2 (Thu Sep 19 2002 - 12:27:48 CDT)
• priestle
  • RE: What's this "interface" the tutorial talks about? (Wed Aug 28 2002 - 14:02:52 CDT)
• pu xuemei
  • disulfide bond link between two chains (Mon Dec 16 2002 - 06:50:35 CST)
• Qing Zhang
  • Amber 7 MM-PBSA for Amber 6 trajectories (Thu Dec 12 2002 - 13:52:23 CST)
  • Re: PROTON_INFO (Sat Aug 03 2002 - 20:12:24 CDT)
  • water molecules diffuse during equilibration (Tue Jul 16 2002 - 18:56:53 CDT)
  • Re: simulated annealing example (Wed Jul 10 2002 - 21:59:20 CDT)
  • heat up at constant pressure (Mon Jul 08 2002 - 17:05:19 CDT)
  • van der Waals, hydrogen bond energy (Fri Jun 28 2002 - 17:57:10 CDT)
  • taupt: time constant for heat bath coupling for the SOLUTE (Fri Jun 21 2002 - 18:44:55 CDT)
  • how to keep aromatic ring flat (Fri Jun 14 2002 - 18:00:51 CDT)
  • free energy for binding (Fri Jun 14 2002 - 17:50:54 CDT)
  • Re: model molecules for getting charges of DNA (Sun Jun 09 2002 - 14:47:04 CDT)
  • RESP on Deoxy-ADE (Tue Apr 23 2002 - 20:34:23 CDT)
  • RESP on Deoxy-ADE (Tue Apr 23 2002 - 20:34:23 CDT)
  • Re: RESP-ivary (Fri Apr 19 2002 - 11:15:27 CDT)
• quch quch
  • compile AMBER on cygwin? (Thu Feb 07 2002 - 13:46:43 CST)
• R.Sathyapriya
  • Clarification (Tue Jun 04 2002 - 02:45:19 CDT)
• Raik Grunberg
  • GBSA and surface crystal waters (Tue Sep 10 2002 - 09:44:20 CDT)
  • group selection for all heavy atoms ? (Fri Sep 06 2002 - 11:23:33 CDT)
  • Re: Follow distances during MD (Thu Apr 11 2002 - 07:49:16 CDT)
  • Re: removing rotational motion (Tue Feb 19 2002 - 06:30:00 CST)
  • Re: removing rotational motion (Tue Feb 19 2002 - 06:30:00 CST)
  • Re: Amino acid unit "NHE" problem ? (Thu Jan 17 2002 - 09:23:30 CST)
• Raja Swaminathan
  • average structure (Thu Sep 05 2002 - 12:16:03 CDT)
• Rajesh Korde
  • Amber 7 Installation (Tue Jul 09 2002 - 11:45:36 CDT)
• ramon kleber da rocha
  • compiling amber 7 with Intel Fortran Compiler 6.0 (Wed Sep 25 2002 - 14:23:21 CDT)
  • Re: compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 18:11:55 CDT)
  • compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 15:46:43 CDT)
  • problems runing gibbs on a IBM SP2 machine (Fri Aug 09 2002 - 09:48:11 CDT)
  • problemas running amber7 tests on a SP2 machine (Tue Jul 23 2002 - 15:33:28 CDT)
  • new problems compiling amber 7 (Thu Jul 11 2002 - 12:30:07 CDT)
  • new problems compiling amber 7 (Wed Jul 10 2002 - 08:11:52 CDT)
  • problems compiling Amber 7 (Fri Jul 05 2002 - 12:52:45 CDT)
  • Re: problems compiling Amber 7 (Tue Jul 02 2002 - 09:42:05 CDT)
  • problems compiling Amber 7 (Thu Jun 27 2002 - 12:18:50 CDT)
  • compiling amber 6.0 in a Sun starfire ENT10000 (Tue Apr 16 2002 - 14:08:54 CDT)
  • Are the programs sander and gibbs in Amber 7 parallel? (Wed Mar 06 2002 - 13:28:01 CST)
• Randy M. Wadkins
  • Re: BLOWUP after 100 ns??? (Thu Sep 19 2002 - 20:41:16 CDT)
  • Re: BLOWUP after 100 ns??? (Thu Sep 19 2002 - 16:39:48 CDT)
  • BLOWUP after 100 ns??? (Thu Sep 19 2002 - 15:51:28 CDT)
  • igb=2 in amber7 (Fri Aug 02 2002 - 17:28:48 CDT)
  • Re: sander input for a newbie (Wed Jun 12 2002 - 08:04:55 CDT)
  • sander input for a newbie (Tue Jun 11 2002 - 18:21:22 CDT)
  • Re: amber on MAC OSX (Fri Jun 07 2002 - 14:29:58 CDT)
  • Mac OS X compiliation? (Thu Jun 06 2002 - 16:58:18 CDT)
• Rebecca Perlow
  • Solvent exposed surface area over a trajectory (Thu Oct 17 2002 - 13:20:03 CDT)
  • Comparing simulations using Amber 5 and Amber 6 (Thu May 30 2002 - 09:18:36 CDT)
• Renee olano
  • Re: compile Moil-View, GL header files (Tue Sep 03 2002 - 11:54:57 CDT)
• rhertadi_at_bio.titech.ac.jp
  • Problem with atom type (Thu Mar 28 2002 - 15:55:33 CST)
• Richard Henchman
  • Re: SUMMARY: solvating a protein with large cavity (Wed Dec 18 2002 - 13:56:20 CST)
  • Re: loss of disulfide bonds (Mon Oct 14 2002 - 12:44:30 CDT)
• Richard Kho
  • help please :) (Fri Mar 15 2002 - 18:59:23 CST)
• Richard Stefl
  • RDC restraints (Mon Jul 08 2002 - 10:01:39 CDT)
• rino ragno
  • Amber tutorial (Sat Jun 15 2002 - 04:53:53 CDT)
• Robert Duke
  • Re: The atom number mismatch in coord and topology file in AMBER6. (Fri Jun 14 2002 - 11:27:00 CDT)
  • Re: Intel ifc Compiler (Thu May 30 2002 - 08:13:59 CDT)
• Robert G. Endres
  • default GB radii (Fri Dec 06 2002 - 15:00:31 CST)
• root
  • installing MPICH for AMBER on Linux CLuster (Mon Jul 08 2002 - 05:02:52 CDT)
• Rosalia Pascual
  • SHAKE problem (Wed Aug 07 2002 - 10:13:12 CDT)
  • NON-BONDED INTERACTION (Tue Jul 30 2002 - 09:41:49 CDT)
• Ross Walker
  • RE: PARMSET (Thu Nov 21 2002 - 08:30:36 CST)
  • RE: P4_GLOBMEMSIZE problem (Tue Nov 05 2002 - 17:04:03 CST)
