AMBER Archive (2006) - Nov 2006 By DateMost recent messages
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Starting: Wed Nov 01 2006 - 02:38:55 CST
Ending: Thu Nov 30 2006 - 19:28:10 CST
- AMBER: Mass weights Sergey Samsonov (Wed Nov 01 2006 - 02:41:33 CST)
- Re: AMBER: Closest(closest water) Sergey Samsonov (Wed Nov 01 2006 - 02:38:55 CST)
- AMBER: How to start a Simulation of a peptide in bilayer nur avneet (Wed Nov 01 2006 - 03:28:31 CST)
- AMBER: ab initio terminology query HL Eastwood (Wed Nov 01 2006 - 05:38:24 CST)
- Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 05:59:04 CST)
- AMBER: PCA and projections Miguel Ferreira (Wed Nov 01 2006 - 08:11:57 CST)
- AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Wed Nov 01 2006 - 10:22:54 CST)
- AMBER: grid output Sergey Samsonov (Wed Nov 01 2006 - 10:31:34 CST)
- AMBER: GBSA implicit chloroform nadiav_at_soton.ac.uk (Wed Nov 01 2006 - 10:41:18 CST)
- RE: AMBER: ab initio terminology query Ross Walker (Wed Nov 01 2006 - 10:44:22 CST)
- Re: AMBER: ab initio terminology query Gustavo Seabra (Wed Nov 01 2006 - 10:50:27 CST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft David A. Case (Wed Nov 01 2006 - 10:54:06 CST)
- Re: AMBER: GBSA implicit chloroform David A. Case (Wed Nov 01 2006 - 10:56:07 CST)
- AMBER: NEWPDB.PDB from antechamber Esther Brugger (Wed Nov 01 2006 - 10:59:29 CST)
- AMBER: too big EEL values in the minimisation output Rachel (Wed Nov 01 2006 - 11:01:17 CST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Wed Nov 01 2006 - 11:02:26 CST)
- Re: AMBER: GBSA implicit chloroform nadiav_at_soton.ac.uk (Wed Nov 01 2006 - 11:13:22 CST)
- RE: AMBER: NEWPDB.PDB from antechamber Junmei Wang (Wed Nov 01 2006 - 11:19:27 CST)
- RE: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Ross Walker (Wed Nov 01 2006 - 11:21:02 CST)
- Re: AMBER: GBSA implicit chloroform Adrian Roitberg (Wed Nov 01 2006 - 11:22:14 CST)
- Re: AMBER: ab initio terminology query David A. Case (Wed Nov 01 2006 - 11:30:50 CST)
- Re: AMBER: mm_pbsa does not terminate Holly Freedman (Wed Nov 01 2006 - 11:56:28 CST)
- Re: AMBER: too big EEL values in the minimisation output darden (Wed Nov 01 2006 - 12:08:27 CST)
- Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 12:27:44 CST)
- Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 12:34:57 CST)
- RE: AMBER: ab initio terminology query Yong Duan (Wed Nov 01 2006 - 12:53:39 CST)
- Re: AMBER: ab initio terminology query Adrian Roitberg (Wed Nov 01 2006 - 13:01:38 CST)
- RE: AMBER: NEWPDB.PDB from antechamber Esther Brugger (Wed Nov 01 2006 - 13:10:20 CST)
- Re: AMBER: mm_pbsa does not terminate Holly Freedman (Wed Nov 01 2006 - 13:34:17 CST)
- Re: AMBER: ab initio terminology query Jiri Sponer (Wed Nov 01 2006 - 13:43:13 CST)
- RE: AMBER: NEWPDB.PDB from antechamber Junmei Wang (Wed Nov 01 2006 - 13:42:42 CST)
- AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Wed Nov 01 2006 - 13:50:28 CST)
- RE: AMBER: ab initio terminology query Hayden Eastwood (Wed Nov 01 2006 - 14:12:49 CST)
- RE: AMBER: ab initio terminology query Ilyas Yildirim (Wed Nov 01 2006 - 14:38:58 CST)
- Re: AMBER: ab initio terminology query David A. Case (Wed Nov 01 2006 - 14:42:23 CST)
- RE: AMBER: ab initio terminology query Ross Walker (Wed Nov 01 2006 - 14:51:43 CST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Wed Nov 01 2006 - 15:36:17 CST)
- AMBER: How the ensemble average calculated in Gibbs, AMBER7? Yongmei Pan (Wed Nov 01 2006 - 16:06:09 CST)
- RE: AMBER: ab initio terminology query Yong Duan (Wed Nov 01 2006 - 17:17:43 CST)
- [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Wed Nov 01 2006 - 17:25:25 CST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Wed Nov 01 2006 - 18:04:28 CST)
- Re: AMBER: problem installing amber9 with g95 gcc on a fc5 m/c Sayandeep Purkayasth (Thu Nov 02 2006 - 00:48:03 CST)
- [RE]RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Lee Kyung-koo (Thu Nov 02 2006 - 02:53:53 CST)
- AMBER: leap usage Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Nov 02 2006 - 03:41:34 CST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Rafi Ahmad (Thu Nov 02 2006 - 03:51:18 CST)
- AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 wenfei Li (Thu Nov 02 2006 - 06:44:18 CST)
- Re: AMBER: leap usage Mark Williamson (Thu Nov 02 2006 - 09:26:42 CST)
- Re: AMBER: leap usage Angelo (Thu Nov 02 2006 - 10:39:57 CST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Thu Nov 02 2006 - 11:05:38 CST)
- RE: AMBER: Problem of QM/MM calculation with amber 9 parallel version Ross Walker (Thu Nov 02 2006 - 11:17:42 CST)
- Re: AMBER: too big EEL values in the minimisation output Rachel (Thu Nov 02 2006 - 12:08:00 CST)
- Re: AMBER: too big EEL values in the minimisation output darden (Thu Nov 02 2006 - 13:13:29 CST)
- Re: AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8 Carlos Simmerling (Thu Nov 02 2006 - 14:28:33 CST)
- AMBER: Interaction Energy Calculation Varsha Goyal (Thu Nov 02 2006 - 15:34:28 CST)
- Re: AMBER: Interaction Energy Calculation Vitor Manuel Sousa F?x (Thu Nov 02 2006 - 16:08:01 CST)
- Re: AMBER: Interaction Energy Calculation Varsha Goyal (Thu Nov 02 2006 - 17:04:12 CST)
- AMBER: ntt=1 in simulated annealing Tanya Johannsen (Thu Nov 02 2006 - 21:44:19 CST)
- AMBER: how to choose the parameter for the production/sampling run after the equilibration run hbluo (Fri Nov 03 2006 - 19:57:01 CST)
- Re: AMBER: ntt=1 in simulated annealing Carlos Simmerling (Fri Nov 03 2006 - 05:48:06 CST)