  • RE: P4_GLOBMEMSIZE problem (Tue Nov 05 2002 - 11:16:55 CST)
  • RE: Not able to use xleap ... (Sat Oct 19 2002 - 04:51:30 CDT)
  • RE: Sander multiprocessors running problem with MPI (Wed Oct 02 2002 - 12:52:27 CDT)
  • RE: compiling without ISTAR2 (Thu Sep 19 2002 - 12:50:49 CDT)
  • RE: Beowulf killing jobs (Mon Sep 16 2002 - 09:46:45 CDT)
  • RE: Changing MAXINT (Mon Sep 16 2002 - 09:39:36 CDT)
  • RE: mpirun (Sun Sep 01 2002 - 17:36:24 CDT)
  • RE: trajectory file limit??? (Thu Aug 15 2002 - 16:48:30 CDT)
  • RE: Amber+Mosix (Sun Aug 11 2002 - 16:33:04 CDT)
  • RE: Amber/Gentoo linux (Sun Aug 11 2002 - 16:32:37 CDT)
  • RE: Dual AMD motherboards (Tue Jul 16 2002 - 02:31:56 CDT)
  • RE: RESP charges (Wed Apr 17 2002 - 10:28:58 CDT)
  • RE: RESP charges (Wed Apr 17 2002 - 08:21:37 CDT)
  • RE: Roar 2.1 with Amber7 (Wed Apr 10 2002 - 00:48:43 CDT)
• Rudesh Toofanny
  • Periodic water box (Fri Jun 14 2002 - 07:41:01 CDT)
• Rukman Hertadi
  • Re: Error decoding variable (Wed Jul 31 2002 - 20:50:27 CDT)
  • Error decoding variable (Wed Jul 31 2002 - 05:52:02 CDT)
  • nmropt problem in AMBER7 (Mon Mar 25 2002 - 03:51:22 CST)
  • combining trajectory file (Tue Mar 12 2002 - 03:48:49 CST)
  • rdparm error message (Sun Mar 10 2002 - 02:46:53 CST)
• S. Jang
  • Amino acid unit "NHE" problem ? (Thu Jan 17 2002 - 06:27:19 CST)
  • I can not see text in xleap ! (Wed Jan 16 2002 - 00:56:04 CST)
• S. Yamasaki
  • Using TIP4P water (Thu Jun 13 2002 - 20:05:48 CDT)
• Salinthip Thipayang
  • Questions about xleap and mm_pbsa (cont.2) (Tue Jul 23 2002 - 10:21:23 CDT)
  • Questions about xleap and mm_pbsa(cont.) (Tue Jul 23 2002 - 09:46:20 CDT)
  • Questions about xleap and mm_pbsa] (Fri Jul 19 2002 - 12:49:08 CDT)
  • help/suggestions needed with PROFEC (Fri May 03 2002 - 10:03:47 CDT)
  • Help/suggestions needed with PROFEC (Fri May 03 2002 - 09:40:41 CDT)
  • To PROFEC users (Fri Apr 19 2002 - 09:13:11 CDT)
• sam_008_at_www.com
  • RE:SAMUEL METU (Thu Oct 03 2002 - 20:46:51 CDT)
  • RE:SAMUEL METU (Thu Oct 03 2002 - 20:46:50 CDT)
• Samantha
  • Re: MS program ... (Sat Mar 23 2002 - 11:09:14 CST)
  • Lipid simulation, DMPC (Wed Feb 13 2002 - 10:24:20 CST)
• samantha hughes
  • Octane Box (equilibrated) (Wed Jul 24 2002 - 10:27:53 CDT)
  • Cholesterol PREP file (Wed Feb 27 2002 - 09:28:46 CST)
• Anonymous
  • non-zero 10-12 coefficient (Thu Nov 14 2002 - 18:18:34 CST)
• Sanjeev B.S.
  • Re: carnal output trajectory (Wed Oct 30 2002 - 07:50:45 CST)
  • Re: number of H-bonds (Sun Oct 20 2002 - 00:14:32 CDT)
  • Re: Solvent exposed surface area over a trajectory (Thu Oct 17 2002 - 14:18:56 CDT)
  • Imaging & fitting in carnal (Thu Oct 17 2002 - 06:01:55 CDT)
  • Re: crdgrow (Tue Oct 08 2002 - 12:24:09 CDT)
  • Re: restart without velocities (Wed Oct 02 2002 - 02:44:57 CDT)
  • Re: Carnal+HBond confusion (Tue Sep 24 2002 - 07:13:05 CDT)
  • Carnal+HBond confusion (Wed Sep 18 2002 - 23:18:36 CDT)
  • Re: ES40 hangs amber7 jobs. (Mon Sep 02 2002 - 21:29:45 CDT)
  • ES40 hangs amber7 jobs. (Thu Aug 29 2002 - 22:09:13 CDT)
  • Re: Scaling of Sander on Linux Clusters (fwd) (Tue Aug 27 2002 - 12:59:51 CDT)
  • amber7: ES40s (Tue Aug 27 2002 - 08:08:49 CDT)
  • Re: Scaling of Sander on Linux Clusters (fwd) (Tue Aug 27 2002 - 03:56:15 CDT)
  • Running amber7 on Param10000 (Wed Aug 14 2002 - 10:38:34 CDT)
  • Re: Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. (Wed Aug 07 2002 - 23:46:08 CDT)
  • Re: "number of processors must be a power of two" (Tue Aug 06 2002 - 11:17:35 CDT)
  • Benchmarks (Sat Aug 03 2002 - 00:48:09 CDT)
  • Re: new problems compiling amber 7 (Wed Jul 10 2002 - 09:57:40 CDT)
  • Re: Problem getting sander started (Wed Jul 10 2002 - 07:26:39 CDT)
  • Re: Amber 7 Installation (Tue Jul 09 2002 - 12:38:16 CDT)
  • Re: bug in .../sander/egb.f ? (Mon Jul 08 2002 - 14:08:09 CDT)
  • Re: Compilation ov Amber 7 (Sun Jun 30 2002 - 12:42:28 CDT)
  • Re: topology file generation (Mon May 06 2002 - 07:24:30 CDT)
  • topology file generation (Mon May 06 2002 - 00:36:36 CDT)
  • Re: How to run the leap module (Tue Apr 30 2002 - 05:37:11 CDT)
  • Amber6 & ES40 incompatability (Wed Mar 20 2002 - 01:01:17 CST)
  • leap:segmentation fault (Tue Feb 26 2002 - 10:30:45 CST)
  • restrt problem (Tue Feb 19 2002 - 07:50:41 CST)
  • MPICH/LAM on sparc (Sat Feb 16 2002 - 06:23:26 CST)
  • Latest parm + getting parm98 as default in LEaP (Mon Jan 21 2002 - 00:43:42 CST)
  • Amber6 + IBM SP3 (Sat Jan 19 2002 - 08:59:58 CST)
  • Re: removing rotational motion in MD (Wed Jan 09 2002 - 12:54:55 CST)
• Sankha Subhra Som
  • question (Tue Aug 27 2002 - 01:24:32 CDT)