- Re: AMBER: too big EEL values in the minimisation output Rachel (Fri Nov 03 2006 - 06:09:54 CST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Fri Nov 03 2006 - 09:18:35 CST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Ross Walker (Fri Nov 03 2006 - 10:39:22 CST)
- AMBER: Problems with equilibrating the starting density Markus Weingarth (Fri Nov 03 2006 - 11:32:20 CST)
- AMBER: Simulation a small chain of amino acids - error in MD simulation Dave, Sonya (Fri Nov 03 2006 - 11:54:06 CST)
- Re: AMBER: Simulation a small chain of amino acids - error in MD simulation Carlos Simmerling (Fri Nov 03 2006 - 12:05:22 CST)
- RE: AMBER: Simulation a small chain of amino acids - error in MD simulation Ross Walker (Fri Nov 03 2006 - 12:32:27 CST)
- AMBER: pmemd installation problem Ed Pate (Fri Nov 03 2006 - 12:51:36 CST)
- Re: AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft Yu Chen (Fri Nov 03 2006 - 13:05:55 CST)
- Re: AMBER: pmemd installation problem Robert Duke (Fri Nov 03 2006 - 13:09:52 CST)
- RE: AMBER: Simulation a small chain of amino acids - error in MD simulation Dave, Sonya (Fri Nov 03 2006 - 13:20:55 CST)
- RE: AMBER: Problems with equilibrating the starting density Ross Walker (Fri Nov 03 2006 - 13:41:55 CST)
- AMBER: Re: Fluorine and Bromine Parameters in Amber 9 Philip Cheung (Fri Nov 03 2006 - 13:56:52 CST)
- Re: AMBER: ntt=1 in simulated annealing Tanya Johannsen (Fri Nov 03 2006 - 18:38:38 CST)
- RE: AMBER: ntt=1 in simulated annealing Ross Walker (Fri Nov 03 2006 - 20:04:08 CST)
- AMBER: I got the error meassage in testcase of QMMM Lee Kyung-koo (Fri Nov 03 2006 - 23:33:44 CST)
- AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Sat Nov 04 2006 - 02:45:25 CST)
- AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Sat Nov 04 2006 - 02:58:25 CST)
- AMBER: Unable to find solution for an error - "cannot successfully assign bond type" Rama krishnan (Sat Nov 04 2006 - 04:06:51 CST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Adrian Roitberg (Sat Nov 04 2006 - 07:00:40 CST)
- AMBER: Ross Walker (Sat Nov 04 2006 - 11:35:43 CST)
- AMBER: RE: I got the error meassage in testcase of QMMM Ross Walker (Sat Nov 04 2006 - 12:09:13 CST)
- AMBER: ACS Chicago potential symposia and OASYS abstracts Thomas Cheatham (Sat Nov 04 2006 - 15:04:47 CST)
- AMBER: Amber: disufide bond Fenghui Fan (Sat Nov 04 2006 - 22:29:57 CST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Fenghui Fan (Sun Nov 05 2006 - 00:31:25 CST)
- RE: AMBER: Amber: disufide bond hayden (Sun Nov 05 2006 - 07:03:23 CST)
- RE: AMBER: Amber: disufide bond Fenghui Fan (Sun Nov 05 2006 - 08:02:48 CST)
- AMBER: trajout script Fenghui Fan (Sun Nov 05 2006 - 10:23:57 CST)
- AMBER: Combine amber-force field and gaff94 for one molecule? Michel Becker (Sun Nov 05 2006 - 11:45:05 CST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Fenghui Fan (Sun Nov 05 2006 - 12:30:27 CST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? M. L. Dodson (Sun Nov 05 2006 - 13:35:34 CST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Fenghui Fan (Sun Nov 05 2006 - 14:13:57 CST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? M. L. Dodson (Sun Nov 05 2006 - 14:47:22 CST)
- Re: AMBER: Combine amber-force field and gaff94 for one molecule? Jiri Sponer (Sun Nov 05 2006 - 16:01:27 CST)
- AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung (Sun Nov 05 2006 - 17:16:34 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Peter Gannett (Sun Nov 05 2006 - 17:40:18 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Fenghui Fan (Sun Nov 05 2006 - 18:22:26 CST)
- Re: AMBER: How the ensemble average calculated in Gibbs, AMBER7? David A. Case (Sun Nov 05 2006 - 21:26:02 CST)
- AMBER: Zn metal library Fenghui Fan (Sun Nov 05 2006 - 21:51:19 CST)
- AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Sun Nov 05 2006 - 23:59:38 CST)
- RE: AMBER: Zn metal library Ross Walker (Mon Nov 06 2006 - 00:08:20 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Andreas Svrcek-Seiler (Mon Nov 06 2006 - 03:17:11 CST)
- AMBER: Potential Energy Calculation sangeeta (Mon Nov 06 2006 - 06:11:30 CST)
- Re: AMBER: Zn metal library Carlos Simmerling (Mon Nov 06 2006 - 06:26:52 CST)
- Re: AMBER: Potential Energy Calculation Carlos Simmerling (Mon Nov 06 2006 - 06:32:35 CST)
- RE: AMBER: Potential Energy Calculation Hayden Eastwood (Mon Nov 06 2006 - 06:47:00 CST)
- AMBER: problem with NAD+ parameters Urszula Uciechowska (Mon Nov 06 2006 - 08:27:16 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Margaret S. Cheung (Mon Nov 06 2006 - 09:23:29 CST)
- AMBER: PCA results with explicit Vs Implicit solvation Keerthi Gottipati (Mon Nov 06 2006 - 10:32:16 CST)
- Re: AMBER: PCA results with explicit Vs Implicit solvation Angelo (Mon Nov 06 2006 - 11:14:47 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Andreas Svrcek-Seiler (Mon Nov 06 2006 - 11:13:37 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Scott Pendley (Mon Nov 06 2006 - 11:20:43 CST)
- Re: AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5? Scott Pendley (Mon Nov 06 2006 - 11:28:48 CST)
- Re: AMBER: trajout script Thomas Cheatham (Mon Nov 06 2006 - 14:39:04 CST)
- Re: AMBER: Potential Energy Calculation Mingfeng Yang (Mon Nov 06 2006 - 15:06:18 CST)
- AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Mon Nov 06 2006 - 15:40:50 CST)
- Re: AMBER: Mutual exclusion of atoms Thomas Steinbrecher (Mon Nov 06 2006 - 16:02:47 CST)
- Re: AMBER: problem with NAD+ parameters Cenk Andac (Mon Nov 06 2006 - 16:05:52 CST)
- Re: AMBER: Mutual exclusion of atoms Nitin Bhardwaj (Mon Nov 06 2006 - 16:27:49 CST)