  • Im lost (Tue Aug 20 2002 - 00:16:00 CDT)
• sara nunez
  • PARMSET (Thu Nov 21 2002 - 08:08:12 CST)
  • gibbs (Wed Aug 28 2002 - 14:52:56 CDT)
  • minimising WATBOX216 (Tue Jan 15 2002 - 13:11:04 CST)
  • xleap (Fri Jan 04 2002 - 17:28:14 CST)
• Sarah Tschampel
  • Re: not compiled with -DHAS_10_12!! (Thu Dec 05 2002 - 10:43:40 CST)
  • restraints in parm in amber7 (Tue Aug 27 2002 - 16:57:33 CDT)
  • Extra points (Thu Aug 15 2002 - 15:25:45 CDT)
  • Re:Re: Running TIP5P with PBC (Tue Jul 09 2002 - 12:32:32 CDT)
  • Running TIP5P with PBC (Wed Jul 03 2002 - 14:47:41 CDT)
• Sarangan Ravichandran
  • GBSA with IGB=2, setting the PBradii bondi (Fri Aug 30 2002 - 16:55:28 CDT)
  • Re: Minimization in GB-SA-E-Spikes, LINMIN (Tue Jul 16 2002 - 12:11:27 CDT)
  • Minimization in GB-SA-E-Spikes, LINMIN (Tue Jul 16 2002 - 10:02:58 CDT)
  • antechamber created prep file--Problem in xleap--additional info (Tue Jul 16 2002 - 09:06:31 CDT)
  • antechamber created prep file--Problem in xleap (Tue Jul 16 2002 - 08:54:45 CDT)
  • Net Charge is Different In The Sander Output!! (Tue Jul 09 2002 - 20:19:00 CDT)
  • eedmeth variable in AMBER7 (Tue Jul 09 2002 - 09:30:28 CDT)
  • Distance dependent vaccum energy minimization in AMBER7 (Fri Jul 05 2002 - 10:29:40 CDT)
  • TEST (Fri Jul 05 2002 - 07:43:37 CDT)
• Scott Brozell
  • Re: MPI_BCAST error (Wed Dec 18 2002 - 15:24:55 CST)
  • Re: Overwrite files (Thu Dec 05 2002 - 15:39:23 CST)
  • Re: amber on RH8 (Thu Nov 07 2002 - 15:13:14 CST)
  • Re: 64-bit Compilation SUN's forte compiler (Mon Oct 28 2002 - 18:00:08 CST)
  • Re: compiling amber 7 with Intel Fortran Compiler 6.0 (Wed Sep 25 2002 - 15:05:45 CDT)
  • Re: compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 19:16:40 CDT)
  • Re: compiling amber on a linux box using DMEM-ALLOC (Fri Sep 06 2002 - 17:01:27 CDT)
  • Re: parallel jobs die with no error message from sander (Mon Jul 29 2002 - 17:43:51 CDT)
• Sebastian Jayaraj
  • Amber on Tru64 (Tue Jan 08 2002 - 13:22:43 CST)
• SEKIJIMA Masakazu
  • Re: TIP4P (Fri May 31 2002 - 02:32:08 CDT)
  • TIP4P (Thu May 30 2002 - 03:43:14 CDT)
• sepideh ameli
  • (no subject) (Sun Aug 04 2002 - 14:01:20 CDT)
• Service
  • New Promotion Products at American Disc Corporation (Thu Jul 25 2002 - 14:56:47 CDT)
• shailendra singh
  • Re: Amber (Mon Mar 18 2002 - 23:57:48 CST)
• Shimono Fumihiro
  • Re: about AMBER parallel edition (Thu Oct 03 2002 - 06:46:14 CDT)
  • about AMBER parallel edition (Thu Oct 03 2002 - 06:07:36 CDT)
• Shixiang Yan
  • Re: corrupted trajectory (Tue Dec 03 2002 - 17:36:37 CST)
  • re: the removal of global motion (Tue Nov 12 2002 - 10:44:38 CST)
  • binding site volume (Thu Sep 12 2002 - 18:38:41 CDT)
  • Re: How to check whether the trajectory file matches the coordinates file or not? (Mon Sep 09 2002 - 13:53:04 CDT)
  • Re: problem with amber7 mpi (Thu Aug 01 2002 - 08:29:58 CDT)
  • RE: Water molecule numbering (Thu Jul 25 2002 - 21:28:02 CDT)
  • Re: Water molecule numbering (Thu Jul 25 2002 - 18:25:08 CDT)
  • Re: water box size (Fri Jul 19 2002 - 18:02:32 CDT)
  • s-matrix format and ftnmr (Wed Mar 27 2002 - 15:49:50 CST)
  • linux? (Thu Jan 03 2002 - 20:17:46 CST)
• Shunzhou Wan
  • period boundary (Fri Oct 11 2002 - 10:50:39 CDT)
• Sichun Yang
  • the tree name? (Tue Nov 26 2002 - 21:29:27 CST)
  • leap for peptide (Fri Nov 22 2002 - 16:33:51 CST)
  • targeted MD for more than 2 groups (Thu Nov 21 2002 - 15:20:44 CST)
  • makeDIST_RST? (Mon Nov 18 2002 - 17:44:09 CST)
  • saveAmberParm of leap (Mon Nov 11 2002 - 13:27:16 CST)
  • question on belly and restraint (Wed Oct 30 2002 - 14:54:37 CST)
  • Re: question on ouput of sander (Mon Oct 21 2002 - 13:45:29 CDT)
  • question on ouput of sander (Mon Oct 21 2002 - 13:19:17 CDT)
  • docking in amber? (Thu Oct 10 2002 - 18:44:45 CDT)
  • Some error message on Leap (Thu Oct 10 2002 - 15:15:43 CDT)
• Snyder, James
  • RE: AMBER7 and Movie (Fri Jul 19 2002 - 17:25:37 CDT)
  • simulated annealing example (Wed Jul 10 2002 - 15:42:43 CDT)
  • (no subject) (Sun Jun 09 2002 - 19:45:03 CDT)
• software_at_kagaku.com
  • Inquiry (Sun Nov 24 2002 - 21:44:51 CST)
• Soonmin Jang
  • RMSD calculation question (Fri Oct 04 2002 - 02:02:37 CDT)
  • Re: Strange MD simulation results with GB solvation at high temp. (Fri Sep 13 2002 - 00:21:32 CDT)
  • Re: Strange MD simulation results with GB solvation at high temp. (Tue Sep 10 2002 - 10:56:53 CDT)
  • Strange MD simulation results with GB solvation at high temp. (Tue Sep 10 2002 - 05:09:06 CDT)
  • PC (principal component) analysis (Tue Aug 20 2002 - 03:02:24 CDT)
  • Import of CHARMM force field and GB potential parameters into Amber7 (Sun Aug 04 2002 - 21:19:20 CDT)
  • Generalized Born and OPLS potential (Sat Aug 03 2002 - 03:05:27 CDT)
  • Re: "crd" file created with VMD (Wed Jul 24 2002 - 02:28:27 CDT)
  • "crd" file created with VMD (Tue Jul 23 2002 - 19:47:04 CDT)
  • "crd" file created with VMD (Tue Jul 23 2002 - 11:23:56 CDT)
  • Energy conservation in NVE simulation ? (Tue May 21 2002 - 00:42:40 CDT)
  • Amber7 compilation on IBM sp3 machine (Tue Apr 30 2002 - 23:33:05 CDT)
  • Amber7 and VMD (Wed Apr 10 2002 - 03:40:37 CDT)
  • Roar 2.1 with Amber7 (Tue Apr 09 2002 - 22:39:07 CDT)
• Sophia Kondratova
  • ptraj - BONDS_WITHOUT_HYDROGEN (Wed Sep 25 2002 - 11:54:48 CDT)
  • image command (Thu Aug 29 2002 - 12:46:01 CDT)
  • iwrap and image (Wed Aug 28 2002 - 07:55:36 CDT)
  • ewald bomb in md equilibration (Mon Aug 26 2002 - 17:54:37 CDT)
  • am1-bcc charges (Tue Aug 06 2002 - 13:26:22 CDT)
  • am1-bcc charges, antechamber (Wed Jul 24 2002 - 14:02:02 CDT)
  • md equilibration in chloroform (Mon Jul 08 2002 - 08:38:27 CDT)
  • (no subject) (Tue May 21 2002 - 13:37:24 CDT)
  • (no subject) (Mon May 06 2002 - 08:13:53 CDT)
  • valine to alanine example (Tue Apr 30 2002 - 10:23:21 CDT)
  • PMF calculations (Thu Apr 25 2002 - 08:30:11 CDT)
  • INTPRT and PMF (Tue Apr 23 2002 - 13:23:36 CDT)
  • frcmod file format (Mon Feb 11 2002 - 12:16:23 CST)
  • (no subject) (Mon Jan 14 2002 - 12:28:01 CST)
  • SCEE parameter (Wed Jan 09 2002 - 10:49:36 CST)
• SPEROLEEM_at_aol.com
  • (no subject) (Thu May 30 2002 - 17:51:26 CDT)
  • (no subject) (Mon Apr 22 2002 - 13:47:28 CDT)
  • Re: Release of Amber, version 7 (fwd) (Tue Mar 05 2002 - 16:16:27 CST)
• Stefan Andreev Andreev
  • mpi version of sander in Amber 6.0 with constraints (Wed Aug 14 2002 - 17:13:26 CDT)
  • Nanotubes with AMBER (Sun Aug 11 2002 - 18:59:26 CDT)
• Stéphane Teletchéa
  • Re: question (Tue Nov 19 2002 - 06:43:04 CST)
  • Re: help on VMD movie (Wed Nov 13 2002 - 07:12:58 CST)
  • Re: residue cross-correlation (Tue Nov 12 2002 - 04:57:10 CST)
  • Re: carnal (Mon Nov 04 2002 - 04:09:10 CST)
  • Re: carnal output trajectory (Wed Oct 30 2002 - 07:50:19 CST)
  • Re: Not able to use xleap ... (Mon Oct 21 2002 - 10:02:25 CDT)
  • Re: Not able to use xleap ... (Mon Oct 21 2002 - 02:08:12 CDT)
  • Re: Not able to use xleap ... (Fri Oct 18 2002 - 12:24:38 CDT)
  • Not able to use xleap ... (Fri Oct 18 2002 - 10:58:21 CDT)
  • Re: Dual Processor AMD vs. Single Processor (Thu Sep 12 2002 - 03:09:58 CDT)
  • Re: Scaling of Sander on Linux Clusters (fwd) (Tue Aug 27 2002 - 04:31:16 CDT)
  • Re: Scaling of Sander on Linux Clusters (fwd) (Tue Aug 27 2002 - 03:41:06 CDT)
  • Benchmark (Mon Jul 22 2002 - 11:55:14 CDT)
  • Re: Not able to image a snapshot. (Thu Jul 11 2002 - 03:24:48 CDT)
  • Not able to image a snapshot. (Wed Jul 10 2002 - 10:28:12 CDT)
  • Re: Origin300, Linux Cluster (Mon Jul 08 2002 - 07:37:37 CDT)
  • Re: Origin300, Linux Cluster (Fri Jul 05 2002 - 03:48:03 CDT)
  • Re: sander parallel (Fri Jun 14 2002 - 03:58:53 CDT)
  • Re: SHAKE troubles (Fri May 31 2002 - 04:45:48 CDT)
  • Re: MPich error (Wed May 29 2002 - 09:00:44 CDT)
  • Re: SHAKE troubles (Wed May 29 2002 - 05:50:12 CDT)
  • Re: Protonate doesn-t recognize by pdb input file (Thu May 23 2002 - 07:23:31 CDT)
  • Re: Protonate doesn-t recognize my pdb input file (Wed May 22 2002 - 06:41:08 CDT)
  • Re: "Unit 5 Error" with a Linux/MPICH Amber7 (Mon May 06 2002 - 11:22:42 CDT)
  • Re: sander mpich hangs (Fri Apr 26 2002 - 06:54:01 CDT)
  • Re: Initial Amber 7 benchmark timings (Thu Apr 04 2002 - 03:36:23 CST)
  • Still no bench (Tue Mar 19 2002 - 09:17:45 CST)
  • Re: Cholesterol PREP file (Thu Feb 28 2002 - 03:48:16 CST)
  • The link is out (Tue Feb 19 2002 - 10:58:44 CST)
  • Re: removing rotational motion (Tue Feb 19 2002 - 07:15:10 CST)
  • MP_Lite (Thu Jan 24 2002 - 11:44:40 CST)
  • Maxwell Boltzmann Distribution (Thu Jan 17 2002 - 08:48:02 CST)
  • Re: removing rotational motion in MD (Thu Jan 10 2002 - 02:35:54 CST)
  • Re: removing rotational motion in MD (Wed Jan 09 2002 - 12:04:30 CST)
  • Re: Not able to do parallel run (again) (Tue Jan 08 2002 - 10:21:07 CST)
  • Re: Not able to do parallel run (again) (Mon Jan 07 2002 - 11:08:17 CST)
• Sudhakar Pamidighantam
  • Re: Amber in a distributed environment (Wed Apr 17 2002 - 08:55:34 CDT)
• Sue Heavner
  • mm_pbsa-amber7 (Tue Oct 22 2002 - 14:06:01 CDT)
  • mm_pbsa (Fri Sep 20 2002 - 15:00:36 CDT)
  • Z DNA (Tue Sep 17 2002 - 14:55:04 CDT)
  • Amber7 nmode (Wed May 01 2002 - 12:23:19 CDT)
  • convergence of MD simulations (Thu Apr 04 2002 - 16:24:05 CST)