- top2mol2.c scanf format string bug Chris Moth (Mon Nov 06 2006 - 18:19:36 CST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data Thomas Cheatham (Mon Nov 06 2006 - 22:18:20 CST)
- Re: AMBER: grid output Thomas Cheatham (Mon Nov 06 2006 - 22:30:25 CST)
- Re: AMBER: Mass weights Thomas Cheatham (Mon Nov 06 2006 - 22:58:54 CST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Tue Nov 07 2006 - 00:44:35 CST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data David A. Case (Tue Nov 07 2006 - 01:26:13 CST)
- Re: AMBER: PTRAJ RMS: dumping RMSd vs time data r. a. (Tue Nov 07 2006 - 01:41:35 CST)
- Re: AMBER: Mass weights Sergey Samsonov (Tue Nov 07 2006 - 02:06:14 CST)
- Re: AMBER: grid output Sergey Samsonov (Tue Nov 07 2006 - 02:35:28 CST)
- AMBER: leap - compilation error Tomas Kubar (Tue Nov 07 2006 - 03:47:33 CST)
- Re: AMBER: ntt=1 in simulated annealing Steven Winfield (Tue Nov 07 2006 - 05:26:28 CST)
- AMBER: klambda for TI method. Biswa Ranjan Meher (Tue Nov 07 2006 - 06:59:15 CST)
- Re: AMBER: klambda for TI method. David A. Case (Tue Nov 07 2006 - 10:06:21 CST)
- Re: AMBER: top2mol2.c scanf format string bug David A. Case (Tue Nov 07 2006 - 10:18:43 CST)
- Re: AMBER: grid output Thomas Cheatham (Tue Nov 07 2006 - 10:25:39 CST)
- Re: AMBER: grid output Sergey Samsonov (Tue Nov 07 2006 - 10:46:07 CST)
- [RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo (Tue Nov 07 2006 - 10:46:25 CST)
- AMBER: building a box kepa koldo burusco (Tue Nov 07 2006 - 10:52:28 CST)
- [RE]AMBER: RE: I got the error meassage in testcase of QMMM Lee Kyung-koo (Tue Nov 07 2006 - 10:59:16 CST)
- Re: AMBER: building a box Fenghui Fan (Tue Nov 07 2006 - 11:49:54 CST)
- AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) Nitin Bhardwaj (Tue Nov 07 2006 - 15:08:42 CST)
- AMBER: error about the number of snapshots AYTUG TUNCEL (Tue Nov 07 2006 - 15:11:24 CST)
- Re: AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST) David A. Case (Tue Nov 07 2006 - 19:51:48 CST)
- Re: AMBER: leap - compilation error David A. Case (Tue Nov 07 2006 - 20:25:37 CST)
- AMBER: Atom Exclusion Nitin Bhardwaj (Tue Nov 07 2006 - 23:44:30 CST)
- AMBER: Re: Unit of force Kakali Sen (Wed Nov 08 2006 - 00:41:30 CST)
- AMBER: question about the topology file J. Zhang (Wed Nov 08 2006 - 03:24:10 CST)
- AMBER: Unit of force Kakali Sen (Wed Nov 08 2006 - 05:06:16 CST)
- Re: AMBER: building a box kepa koldo burusco (Wed Nov 08 2006 - 06:08:32 CST)
- Re: AMBER: question about the topology file Carlos Simmerling (Wed Nov 08 2006 - 06:18:58 CST)
- Re: AMBER: Unit of force Adrian Roitberg (Wed Nov 08 2006 - 06:57:00 CST)
- AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Wed Nov 08 2006 - 06:59:00 CST)
- Re: AMBER: Unit of force Kakali Sen (Wed Nov 08 2006 - 07:12:41 CST)
- AMBER: NAD ?? Urszula Uciechowska (Wed Nov 08 2006 - 07:40:15 CST)
- Re: AMBER: NAD ?? David A. Case (Wed Nov 08 2006 - 08:49:31 CST)
- Re: AMBER: NAD ?? Cenk Andac (Wed Nov 08 2006 - 09:55:38 CST)
- AMBER: simulating a small chain protein in water box Dave, Sonya (Wed Nov 08 2006 - 10:03:46 CST)
- AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion Rajesh Murarka (Wed Nov 08 2006 - 09:59:36 CST)
- Re: AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion David A. Case (Wed Nov 08 2006 - 10:35:24 CST)
- AMBER: Problems amber mask in distance? Sergey Samsonov (Wed Nov 08 2006 - 10:39:18 CST)
- AMBER: big bond energy change from minimization and md (heating) Rachel (Wed Nov 08 2006 - 10:40:12 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Wed Nov 08 2006 - 10:48:01 CST)
- Re: AMBER: Problems amber mask in distance? Viktor Hornak (Wed Nov 08 2006 - 10:50:59 CST)
- Re: AMBER: Problems amber mask in distance? Sergey Samsonov (Wed Nov 08 2006 - 10:57:20 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Wed Nov 08 2006 - 11:31:12 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Wed Nov 08 2006 - 11:46:27 CST)
- Re: AMBER: simulating a small chain protein in water box Carlos Simmerling (Wed Nov 08 2006 - 11:50:59 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Wed Nov 08 2006 - 12:35:21 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Wed Nov 08 2006 - 15:35:10 CST)
- AMBER: problem in calculating EGB using sander for ligand containing F atom VANDANA KUMARI (Wed Nov 08 2006 - 21:36:52 CST)
- AMBER: Amber H-bond print? Andres Palencia (Thu Nov 09 2006 - 03:07:46 CST)
- AMBER: Probelm with running Amber 9 parallelly Rafi Ahmad (Thu Nov 09 2006 - 06:59:56 CST)
- AMBER: Biomolecular Simulation 2007 Angelo (Thu Nov 09 2006 - 10:03:43 CST)
- Re: AMBER: problem in calculating EGB using sander for ligand containing F atom David A. Case (Thu Nov 09 2006 - 10:14:06 CST)
- AMBER: Building Library Steve Seibold (Thu Nov 09 2006 - 10:52:08 CST)
- AMBER: Steve Seibold (Thu Nov 09 2006 - 11:03:14 CST)
- AMBER: saltconc for explicit solvent calculation. a a (Thu Nov 09 2006 - 11:51:36 CST)
- Re: AMBER: saltconc for explicit solvent calculation. Carlos Simmerling (Thu Nov 09 2006 - 12:14:21 CST)
- Re: AMBER: David A. Case (Thu Nov 09 2006 - 12:11:55 CST)
- Re: AMBER: saltconc for explicit solvent calculation. David A. Case (Thu Nov 09 2006 - 12:13:05 CST)
- Re: AMBER: Building Library Fenghui Fan (Thu Nov 09 2006 - 12:21:57 CST)
- AMBER: antechamber:tutorial Lwin, ThuZar (Thu Nov 09 2006 - 12:48:58 CST)
- Re: AMBER: antechamber:tutorial Mark Williamson (Thu Nov 09 2006 - 13:06:24 CST)
- Re: AMBER: antechamber:tutorial Fenghui Fan (Thu Nov 09 2006 - 13:10:17 CST)
- AMBER: FW: antechamber:tutorial Lwin, ThuZar (Thu Nov 09 2006 - 13:03:46 CST)
- AMBER: Building Library Steve Seibold (Thu Nov 09 2006 - 13:40:30 CST)
- AMBER: strange temperature behavior when changing to constant pressure Joshua (Thu Nov 09 2006 - 13:52:33 CST)
- RE: AMBER: antechamber:tutorial. . Lwin, ThuZar (Thu Nov 09 2006 - 14:02:28 CST)
- Re: AMBER: NAD ?? Urszula Uciechowska (Fri Nov 10 2006 - 03:36:15 CST)
- AMBER: sander error: rst file crash jitrayut jitonnom (Fri Nov 10 2006 - 06:52:19 CST)
- Re: AMBER: sander error: rst file crash Carlos Simmerling (Fri Nov 10 2006 - 07:26:16 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Fri Nov 10 2006 - 08:42:31 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Carlos Simmerling (Fri Nov 10 2006 - 08:58:26 CST)
- Fwd: AMBER: sander error: rst file crash jitrayut jitonnom (Fri Nov 10 2006 - 09:52:00 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Fri Nov 10 2006 - 09:54:26 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity David A. Case (Fri Nov 10 2006 - 10:34:45 CST)
- AMBER: PTRAJ: radius of gyration kepa koldo burusco (Fri Nov 10 2006 - 11:05:09 CST)
- Re: AMBER: PTRAJ: radius of gyration Bill Ross (Fri Nov 10 2006 - 13:04:06 CST)
- Re: AMBER: sander error: rst file crash David A. Case (Fri Nov 10 2006 - 15:11:15 CST)
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Fri Nov 10 2006 - 15:55:23 CST)
- Re: AMBER: NAD ?? Cenk Andac (Fri Nov 10 2006 - 17:27:35 CST)
- Re: AMBER: NAD ?? Cenk Andac (Fri Nov 10 2006 - 17:20:53 CST)
- AMBER: bond command between Zn and a CYM residue in one chain of a protein complex Fenghui Fan (Fri Nov 10 2006 - 23:25:01 CST)
- Fwd: AMBER: sander error: rst file crash jitrayut jitonnom (Sat Nov 11 2006 - 05:16:37 CST)
- Re: Fwd: AMBER: sander error: rst file crash Carlos Simmerling (Sat Nov 11 2006 - 06:38:52 CST)
- Re: AMBER: sander error: rst file crash jitrayut jitonnom (Sat Nov 11 2006 - 11:22:20 CST)
- Re: Re: AMBER: question about the topology file J. Zhang (Sun Nov 12 2006 - 19:42:20 CST)
- AMBER: ZN-CYS prepin and frcmd file Fenghui Fan (Sun Nov 12 2006 - 20:16:37 CST)
- Re: Fwd: AMBER: sander error: rst file crash David A. Case (Sun Nov 12 2006 - 20:44:48 CST)
- AMBER: The plc.frcmod file in the old version tutorial Fenghui Fan (Sun Nov 12 2006 - 20:50:29 CST)
- Re: AMBER: NAD ?? Urszula Uciechowska (Mon Nov 13 2006 - 03:08:45 CST)
- AMBER: <kein Betreff> Michel Becker (Mon Nov 13 2006 - 05:21:58 CST)
- Re: AMBER: NAD ?? Cenk Andac (Mon Nov 13 2006 - 08:46:47 CST)
- RE: AMBER: The plc.frcmod file in the old version tutorial Ross Walker (Mon Nov 13 2006 - 10:29:26 CST)
- RE: AMBER: <kein Betreff> Ross Walker (Mon Nov 13 2006 - 10:44:03 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Mon Nov 13 2006 - 11:09:22 CST)
- Re: AMBER: <kein Betreff> Gustavo Seabra (Mon Nov 13 2006 - 11:52:55 CST)
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Mon Nov 13 2006 - 19:56:29 CST)
- AMBER: what to do with the counter ions when minimizing average structure of DNA? Chengwen Chen (Tue Nov 14 2006 - 05:09:25 CST)
- AMBER: how to remove the rotation of system in periodic condition? ÕÅÓÂ (Tue Nov 14 2006 - 06:10:22 CST)
- AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Tue Nov 14 2006 - 08:35:21 CST)
- Re: AMBER: gfortran/gcc versus ifort/icc Fenghui Fan (Tue Nov 14 2006 - 11:40:13 CST)
- AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 12:10:39 CST)
- AMBER: Acetone box SERGIO MIGUEL FERNANDES DOS SANTOS (Tue Nov 14 2006 - 12:34:24 CST)
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Thomas Cheatham (Tue Nov 14 2006 - 12:34:57 CST)
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 12:50:01 CST)
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Austin B. Yongye (Tue Nov 14 2006 - 13:02:27 CST)
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Thomas Cheatham (Tue Nov 14 2006 - 13:17:40 CST)
- AMBER: Restraints of the strand-endings? Michel Becker (Tue Nov 14 2006 - 14:22:36 CST)
- Re: AMBER: Ptraj: radial distribution and correlation coefficient Andres Palencia (Tue Nov 14 2006 - 14:13:39 CST)
- Re: AMBER: Restraints of the strand-endings? Bill Ross (Tue Nov 14 2006 - 16:19:06 CST)
- Re: AMBER: vlimit exceeded for step 0, vmax = infinity Rachel (Tue Nov 14 2006 - 16:44:44 CST)
- RE: AMBER: vlimit exceeded for step 0, vmax = infinity Yong Duan (Tue Nov 14 2006 - 17:05:08 CST)
- Re: AMBER: ntt=1 in simulated annealing Tanya Johannsen (Tue Nov 14 2006 - 17:59:04 CST)
- AMBER: error in tleap test Christian Roth (Tue Nov 14 2006 - 18:40:24 CST)
- Re: AMBER: ntt=1 in simulated annealing Sergey Samsonov (Wed Nov 15 2006 - 01:09:15 CST)
- Re: AMBER: ntt=1 in simulated annealing kepa koldo burusco (Wed Nov 15 2006 - 05:53:27 CST)
- Re: AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Wed Nov 15 2006 - 09:37:27 CST)
- Re: AMBER: how to remove the rotation of system in periodic condition? David A. Case (Wed Nov 15 2006 - 10:34:01 CST)
- Re: AMBER: ntt=1 in simulated annealing David A. Case (Wed Nov 15 2006 - 10:46:58 CST)
- RE: AMBER: gfortran/gcc versus ifort/icc Jordi Camps (Wed Nov 15 2006 - 11:50:54 CST)
- Re: AMBER: error in tleap test Scott Brozell (Wed Nov 15 2006 - 11:55:07 CST)
- RE: AMBER: error in tleap test Christian Roth (Wed Nov 15 2006 - 12:18:07 CST)
- Re: AMBER: gfortran/gcc versus ifort/icc Luis Gracia (Wed Nov 15 2006 - 12:34:36 CST)
- AMBER: ptraj and mdvel question Jianhui (Wed Nov 15 2006 - 13:07:06 CST)
- AMBER: H-Bond Terms in amber force field Ilyas Yildirim (Wed Nov 15 2006 - 13:28:06 CST)
- AMBER: Error in compliling LEAP on Fedora 5 Pankaj Daga (Wed Nov 15 2006 - 16:56:58 CST)