  • convergence of MD simulations (Sat Mar 30 2002 - 17:02:16 CST)
  • quasih (Wed Feb 06 2002 - 09:16:25 CST)
  • "flags" in .lib files (Wed Jan 23 2002 - 10:22:08 CST)
• Susanna Monti
  • box_size (Tue Jan 29 2002 - 04:34:22 CST)
• suvendu lomash
  • BondEn shoots in solvent minimization (Mon Sep 30 2002 - 10:50:39 CDT)
  • Is H-bonding really there? (Fri Sep 27 2002 - 14:59:48 CDT)
  • Pressure probs in MD (Thu Jul 25 2002 - 02:49:28 CDT)
• sxzheng
  • choose dt in gibbs (Sun Nov 17 2002 - 21:06:34 CST)
  • problem about cut and cap (Sun Nov 03 2002 - 06:40:25 CST)
  • How to choose the box and cap size (Thu Oct 31 2002 - 00:42:27 CST)
  • Can I use belly and ntr at the same time? (Wed Oct 16 2002 - 10:21:10 CDT)
  • volume of ucell too big!! (Fri Oct 11 2002 - 10:06:52 CDT)
  • about dummy parameter of multiplicity (Thu Oct 10 2002 - 02:55:15 CDT)
  • Re: Re:ERROR TERMINATION DUE TO SHAKE OR TORCON (Fri Jan 11 2002 - 21:21:30 CST)
• sychen
  • Re: a question about force field in AMBER (Sat Dec 14 2002 - 23:17:59 CST)
• Tadashi Takemori
  • Re: sander (CAP) chokes on efc (Itanium2/Linux) (Wed Dec 18 2002 - 03:38:25 CST)
  • sander (CAP) chokes on efc (Itanium2/Linux) (Tue Dec 17 2002 - 01:11:14 CST)
• Tali
  • Matching Patterns (Wed Apr 10 2002 - 16:57:59 CDT)
• telesales
  • Vulgar Models Do Everything And Love It!!! (Mon Apr 15 2002 - 19:03:45 CDT)
• thenmalar rathinavelan
  • regarding resp-doubts (Thu Oct 03 2002 - 03:21:51 CDT)
  • high electrostatic energy (Thu Mar 07 2002 - 23:13:40 CST)
• Therese Malliavin
  • offset of temperature when running MD with CAP and no periodic conditions (Thu Sep 19 2002 - 10:44:24 CDT)
  • electrostatics truncation in AMBER (Fri Jul 19 2002 - 08:21:59 CDT)
• Thijs Beuming
  • nmode vectors (Mon Jan 21 2002 - 06:24:48 CST)
  • multiple improper torsion terms (Fri Jan 11 2002 - 21:37:58 CST)
• Thomas A. Spraggins
  • RE: installing MPICH for AMBER on Linux CLuster (Mon Jul 08 2002 - 08:15:23 CDT)
  • RE: problems compiling Amber 7 (Fri Jul 05 2002 - 13:42:32 CDT)
  • Passing arguments with SP2 LoadLeveler (Mon Jun 24 2002 - 09:41:26 CDT)
  • bug in .../sander/egb.f ? (Thu Jun 20 2002 - 12:45:28 CDT)
  • RE: xaLeap make fails on AIX (Mon Jun 10 2002 - 11:13:01 CDT)
  • Parallel Amber on Solaris 2.6 (Mon Jun 03 2002 - 09:49:45 CDT)
• Thomas Cheatham
  • Re: problem in restrt (Fri Nov 22 2002 - 11:55:27 CST)
  • Re: Equilibration output Amber7 (Fri Nov 22 2002 - 11:49:55 CST)
  • Re: limit of RMSD value (Tue Nov 19 2002 - 11:51:53 CST)
  • Re: Sander: check COM velocity, temp: 0.000000 0.00(Removed) (Fri Nov 08 2002 - 23:49:21 CST)
  • Re: residue cross-correlation (Fri Nov 08 2002 - 14:50:42 CST)
  • Re: average and runningaverage in ptraj (Wed Nov 06 2002 - 11:36:56 CST)
  • Re: Is H-bonding really there? (Fri Sep 27 2002 - 15:53:24 CDT)
  • Re: watershell in ptraj (Tue Sep 24 2002 - 14:28:09 CDT)
  • Re: vlimit and vmax (Fri Sep 20 2002 - 14:14:11 CDT)
  • Re: Dynamic Movement of Molecule (Fri Sep 20 2002 - 14:01:39 CDT)
  • Re: Potential Energy and RMS-Deviation Issues (Thu Aug 01 2002 - 11:08:09 CDT)
  • RE: ptraj (Fri Jul 26 2002 - 14:15:04 CDT)
  • Re: PTRAJ: radial distribution function (Wed Jul 17 2002 - 16:47:24 CDT)
  • Re: ptraj problem (Mon Jun 24 2002 - 12:24:30 CDT)
  • Re: Periodic water box (Wed Jun 19 2002 - 22:57:04 CDT)
  • Re: vlimit exceeded (Wed Jun 12 2002 - 14:35:53 CDT)
  • Re: Amber7 and VMD (Wed Apr 10 2002 - 08:55:46 CDT)
  • Re: combining trajectory file (Tue Mar 12 2002 - 12:30:51 CST)
• Thomas E. Cheatham, III
  • Re: ion distances (Thu Nov 21 2002 - 17:54:46 CST)
  • Re: periodic box (Wed Jul 31 2002 - 09:26:49 CDT)
• Thomas Steinbrecher
  • MM-PBSA: .crg file for Delphi (Wed Dec 11 2002 - 12:08:40 CST)
  • ptraj rmsd calculation (Thu Dec 05 2002 - 14:15:40 CST)
  • Calculating atomic charges for AMBER with Gaussian98W (Sat Nov 23 2002 - 07:52:47 CST)
  • Re: equilibrium problem about cut and belly (Tue Nov 05 2002 - 11:24:54 CST)
  • Sander Recompilation for the Biotin-Streptavidin Tutorial? (Wed Oct 30 2002 - 09:46:30 CST)
  • old prmtop (Wed Sep 04 2002 - 10:56:47 CDT)
  • sander mpirun hangs with 4 CPU, but not with 2 (Tue Jul 30 2002 - 10:09:03 CDT)
  • compiling MPICH (Thu Jul 11 2002 - 07:46:12 CDT)
  • Problem getting sander started (Wed Jul 10 2002 - 07:24:00 CDT)
  • Re: installing MPICH for AMBER on Linux CLuster update (Mon Jul 08 2002 - 08:46:48 CDT)
• Thomas.Fox_at_bc.boehringer-ingelheim.com
  • parameters for cyclic nucleotides (Fri Nov 29 2002 - 04:11:43 CST)
  • parmchk -p option (Fri Nov 29 2002 - 04:09:09 CST)
  • RE: md equilibration in chloroform (Thu Jul 11 2002 - 12:51:47 CDT)
• Ting Wang
  • Re: Anal in AMBER7 (Mon Jul 22 2002 - 04:19:16 CDT)
  • Re: Anal in AMBER7 (Tue May 21 2002 - 07:48:48 CDT)
• TL Poulos
  • Question (Wed Jun 05 2002 - 10:49:10 CDT)
• Tod Pascal
  • simulating dna (Fri Nov 15 2002 - 19:23:54 CST)
  • Amber Perl module (Thu Nov 14 2002 - 15:33:01 CST)
  • Amber Crd format (Tue Oct 22 2002 - 13:21:05 CDT)
  • Amber 4 question (Fri Oct 18 2002 - 17:42:40 CDT)
• Tom Bishop
  • SUMMARY: solvating a protein with large cavity (Wed Dec 18 2002 - 09:03:27 CST)
  • solvating a protein with large cavity (Sat Dec 14 2002 - 09:42:38 CST)
  • Re: Visualizing AMBER coordinates trajectory in VMD (Tue Nov 05 2002 - 05:36:41 CST)
  • IGB =4 with GAFF and bugfix24 incomplete? (Wed Oct 16 2002 - 13:12:37 CDT)
  • IBELLY and NMROPT in sander (Thu Oct 10 2002 - 11:54:43 CDT)
  • geometry optimization/turning off Elec and Vdw terms (Mon Oct 07 2002 - 15:17:52 CDT)
  • antechamber best practices/charge equivalence w/ AM1-BCC (Mon Sep 23 2002 - 16:28:57 CDT)
  • simulation management tools (Fri Jul 05 2002 - 10:58:59 CDT)
• Toshikazu Matsuoka
  • Cyclodextrin (Wed May 29 2002 - 01:48:19 CDT)
• Tru
  • Re: problem compiling roar (mop7mm) on alpha (Tue Jul 23 2002 - 12:05:08 CDT)
  • Re: amber on MAC OSX (Mon Jun 10 2002 - 04:18:03 CDT)
  • Re: Sander, Setup for Parallel SMP Linux Cluster (Wed May 15 2002 - 14:40:45 CDT)
• UMEMOTO kimiko
  • resizing and recompiling sander (Mon Jan 14 2002 - 19:12:02 CST)
• Uwe Richter
  • RESP charges for phosphorylated residues (Tue May 28 2002 - 11:05:05 CDT)
  • atom connection, .off file problem (Wed Mar 20 2002 - 07:48:07 CST)
  • minimization problem (Tue Mar 19 2002 - 06:22:06 CST)
  • MPI sander (Thu Feb 21 2002 - 07:13:52 CST)
  • restart md simulation (Tue Jan 29 2002 - 03:35:50 CST)
  • sander (Amber5) vs sander_classic (Amber6) (Wed Jan 16 2002 - 05:33:32 CST)
  • azobenzene parameters (Tue Jan 15 2002 - 04:18:03 CST)
• vannajan_at_chiangmai.ac.th
  • RST file for nonstandard residue (Tue Dec 17 2002 - 03:07:04 CST)
  • C60 parameter (Thu Nov 28 2002 - 02:47:47 CST)
• Venkanna Belde
  • Sir, (Thu Oct 17 2002 - 04:33:18 CDT)
• Vickie Tsui
  • Re: makeDIP_RST.dna (Wed Jul 24 2002 - 18:49:57 CDT)
  • RE: automated rescoring of ligands (Tue May 14 2002 - 16:23:29 CDT)
• vijay dasa
  • Hello Amber, (Mon Oct 28 2002 - 04:20:24 CST)
  • Amber (Mon Oct 28 2002 - 00:51:02 CST)
• Viktor Hornak
  • Re: compile Moil-View, GL header files (Tue Sep 03 2002 - 11:12:22 CDT)
  • Re: Linux Parallel compilation Linux Mpich PGI (Mon May 27 2002 - 09:56:24 CDT)
• Vincent BOSQUIER
  • Problems with parallel computing in Amber7 (Tue May 14 2002 - 09:28:10 CDT)
  • RE: "Unit 5 Error" with a Linux/MPICH Amber7 (Mon May 06 2002 - 11:44:09 CDT)
  • "Unit 5 Error" with a Linux/MPICH Amber7 (Mon May 06 2002 - 10:50:07 CDT)
  • Compilation on RedHat-7.2 with MPICH (Thu May 02 2002 - 11:29:32 CDT)
  • RE: Problems with AMBER7 and Multiple Processors on SGI servers (Thu May 02 2002 - 03:55:45 CDT)
  • RE: Problems with AMBER7 and Multiple Processors on SGI servers (Tue Apr 30 2002 - 04:59:11 CDT)
  • Problems with AMBER7 and Multiple Processors on SGI servers (Fri Apr 26 2002 - 03:39:35 CDT)
• Vlad
  • Bug in reading binary restart file with BOX parameters (Tue Oct 15 2002 - 21:58:54 CDT)
  • Potential bug in gbsa.h of sander-7 (Mon Oct 14 2002 - 19:35:58 CDT)
• Vlad Cojocaru
  • ambpdb (Thu Dec 12 2002 - 16:01:23 CST)
  • positional restraints (Fri Dec 06 2002 - 06:55:05 CST)
  • DIANA like files (Wed Dec 04 2002 - 14:24:12 CST)
  • restrained MD (Wed Dec 04 2002 - 12:18:54 CST)
  • carnal amber 7.0 (Mon Dec 02 2002 - 02:35:34 CST)
  • defining groups on dif. sets in carnal (Tue Nov 19 2002 - 04:59:06 CST)
  • creating a pdb trajectory with carnal (Mon Nov 18 2002 - 09:29:21 CST)
  • drifting from average structure (Sat Nov 09 2002 - 10:17:38 CST)
  • more about averaging (Fri Nov 08 2002 - 08:12:00 CST)
  • averaging with ptraj and carnal (Fri Nov 08 2002 - 06:31:03 CST)
  • average and runningaverage in ptraj (Wed Nov 06 2002 - 09:40:51 CST)
  • carnal output trajectory (Wed Oct 30 2002 - 07:25:36 CST)
  • carnal output trajectory (Fri Oct 25 2002 - 04:50:55 CDT)
  • carnal output trajectory (Thu Oct 24 2002 - 15:07:35 CDT)
  • a leap question (Thu Oct 17 2002 - 08:20:23 CDT)
  • more information about the previous email (Wed Oct 16 2002 - 12:26:43 CDT)
  • error message (Wed Oct 16 2002 - 12:25:01 CDT)
  • pressure variation coupled with taup value (Mon Oct 14 2002 - 04:36:42 CDT)
  • different counterions for special type of DNA (Thu Sep 26 2002 - 07:59:31 CDT)
  • a freeware to display RMSD matrices (Thu Sep 19 2002 - 07:44:53 CDT)