- Re: AMBER: H-Bond Terms in amber force field Jiri Sponer (Wed Nov 15 2006 - 17:20:18 CST)
- Re: AMBER: ptraj and mdvel question Thomas Cheatham (Wed Nov 15 2006 - 17:37:13 CST)
- Re: AMBER: H-Bond Terms in amber force field Thomas Cheatham (Wed Nov 15 2006 - 17:51:36 CST)
- Re: AMBER: H-Bond Terms in amber force field Ilyas Yildirim (Wed Nov 15 2006 - 18:05:13 CST)
- Re: AMBER: Error in compliling LEAP on Fedora 5 Steven Winfield (Wed Nov 15 2006 - 18:10:33 CST)
- Re: AMBER: H-Bond Terms in amber force field Jiri Sponer (Wed Nov 15 2006 - 18:30:48 CST)
- Re: AMBER: Error in compliling LEAP on Fedora 5 David A. Case (Wed Nov 15 2006 - 19:24:34 CST)
- AMBER: MM_PBSA Varsha Goyal (Wed Nov 15 2006 - 20:27:15 CST)
- AMBER: erroneous placement of TER card Gregory Sandala (Thu Nov 16 2006 - 03:12:43 CST)
- Re: AMBER: erroneous placement of TER card Robert Duke (Thu Nov 16 2006 - 07:56:11 CST)
- AMBER: opls_aa in amber Vitor Manuel Sousa F?x (Thu Nov 16 2006 - 08:29:45 CST)
- RE: AMBER: gfortran/gcc versus ifort/icc Jordi Camps (Thu Nov 16 2006 - 10:22:55 CST)
- Re: AMBER: erroneous placement of TER card David A. Case (Thu Nov 16 2006 - 10:20:32 CST)
- Re: AMBER: MM_PBSA Thomas Steinbrecher (Thu Nov 16 2006 - 10:21:55 CST)
- AMBER: pqr file Seth Lilavivat (Thu Nov 16 2006 - 10:43:55 CST)
- Re: AMBER: erroneous placement of TER card Robert Duke (Thu Nov 16 2006 - 10:47:23 CST)
- Re: AMBER: pqr file David A. Case (Thu Nov 16 2006 - 10:53:46 CST)
- AMBER: GLYCAM and ff98 atom-types Gabbar S. Daaku (Thu Nov 16 2006 - 12:11:05 CST)
- AMBER: Xleap woes Shozeb Haider (Thu Nov 16 2006 - 17:07:01 CST)
- Re: AMBER: Xleap woes David A. Case (Thu Nov 16 2006 - 12:39:39 CST)
- Re: AMBER: erroneous placement of TER card David A. Case (Thu Nov 16 2006 - 12:59:28 CST)
- Re: AMBER: erroneous placement of TER card Bill Ross (Thu Nov 16 2006 - 12:54:50 CST)
- Re: AMBER: erroneous placement of TER card Bill Ross (Thu Nov 16 2006 - 13:06:25 CST)
- Re: AMBER: Xleap woes Fenghui Fan (Thu Nov 16 2006 - 13:22:59 CST)
- Re: AMBER: GLYCAM and ff98 atom-types Fenghui Fan (Thu Nov 16 2006 - 13:16:34 CST)
- AMBER: parameters for beta peptides yipinl_at_umich.edu (Thu Nov 16 2006 - 13:29:08 CST)
- Re: AMBER: GLYCAM and ff98 atom-types] Austin B. Yongye (Thu Nov 16 2006 - 13:53:03 CST)
- Re: AMBER: Xleap woes M. L. Dodson (Thu Nov 16 2006 - 14:14:07 CST)
- Re: AMBER: gfortran/gcc versus ifort/icc Lachele Foley (Lists) (Thu Nov 16 2006 - 14:49:23 CST)
- AMBER: optimatized structure is so much different from the original pdb structure emilia wu (Thu Nov 16 2006 - 23:38:18 CST)
- AMBER: Ethanol Rita Cassia (Fri Nov 17 2006 - 06:13:14 CST)
- AMBER: dihedral angle equation Vitor Manuel Sousa F?x (Fri Nov 17 2006 - 06:41:25 CST)
- Re: AMBER: dihedral angle equation Igor Schapiro (Fri Nov 17 2006 - 08:15:47 CST)
- Re: AMBER: Ethanol FyD (Fri Nov 17 2006 - 08:19:15 CST)
- Re: AMBER: dihedral angle equation Igor Schapiro (Fri Nov 17 2006 - 08:24:29 CST)
- Re: AMBER: optimatized structure is so much different from the original pdb structure Gabbar S. Daaku (Fri Nov 17 2006 - 11:13:04 CST)
- AMBER: reading psf file jojartb_at_pharm.u-szeged.hu (Fri Nov 17 2006 - 17:24:24 CST)
- AMBER: Amber9 installation error Keerthi Gottipati (Fri Nov 17 2006 - 18:12:53 CST)
- Re: AMBER: reading psf file Thomas Cheatham (Fri Nov 17 2006 - 18:28:45 CST)
- Re: AMBER: reading psf file jojartb_at_pharm.u-szeged.hu (Sat Nov 18 2006 - 02:38:26 CST)
- RE: AMBER: Amber9 installation error Ross Walker (Sat Nov 18 2006 - 11:20:39 CST)
- AMBER: gfortran and amber9 success on FreeBSD M. L. Dodson (Sat Nov 18 2006 - 16:02:16 CST)
- AMBER: parameters for silicon atom Chengwen Chen (Mon Nov 20 2006 - 01:45:07 CST)
- Re: AMBER: reading psf file jojartb_at_pharm.u-szeged.hu (Sat Nov 18 2006 - 03:40:37 CST)
- AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 06:59:07 CST)
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan (Mon Nov 20 2006 - 07:57:10 CST)
- Re: AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 08:23:30 CST)
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan (Mon Nov 20 2006 - 09:06:53 CST)
- AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier (Mon Nov 20 2006 - 11:09:13 CST)
- Re: AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 11:18:00 CST)
- Re: AMBER: Combining Residues in LEaP for Lipid Bilayers David A. Case (Mon Nov 20 2006 - 11:35:04 CST)
- Re: AMBER: problems with saving self-built molecules parameters David A. Case (Mon Nov 20 2006 - 11:33:25 CST)
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers Matthew Tessier (Mon Nov 20 2006 - 11:48:32 CST)
- Re: AMBER: problems with saving self-built molecules parameters Fenghui Fan (Mon Nov 20 2006 - 12:10:21 CST)
- Re: AMBER: problems with saving self-built molecules parameters Rachel (Mon Nov 20 2006 - 12:42:10 CST)
- Re: AMBER: problems with saving self-built molecules parameters Bill Ross (Mon Nov 20 2006 - 12:55:00 CST)
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers Bill Ross (Mon Nov 20 2006 - 12:58:11 CST)
- AMBER: the energy and temperature both increasing during the simulation with NTT=0 Xiaowei (David) Li (Mon Nov 20 2006 - 12:50:00 CST)
- Re: AMBER: the energy and temperature both increasing during the simulation with NTT=0 David A. Case (Tue Nov 21 2006 - 00:09:28 CST)
- AMBER: matrix correl Jardas sucuriba (Tue Nov 21 2006 - 07:05:41 CST)
- AMBER: Quantifying pi-pi interactions zachary hartman (Tue Nov 21 2006 - 09:51:30 CST)
- Re: AMBER: Quantifying pi-pi interactions Jiri Sponer (Tue Nov 21 2006 - 10:14:32 CST)