  • the amino group of 2amino purine has strange behaviour (Thu Sep 12 2002 - 13:42:10 CDT)
  • sorry this is just a test (Thu Sep 12 2002 - 10:23:24 CDT)
  • just a test (Wed Sep 11 2002 - 08:39:59 CDT)
  • parameterization of a new class of compounds (nucleic acid base analogues) (Mon Sep 09 2002 - 04:40:05 CDT)
  • carnal averaging (Mon Sep 02 2002 - 06:43:33 CDT)
  • ewald bomb (Fri Aug 30 2002 - 08:38:49 CDT)
  • sorry!!!!maybe another stupid question (Wed Aug 28 2002 - 17:48:03 CDT)
  • a missing variable (Wed Aug 28 2002 - 15:43:04 CDT)
  • difference 94 99 force field (Tue Aug 27 2002 - 08:34:11 CDT)
  • segmentation fault (Tue Aug 20 2002 - 16:21:30 CDT)
  • trajectory file limit??? (Thu Aug 15 2002 - 11:43:54 CDT)
  • a question about carnal (Wed Aug 14 2002 - 11:39:36 CDT)
  • Carnal stream problem (Wed Aug 14 2002 - 09:45:04 CDT)
  • a problem with AMBER7 (Thu Jun 27 2002 - 05:12:58 CDT)
  • ptraj problem (Mon Jun 24 2002 - 10:54:32 CDT)
  • CARNAL (Thu May 23 2002 - 05:35:29 CDT)
  • crdgrow (Sat May 04 2002 - 15:06:32 CDT)
  • new RNA residues (Thu May 02 2002 - 14:07:32 CDT)
  • parmjoin (Mon Apr 29 2002 - 11:53:01 CDT)
  • a more general question (Tue Apr 23 2002 - 09:20:34 CDT)
  • a problem (Mon Apr 22 2002 - 10:56:48 CDT)
  • RESP (Mon Apr 22 2002 - 05:17:17 CDT)
  • RESP-ivary (Fri Apr 19 2002 - 06:26:22 CDT)
  • RESP charges (Wed Apr 17 2002 - 07:36:43 CDT)
  • RESP charges (Wed Apr 17 2002 - 05:53:27 CDT)
  • new residues (Thu Apr 04 2002 - 07:03:37 CST)
  • new units (Fri Mar 08 2002 - 08:35:46 CST)
  • parameter estimation (Thu Mar 07 2002 - 12:32:25 CST)
  • converting some files (Thu Mar 07 2002 - 05:00:00 CST)
  • a question about .in files (Wed Mar 06 2002 - 09:00:02 CST)
• Vojta Klusak
  • scaleCharges (Mon Mar 11 2002 - 03:45:54 CST)
• Walter Langel
  • Re: installing MPICH for AMBER on Linux CLuster (Mon Jul 08 2002 - 07:26:36 CDT)
• wang lan
  • new telescopes-Maksutov-Cassegrain, reflector, refractor (Tue Oct 15 2002 - 06:42:50 CDT)
  • new telescopes-Maksutov-Cassegrain, reflector, refractor (Tue Oct 15 2002 - 06:13:49 CDT)
• wentaofu
  • mm_pbsa question. (Tue Sep 17 2002 - 10:35:59 CDT)
• Wiktor Jurkowski
  • leap - sander information flow (Mon Oct 28 2002 - 06:34:51 CST)
  • Re: regarding resp-doubts (Thu Oct 03 2002 - 10:41:13 CDT)
• William Gropp
  • Re: Parallel Amber on Solaris 2.6 (Mon Jun 03 2002 - 14:20:26 CDT)
• William Wei
  • RESTARTED DUE TO LINMIN FAILURE (Thu Dec 19 2002 - 13:33:07 CST)
  • mm_pbsa error message! (Wed Dec 18 2002 - 11:17:16 CST)
  • not compiled with -DHAS_10_12!! (Thu Dec 05 2002 - 10:29:22 CST)
  • Amber 7 bugfix 27 !! urgent (Wed Dec 04 2002 - 14:45:13 CST)
  • Bugfixes (Wed Nov 06 2002 - 03:50:35 CST)
  • Sander multiprocessors running problem with MPI (Wed Oct 02 2002 - 13:09:49 CDT)
  • Can we get trajectories coordinates after FIT in Carnal? (Wed Aug 14 2002 - 16:52:34 CDT)
  • Memory and swap in sander (Mon Aug 12 2002 - 10:11:35 CDT)
  • RE: correction about solvateOct (Fri Jul 19 2002 - 10:18:53 CDT)
  • Suggestion to Bill and Case (Fri Jun 07 2002 - 15:49:10 CDT)
  • RE: Mutations - Molecular Dynamics (Mon May 27 2002 - 10:21:04 CDT)
  • Mutations - Molecular Dynamics (Thu May 16 2002 - 18:11:36 CDT)
  • RE: Carnal BUG?? --- How can I get the correct residue number? (Thu May 02 2002 - 12:48:10 CDT)
  • RE: Carnal BUG?? --- How can I get the correct residue number? (Thu May 02 2002 - 11:09:21 CDT)
  • Carnal BUG?? (Wed May 01 2002 - 22:19:03 CDT)
  • Fail message:Segmantation fault and Bus error? (Mon Apr 29 2002 - 14:38:48 CDT)
  • About Group in Carnal (Thu Apr 25 2002 - 10:50:08 CDT)
  • What is the atoms limit for Amber 7? (Wed Mar 27 2002 - 16:19:34 CST)
• Wolfe, Jennifer
  • Post-doctoral position (Mon Mar 18 2002 - 10:33:11 CST)
• Wu, JianHui(IAF)(LAVAL)
  • Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) (Thu Mar 28 2002 - 11:56:04 CST)
• X. Tan
  • Re: polarizabitlity (Tue Nov 19 2002 - 12:08:31 CST)
  • polarizabitlity (Fri Nov 15 2002 - 19:41:37 CST)
  • dummy torsional parameters again. (Thu Oct 17 2002 - 11:52:05 CDT)
  • image (Thu Sep 19 2002 - 12:32:15 CDT)
  • how to detect bad contact? (Wed Sep 04 2002 - 14:14:40 CDT)
  • PME in gibbs module (Tue Jul 16 2002 - 15:29:27 CDT)
  • parameters for Zn2+ bond to CYS- (Wed Jun 19 2002 - 19:23:16 CDT)
  • entropy calculation (Mon Jun 10 2002 - 18:42:59 CDT)
  • mm_pbsa (Mon May 20 2002 - 18:04:52 CDT)
  • about ew_legal.h (Tue Apr 30 2002 - 19:12:01 CDT)
  • question on Gibbs calculation (Tue Mar 12 2002 - 15:50:24 CST)
  • Re: questions about resp (Tue Mar 12 2002 - 15:02:22 CST)