- Re: AMBER: Combining Residues in LEaP for Lipid Bilayers David A. Case (Tue Nov 21 2006 - 10:16:06 CST)
- AMBER: ff03 GLY HAs atom type Sandro Fornili (Tue Nov 21 2006 - 10:21:01 CST)
- RE: AMBER: ff03 GLY HAs atom type Yong Duan (Tue Nov 21 2006 - 11:41:17 CST)
- AMBER: compile amber8 on IBM-sp4 Rachel (Tue Nov 21 2006 - 11:56:13 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Scott Brozell (Tue Nov 21 2006 - 12:38:49 CST)
- AMBER: Ptraj: correlation time Austin B. Yongye (Tue Nov 21 2006 - 15:05:52 CST)
- AMBER: Ptraj: diffusion rate Austin B. Yongye (Tue Nov 21 2006 - 15:03:52 CST)
- RE: AMBER: ff03 GLY HAs atom type mahdi fathi (Tue Nov 21 2006 - 23:46:22 CST)
- AMBER: Some warning !!! during SANDER ? jitrayut jitonnom (Wed Nov 22 2006 - 02:20:36 CST)
- Re: AMBER: Ethanol Rita Cassia (Wed Nov 22 2006 - 03:33:24 CST)
- AMBER: Ptraj syntax change Amber8->Amber9 ? Markus Kaukonen (Wed Nov 22 2006 - 04:35:26 CST)
- AMBER: Radius of gyration r. a. (Wed Nov 22 2006 - 04:11:14 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Rachel (Wed Nov 22 2006 - 04:08:42 CST)
- AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 05:39:18 CST)
- Re: AMBER: Ethanol FyD (Wed Nov 22 2006 - 06:22:28 CST)
- Re: AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 09:42:34 CST)
- AMBER: Re: installation instructions David A. Case (Wed Nov 22 2006 - 10:48:17 CST)
- RE: AMBER: Some warning !!! during SANDER ? Ross Walker (Wed Nov 22 2006 - 10:48:55 CST)
- RE: AMBER: compile amber8 on IBM-sp4 Ross Walker (Wed Nov 22 2006 - 11:55:45 CST)
- RE: AMBER: SHAKE problem after minimization Ross Walker (Wed Nov 22 2006 - 11:59:58 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Rachel (Wed Nov 22 2006 - 12:34:19 CST)
- Re: AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 12:43:50 CST)
- RE: AMBER: SHAKE problem after minimization Hayden Eastwood (Wed Nov 22 2006 - 13:13:24 CST)
- AMBER: Problem with mask when using distance in ptraj Christopher Gaughan (Wed Nov 22 2006 - 13:36:23 CST)
- Re: AMBER: SHAKE problem after minimization Rachel (Wed Nov 22 2006 - 13:37:15 CST)
- RE: AMBER: SHAKE problem after minimization Hayden Eastwood (Wed Nov 22 2006 - 14:33:17 CST)
- RE: AMBER: SHAKE problem after minimization Hayden Eastwood (Wed Nov 22 2006 - 14:47:09 CST)
- Re: AMBER: Problem with mask when using distance in ptraj David A. Case (Wed Nov 22 2006 - 15:07:29 CST)
- Re: AMBER: Problem with mask when using distance in ptraj Thomas Cheatham (Wed Nov 22 2006 - 15:17:12 CST)
- Re: AMBER: Ptraj syntax change Amber8->Amber9 ? David A. Case (Wed Nov 22 2006 - 15:22:37 CST)
- Re: AMBER: SHAKE problem after minimization Steven Winfield (Wed Nov 22 2006 - 15:53:07 CST)
- Re: AMBER: SHAKE problem after minimization David A. Case (Wed Nov 22 2006 - 16:24:44 CST)
- AMBER: problem of the REMD with nmr constraints wenfei Li (Wed Nov 22 2006 - 19:57:32 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Wed Nov 22 2006 - 21:51:57 CST)
- AMBER: ammonia parameters Peter Trodler (Thu Nov 23 2006 - 02:51:39 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 03:56:53 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Thu Nov 23 2006 - 06:21:07 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Thu Nov 23 2006 - 06:26:12 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 07:14:09 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Xuebin Qiao (Thu Nov 23 2006 - 08:23:36 CST)
- Re: AMBER: ammonia parameters Fenghui Fan (Thu Nov 23 2006 - 09:40:05 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 10:37:18 CST)
- AMBER: Restarting with new topology Sergey Samsonov (Thu Nov 23 2006 - 10:39:53 CST)
- AMBER: Snapshots (pdbs) from a trajectory. Jordi Rodrigo De Losada (Thu Nov 23 2006 - 11:11:18 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Martin Peters (Thu Nov 23 2006 - 11:22:06 CST)
- Re: AMBER: Snapshots (pdbs) from a trajectory. Carlos Simmerling (Thu Nov 23 2006 - 11:25:31 CST)
- Re: AMBER: compile amber8 on IBM-sp4 Rachel (Thu Nov 23 2006 - 11:45:04 CST)
- Re: AMBER: SHAKE problem after minimization Rachel (Thu Nov 23 2006 - 12:37:24 CST)
- AMBER: Unable to find mopac charges in divcon.out Rachel (Thu Nov 23 2006 - 13:31:55 CST)
- Re: AMBER: Unable to find mopac charges in divcon.out Mark Williamson (Thu Nov 23 2006 - 16:06:35 CST)
- Re: AMBER: Unable to find mopac charges in divcon.out Rachel (Thu Nov 23 2006 - 17:22:06 CST)
- Re: AMBER: Snapshots (pdbs) from a trajectory. David A. Case (Thu Nov 23 2006 - 21:58:34 CST)
- AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? a a (Fri Nov 24 2006 - 00:13:38 CST)
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? David A. Case (Fri Nov 24 2006 - 01:02:21 CST)
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences? a a (Fri Nov 24 2006 - 03:29:26 CST)
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? cristian obiol (Fri Nov 24 2006 - 04:24:28 CST)
- RE: AMBER: Radius of gyration kepa koldo burusco (Fri Nov 24 2006 - 04:27:01 CST)
- RE: AMBER: Combining Residues in LEaP for Lipid Bilayers kepa koldo burusco (Fri Nov 24 2006 - 05:38:06 CST)
- RE: AMBER: Radius of gyration Andy Purkiss-Trew (Fri Nov 24 2006 - 06:58:53 CST)
- Re: AMBER: Unable to find mopac charges in divcon.out Mark Williamson (Fri Nov 24 2006 - 07:54:34 CST)
- Re: AMBER: problem of the REMD with nmr constraints Carlos Simmerling (Fri Nov 24 2006 - 08:35:25 CST)
- RE: AMBER: Radius of gyration kepa koldo burusco (Fri Nov 24 2006 - 11:45:55 CST)
- AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel (Fri Nov 24 2006 - 11:58:53 CST)
- Re: RE: AMBER: Radius of gyration Carles Jaime Cardiel (Fri Nov 24 2006 - 12:25:02 CST)
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Nicolas Lux Fawzi (Fri Nov 24 2006 - 13:16:01 CST)
- RE: AMBER: Radius of gyration Andy Purkiss-Trew (Fri Nov 24 2006 - 13:34:52 CST)
- Re: RE: AMBER: Radius of gyration Andy Purkiss-Trew (Fri Nov 24 2006 - 13:38:28 CST)
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Rachel (Fri Nov 24 2006 - 13:53:29 CST)
- Re: RE: AMBER: Radius of gyration Elijah Gregory (Fri Nov 24 2006 - 14:33:50 CST)
- AMBER: Antechamber and gaussian questions Fenghui Fan (Fri Nov 24 2006 - 16:04:40 CST)
- AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 In Hee Park (Fri Nov 24 2006 - 16:50:54 CST)
- AMBER: bondtype problem Fenghui Fan (Fri Nov 24 2006 - 18:22:23 CST)
- Re: AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64 David A. Case (Fri Nov 24 2006 - 18:43:20 CST)
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? a a (Fri Nov 24 2006 - 20:27:26 CST)
- Re: AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines Xuebin Qiao (Fri Nov 24 2006 - 22:55:14 CST)
- AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 01:06:49 CST)
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? David A. Case (Sat Nov 25 2006 - 02:51:06 CST)
- Re: AMBER: respin file M. L. Dodson (Sat Nov 25 2006 - 08:37:05 CST)
- AMBER: resp Fenghui Fan (Sat Nov 25 2006 - 15:03:00 CST)
- AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 16:23:46 CST)
- Re: AMBER: respin file Ilyas Yildirim (Sat Nov 25 2006 - 19:07:04 CST)
- Re: AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 19:49:58 CST)
- Re: AMBER: problem of the REMD with nmr constraints wenfei Li (Sat Nov 25 2006 - 19:56:05 CST)
- Re: AMBER: respin file Ilyas Yildirim (Sat Nov 25 2006 - 20:45:37 CST)
- Re: AMBER: respin file Fenghui Fan (Sat Nov 25 2006 - 21:15:53 CST)
- AMBER: how to get complete prepin file Fenghui Fan (Sat Nov 25 2006 - 23:02:20 CST)
- Re: AMBER: respin file Ilyas Yildirim (Sun Nov 26 2006 - 02:03:33 CST)
- Re: AMBER: Problem with mask when using distance in ptraj Christopher Gaughan (Sun Nov 26 2006 - 08:28:29 CST)
- AMBER: how can i treat with long "mask" in ptraj analysis. Changge Ji (Sun Nov 26 2006 - 10:22:00 CST)
- Re: AMBER: respin file Fenghui Fan (Sun Nov 26 2006 - 11:12:01 CST)
- Re: AMBER: respin file Ilyas Yildirim (Sun Nov 26 2006 - 11:45:20 CST)
- Re: AMBER: respin file M. L. Dodson (Sun Nov 26 2006 - 12:05:33 CST)
- AMBER: ZN prepin Fenghui Fan (Sun Nov 26 2006 - 16:29:31 CST)
- Re: AMBER: respin file Fenghui Fan (Sun Nov 26 2006 - 18:42:09 CST)
- AMBER: bond information Fenghui Fan (Sun Nov 26 2006 - 22:10:42 CST)
- AMBER: ptraj grid Hannes Loeffler (Sun Nov 26 2006 - 22:05:05 CST)
- AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it? a a (Mon Nov 27 2006 - 02:50:12 CST)
- Re: AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences? a a (Mon Nov 27 2006 - 04:29:42 CST)
- AMBER: helices in GB simulations Marie-Pierre Durrieu (Mon Nov 27 2006 - 11:43:41 CST)
- Re: AMBER: helices in GB simulations Carlos Simmerling (Mon Nov 27 2006 - 12:12:02 CST)
- AMBER: minimization of Hydrogens with xLeaP rebeca_at_mmb.pcb.ub.es (Mon Nov 27 2006 - 12:38:04 CST)
- AMBER: Problem Installing Amber in SGI Irix 6.5 trudy_at_uoguelph.ca (Mon Nov 27 2006 - 14:29:53 CST)
- AMBER: phantom sander8 in dmesg Lachele Foley (Lists) (Mon Nov 27 2006 - 15:25:57 CST)
- Re: AMBER: helices in GB simulations Ilyas Yildirim (Mon Nov 27 2006 - 16:09:04 CST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 David A. Case (Mon Nov 27 2006 - 19:56:14 CST)
- Re: AMBER: minimization of Hydrogens with xLeaP David A. Case (Mon Nov 27 2006 - 20:19:48 CST)
- AMBER: prepin file nan Fenghui Fan (Mon Nov 27 2006 - 21:28:16 CST)
- AMBER: Problem about dummy atoms when running antechamber ÇÑ ¹Î¿ì (Mon Nov 27 2006 - 21:30:27 CST)
- Re: RE: AMBER: Radius of gyration r. a. (Mon Nov 27 2006 - 22:20:32 CST)
- AMBER: protonated phosphate Einar Uggerud (Tue Nov 28 2006 - 01:11:46 CST)
- AMBER: NONB values adjusted? Dave S Walker (Tue Nov 28 2006 - 01:37:28 CST)
- AMBER: energy minimizations in amber8 vs. amber9 Seongeun Yang (Tue Nov 28 2006 - 01:43:35 CST)
- Re: AMBER: prepin file nan linfu (Tue Nov 28 2006 - 03:00:30 CST)
- AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 05:51:30 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Carlos Simmerling (Tue Nov 28 2006 - 06:11:51 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 07:56:10 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Carlos Simmerling (Tue Nov 28 2006 - 08:07:18 CST)
- AMBER: xleap Steve Seibold (Tue Nov 28 2006 - 08:33:48 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 08:34:36 CST)
- Re: AMBER: prepin file nan Fenghui Fan (Tue Nov 28 2006 - 08:48:33 CST)
- AMBER: uccadco_at_ucl.ac.uk (Tue Nov 28 2006 - 08:48:08 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gustavo Seabra (Tue Nov 28 2006 - 09:18:49 CST)
- AMBER: Modifying a Force Field Seth Lilavivat (Tue Nov 28 2006 - 09:27:08 CST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy_at_uoguelph.ca (Tue Nov 28 2006 - 09:41:07 CST)
- Re: AMBER: David A. Case (Tue Nov 28 2006 - 09:53:48 CST)
- AMBER: nmode output with ptraj nadiav_at_soton.ac.uk (Tue Nov 28 2006 - 09:59:02 CST)
- Re: AMBER: xleap David A. Case (Tue Nov 28 2006 - 10:02:13 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gobind Singh Bisht (Tue Nov 28 2006 - 10:40:53 CST)
- AMBER: Charge fitting in Amber Changge Ji (Tue Nov 28 2006 - 10:50:20 CST)