  • ERROR from RESNBA (Tue Feb 19 2002 - 19:39:21 CST)
  • memory problem on gibbs (Thu Feb 14 2002 - 18:24:55 CST)
  • help on parameters. (Mon Feb 04 2002 - 19:40:52 CST)
  • how to neutralise the system? (Mon Jan 14 2002 - 13:18:14 CST)
  • questions about resp (Tue Jan 08 2002 - 10:31:55 CST)
• x357l
  • Xleap (Tue Feb 19 2002 - 10:03:11 CST)
  • parm94.dat file (Tue Feb 12 2002 - 12:21:44 CST)
• Xavier Deupi
  • Re: building general solvent boxes with leap (Thu Jul 18 2002 - 18:16:17 CDT)
  • building general solvent boxes with leap (Wed Jul 17 2002 - 12:19:28 CDT)
• Xiang Mao
  • pbc in amber (Thu Aug 29 2002 - 08:00:04 CDT)
  • problem in MD (Tue Aug 27 2002 - 19:05:11 CDT)
• xz27
  • inquiry regarding AMBER (Thu Jan 10 2002 - 15:24:08 CST)
• Y Fang
  • Re: AMBER7 and Movie (Mon Jul 22 2002 - 15:58:23 CDT)
  • AMBER7 and Movie (Fri Jul 19 2002 - 16:03:22 CDT)
• yao yong
  • amber question (Mon Sep 16 2002 - 06:03:16 CDT)
• Yi ming Cheng
  • PME box ? (Wed Jun 05 2002 - 07:11:15 CDT)
  • help ..problem about antechamber (Sat Apr 13 2002 - 00:30:26 CDT)
• Ying Zhao
  • How to do 2dRMS in ptraj (Thu Oct 10 2002 - 14:33:43 CDT)
• Yong Duan
  • RE: Overwrite files (Thu Dec 05 2002 - 20:41:37 CST)
  • RE: Please help. Energy suddenly increase. Protein jump out (Wed Nov 27 2002 - 16:52:54 CST)
  • RE: Please help. Energy suddenly increase. Protein jump out (Wed Nov 27 2002 - 12:42:39 CST)
  • RE: question (Fri Nov 15 2002 - 22:40:56 CST)
  • RE: force field name (Thu Aug 15 2002 - 11:11:19 CDT)
  • Re: SHAKE troubles (Wed May 29 2002 - 07:33:14 CDT)
• Yongjun Jiang
  • Trajectory file converted in pdb file (Sun Dec 29 2002 - 19:13:38 CST)
  • combinig two trajectory files. (Mon Dec 02 2002 - 06:18:29 CST)
  • nonpeoridic boundary + mm/gbsa (Mon Nov 11 2002 - 06:49:03 CST)
  • question about nmode again. (Tue Sep 17 2002 - 02:15:54 CDT)
  • why are the results so large difference calculating by mm_pbsaandmm_gbsa? (Thu Sep 12 2002 - 02:25:32 CDT)
  • nmode compile question? (Tue Sep 10 2002 - 07:46:18 CDT)
  • why are the results so large difference calculating by mm_pbsa and mm_gbsa? (Tue Sep 10 2002 - 02:18:46 CDT)
  • test of mm_pbsa (Tue Jun 11 2002 - 22:08:23 CDT)
  • Re: GROUP Specification - Error decoding variable (Thu May 30 2002 - 03:23:57 CDT)
  • dummy atoms. (Sat Apr 20 2002 - 22:20:44 CDT)
• Yu Chen
  • Amber6 and MPI (Wed Oct 23 2002 - 13:10:30 CDT)
• yuann
  • Re: cannot deal with large trajectory? (Mon Dec 30 2002 - 20:55:41 CST)
  • cannot deal with large trajectory? (Sat Dec 28 2002 - 21:17:23 CST)
  • specification for memory requirement (Fri Oct 25 2002 - 19:37:13 CDT)
  • Re: Compiler & Hardware requirement of AMBER7 ? (Tue Oct 22 2002 - 09:30:34 CDT)
  • Compiler & Hardware requirement of AMBER7 ? (Mon Oct 14 2002 - 23:08:12 CDT)
  • non-bonded metal ion in complex (Tue Sep 17 2002 - 01:28:45 CDT)
  • add DUMMY atom into coordinate file (Fri Aug 16 2002 - 04:12:04 CDT)
  • Gibbs tutorial problem (Wed Jul 24 2002 - 19:40:50 CDT)
  • looking for frcmod in AMBER Tutorials (Fri Jul 12 2002 - 04:19:45 CDT)
  • create new atom problem on xleap (Thu Jul 04 2002 - 15:04:01 CDT)
  • box size & 1st equilibrium (Fri Jun 28 2002 - 01:16:51 CDT)
  • GROUP Specification - Error decoding variable (Thu May 30 2002 - 02:43:02 CDT)
  • minimization to fix up hydrogen positions (Wed May 29 2002 - 02:33:23 CDT)
  • Number of WATBOX (Thu Apr 25 2002 - 00:54:02 CDT)
• Yuguang Mu
  • j3 coupling (Fri Jun 21 2002 - 05:38:31 CDT)
  • glucose (Tue May 28 2002 - 10:05:10 CDT)
  • Re: Junmei et al. 1999 (Wed May 22 2002 - 04:30:29 CDT)
  • heterochirical peptides ? (Tue Apr 30 2002 - 10:43:39 CDT)
  • Re: visualizaion program for NMODE! (Thu Feb 28 2002 - 02:56:44 CST)
  • Re: vlimit exceed (Fri Feb 22 2002 - 01:44:53 CST)
• Yuuki Komata
  • Dynamic Movement of Molecule (Fri Sep 20 2002 - 03:03:48 CDT)
• Zhang Jian
  • Re: help! Non bond list overflow! (Wed Nov 13 2002 - 20:10:02 CST)
  • Re: help on VMD movie (Wed Nov 13 2002 - 19:40:14 CST)
  • Re: help on VMD movie (Wed Nov 13 2002 - 09:21:30 CST)
  • help on VMD movie (Wed Nov 13 2002 - 06:44:36 CST)
  • help! Non bond list overflow! (Wed Nov 13 2002 - 04:56:39 CST)
  • Re: belly and EWALD in amber7 (Sun Nov 10 2002 - 19:36:25 CST)
  • belly and EWALD in amber7 (Sat Nov 09 2002 - 21:04:14 CST)
  • about amber and charmm, thanks (Sun Sep 08 2002 - 04:10:57 CDT)
• Zhe SUN
  • One question about how to use the amber (Tue Mar 26 2002 - 06:49:35 CST)
• zhongh_at_umich.edu
  • nmode segmentation fault (Thu Aug 08 2002 - 08:56:08 CDT)
• 남기엽
  • Re: ion distances (Thu Nov 21 2002 - 16:52:55 CST)