- Re: AMBER: NONB values adjusted? Thomas Steinbrecher (Tue Nov 28 2006 - 10:31:33 CST)
- AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 12:06:16 CST)
- Re: AMBER: NONB values adjusted? Dave S Walker (Tue Nov 28 2006 - 13:48:36 CST)
- AMBER: ambpdb -pqr Seth Lilavivat (Tue Nov 28 2006 - 14:52:10 CST)
- RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 14:59:48 CST)
- Re: AMBER: ambpdb -pqr Carlos Simmerling (Tue Nov 28 2006 - 15:03:18 CST)
- Re: AMBER: ambpdb -pqr Ilyas Yildirim (Tue Nov 28 2006 - 15:02:39 CST)
- Re: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Mark Williamson (Tue Nov 28 2006 - 15:04:06 CST)
- Re: AMBER: ambpdb -pqr harianto (Tue Nov 28 2006 - 15:03:26 CST)
- RE: AMBER: Amber9 patch bugfix.all issue on SunOS 5.1 Michael John Hanby (Tue Nov 28 2006 - 15:43:06 CST)
- RE: AMBER: prepin file nan Junmei Wang (Tue Nov 28 2006 - 15:47:03 CST)
- RE: AMBER: Problem about dummy atoms when running antechamber Junmei Wang (Tue Nov 28 2006 - 15:54:42 CST)
- RE: AMBER: bond information Junmei Wang (Tue Nov 28 2006 - 16:16:03 CST)
- AMBER: RE: Amber: ZN-complex file Junmei Wang (Tue Nov 28 2006 - 17:21:40 CST)
- Re: AMBER: RE: Amber: ZN-complex file Fenghui Fan (Tue Nov 28 2006 - 17:47:19 CST)
- RE: AMBER: RE: Amber: ZN-complex file Junmei Wang (Tue Nov 28 2006 - 17:54:56 CST)
- AMBER: Periodic simulations with net charge Jennie Thomas (Tue Nov 28 2006 - 18:47:32 CST)
- Re: AMBER: Periodic simulations with net charge David A. Case (Tue Nov 28 2006 - 20:03:22 CST)
- Re: AMBER: nmode output with ptraj David A. Case (Tue Nov 28 2006 - 20:36:33 CST)
- Re: AMBER: nmode output with ptraj a a (Tue Nov 28 2006 - 21:18:32 CST)
- AMBER: How to apply a force to some atom in a residues? a a (Tue Nov 28 2006 - 21:36:15 CST)
- AMBER: DNA helix end stable? a a (Tue Nov 28 2006 - 21:35:11 CST)
- Re: AMBER: RE: Amber: ZN-complex file FyD (Wed Nov 29 2006 - 01:21:19 CST)
- Re: AMBER: Charge fitting in Amber FyD (Wed Nov 29 2006 - 01:16:38 CST)
- Re: AMBER: DNA helix end stable? Carlos Simmerling (Wed Nov 29 2006 - 06:24:14 CST)
- Re: AMBER: How to apply a force to some atom in a residues? Carlos Simmerling (Wed Nov 29 2006 - 06:26:19 CST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 Joe Nolan (Wed Nov 29 2006 - 06:40:58 CST)
- AMBER: Solvation Energies Ivelin Georgiev (Wed Nov 29 2006 - 08:31:13 CST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy_at_uoguelph.ca (Wed Nov 29 2006 - 08:50:51 CST)
- Re: AMBER: Confusion about PBC Thomas Steinbrecher (Wed Nov 29 2006 - 10:40:05 CST)
- AMBER: Confusion about PBC anna.schrey_at_gmx.de (Wed Nov 29 2006 - 10:26:04 CST)
- AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood (Wed Nov 29 2006 - 12:12:16 CST)
- Re: AMBER: Langevin temperature control vs berendson heat bath Carlos Simmerling (Wed Nov 29 2006 - 13:02:20 CST)
- AMBER: ptraj----radial output files Esther Brugger (Wed Nov 29 2006 - 14:03:20 CST)
- Re: AMBER: How to apply a force to some atom in a residues? a a (Thu Nov 30 2006 - 00:45:04 CST)
- AMBER: How to run MD simulation of a silicon containing complex with AMBER9? Chengwen Chen (Thu Nov 30 2006 - 01:06:54 CST)
- AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it? Gobind Singh Bisht (Thu Nov 30 2006 - 01:34:28 CST)
- AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Chengwen Chen (Thu Nov 30 2006 - 02:07:28 CST)
- AMBER: Performing Interactive Essential Dynamics in Ptraj hbluo (Thu Nov 30 2006 - 18:58:11 CST)
- RE: AMBER: Langevin temperature control vs berendson heat bath Hayden Eastwood (Thu Nov 30 2006 - 05:23:37 CST)
- Re: AMBER: Langevin temperature control vs berendson heat bath Andreas Svrcek-Seiler (Thu Nov 30 2006 - 06:06:22 CST)
- Re: AMBER: How to apply a force to some atom in a residues? Carlos Simmerling (Thu Nov 30 2006 - 06:13:42 CST)
- Re: AMBER: Langevin temperature control vs berendson heat bath Carlos Simmerling (Thu Nov 30 2006 - 06:23:24 CST)
- Re: AMBER: Problem Installing Amber in SGI Irix 6.5 trudy_at_uoguelph.ca (Thu Nov 30 2006 - 09:31:02 CST)
- Re: AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes Gustavo Seabra (Thu Nov 30 2006 - 09:20:00 CST)
- Re: AMBER: How to specify user defined force fields or its parameters in amber?? Gustavo Seabra (Thu Nov 30 2006 - 09:46:42 CST)
- AMBER: amber9 parralel compiling Nikola Trbovic (Thu Nov 30 2006 - 10:31:22 CST)
- Re: AMBER: amber9 parralel compiling David A. Case (Thu Nov 30 2006 - 10:50:47 CST)
- Re: AMBER: amber9 parralel compiling Nikola Trbovic (Thu Nov 30 2006 - 11:06:12 CST)
- AMBER: How to recompile sander for single-processor use in AMBER 8? Peter Anderson (Thu Nov 30 2006 - 15:41:27 CST)
- AMBER: watershell and image commands Esther Brugger (Thu Nov 30 2006 - 16:37:58 CST)
- Re: AMBER: How to recompile sander for single-processor use in AMBER 8? David A. Case (Thu Nov 30 2006 - 17:19:10 CST)
- AMBER: watershell command Esther Brugger (Thu Nov 30 2006 - 17:16:52 CST)
- Re: AMBER: watershell and image commands Thomas Cheatham (Thu Nov 30 2006 - 17:22:59 CST)
- Re: AMBER: amber9 parralel compiling David A. Case (Thu Nov 30 2006 - 17:54:08 CST)
- Re: AMBER: watershell and image commands Esther Brugger (Thu Nov 30 2006 - 18:04:04 CST)
- AMBER: H-bond analysis (Ptraj) Esther Brugger (Thu Nov 30 2006 - 19:28:10 CST)
- AMBER: MM-PBSA problem vanessa wai (Thu Nov 30 2006 - 19:27:06 CST)
- AMBER: Problem about dummy atoms when running antechamber Minwoo Han (Mon Nov 27 2006 - 03:29:29 CST)
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
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