AMBER Archive (2003) - Jan 2003 By ThreadMost recent messages
232 messages sorted by:
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Starting: Thu Jan 02 2003 - 04:37:41 CST
Ending: Fri Jan 31 2003 - 17:49:52 CST
- TFE input Raja Swaminathan (Thu Jan 02 2003 - 04:37:41 CST)
- Sander box error and thanks on previous mdin error kxg2248_at_njit.edu (Thu Jan 02 2003 - 21:41:49 CST)
- JACS 125th and PAK Carlos Simmerling (Fri Jan 03 2003 - 11:02:12 CST)
- Linux cluster Amber7 sander mpi error -- Null communicator, IOT Trap Chris Switzer (Fri Jan 03 2003 - 21:18:11 CST)
- looking for 'pdb_to_mass' yuann (Tue Jan 07 2003 - 00:54:32 CST)
- water reordering in sander Michael Trieb (Tue Jan 07 2003 - 07:43:38 CST)
- Small organic molecules Dvira Segal (Tue Jan 07 2003 - 09:55:31 CST)
- reducing restrains Luis Gracia (Tue Jan 07 2003 - 10:14:43 CST)
- virtual box eric hu (Tue Jan 07 2003 - 17:26:15 CST)
- mm_pbsa question wentaofu (Tue Jan 07 2003 - 18:17:08 CST)
- the unit of velocity Jian Zhang (Tue Jan 07 2003 - 22:36:58 CST)
- nmanal & quasih question yuann (Wed Jan 08 2003 - 01:16:56 CST)
- building molecules by script files for leap Dvira Segal (Wed Jan 08 2003 - 10:07:57 CST)
- mm_gbsa error message Mahadevan Seetharaman (Wed Jan 08 2003 - 12:17:23 CST)
- Predefined Water_cap with xleap Jose Ramon Blas (Wed Jan 08 2003 - 12:42:16 CST)
- Amber parameters for Netropsin Manuel Rueda (Wed Jan 08 2003 - 17:48:12 CST)
- GIBBS - Routine TORCON failed. Required change is too large. Miguel de Federico (Thu Jan 09 2003 - 04:11:41 CST)
- free energy perturbation (Gibbs/Amber 5)? meiselba (Thu Jan 09 2003 - 10:49:09 CST)
- MM_pbsa prmtop file wentaofu (Thu Jan 09 2003 - 17:29:38 CST)
- xleap crashes Layi Adekoya (Fri Jan 10 2003 - 06:16:26 CST)
- IDSX0 in free energy calculations Lepsa (Fri Jan 10 2003 - 07:29:04 CST)
- (no subject) amkumar_at_post.its.mcw.edu (Fri Jan 10 2003 - 11:35:12 CST)
- errors in MD trajectories Vlad Cojocaru (Fri Jan 10 2003 - 12:13:03 CST)
- pdb_to_mass Jake Isaacs (Fri Jan 10 2003 - 14:42:35 CST)
- Force Fields Colin Connelly (Fri Jan 10 2003 - 23:44:35 CST)
- electrostatic potential calculations Vlad Cojocaru (Sat Jan 11 2003 - 10:05:07 CST)
- Dummy atoms in free energy calculation Lepsa (Sat Jan 11 2003 - 12:18:44 CST)
- problem with antechamber Craig A Bayse (Sun Jan 12 2003 - 12:54:05 CST)
- xleap crashes Layi Adekoya (Mon Jan 13 2003 - 01:54:20 CST)
- coordinates for quasih Jake Isaacs (Mon Jan 13 2003 - 08:43:54 CST)
- mm_pbsa -- COMPT must be specified (correctly) William Wei (Mon Jan 13 2003 - 12:00:10 CST)
- xleap crashes Layi Adekoya (Tue Jan 14 2003 - 02:46:49 CST)
- chloroform, dichlormethane f.f. Arvid Soederhaell (Tue Jan 14 2003 - 04:24:33 CST)
- MEAD on SuSE 8.1 Vlad Cojocaru (Tue Jan 14 2003 - 09:10:18 CST)
- Summary: mm_pbsa -- COMPT must be specified (correctly) William Wei (Tue Jan 14 2003 - 09:31:07 CST)
- mm_gbsa: Unit 5 Error on OPEN: sander_com.in William Wei (Tue Jan 14 2003 - 11:19:36 CST)
- Moil-view Ling Zhang (Tue Jan 14 2003 - 11:47:14 CST)
- how to stop mapping of N- and C-terminal residues in xleap Michael Ford (Tue Jan 14 2003 - 13:37:27 CST)
- solvatecap GUILLERMINA L ESTIU (Tue Jan 14 2003 - 14:33:16 CST)
- nscm Kristina Furse (Tue Jan 14 2003 - 18:21:52 CST)
- compiling amber: Machine file for new 64 bit HP-Itanium II CPU Ying-Chieh Sun (Tue Jan 14 2003 - 19:40:40 CST)
- solvatecap GUILLERMINA L ESTIU (Wed Jan 15 2003 - 08:48:05 CST)
- Re: how to stop mapping of N- and C-terminal residues in xleap (The RTFM solution) Michael Ford (Wed Jan 15 2003 - 12:02:52 CST)
- mail reflector caldwell_at_heimdal.compchem.ucsf.edu (Thu Jan 16 2003 - 15:07:10 CST)
- solvent free energy, GB Robert G. Endres (Thu Jan 16 2003 - 15:33:36 CST)
- terminal phosphate group in RNA Mahadevan Seetharaman (Thu Jan 16 2003 - 16:10:13 CST)
- Polarization charges -geometry Lepsa (Fri Jan 17 2003 - 02:21:30 CST)
- octahedral volume Peter Varnai (Fri Jan 17 2003 - 04:26:58 CST)
- mm_pbsa Stop at statistics William Wei (Fri Jan 17 2003 - 12:52:48 CST)
- UCSF Network changes to affect Amber Web site. caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 17 2003 - 13:41:19 CST)
- nucleic acid structures Ioana Cozmuta (Fri Jan 17 2003 - 19:12:35 CST)
- Bug found in sander - incorrect conversion factor causes randomized velocities to be too cold John D. Chodera (Sat Jan 18 2003 - 03:26:12 CST)
- High temperature MD A.Madhumalar (Sun Jan 19 2003 - 10:02:41 CST)
- equilibrated solvent box pu xuemei (Mon Jan 20 2003 - 02:54:33 CST)
- equilibrated solvent box pu xuemei (Mon Jan 20 2003 - 02:55:26 CST)
- Has anyone ever used MEAD? Vlad Cojocaru (Mon Jan 20 2003 - 07:58:30 CST)
- CARNAL Lepsa (Mon Jan 20 2003 - 09:22:22 CST)
- Ewald error Miguel de Federico (Mon Jan 20 2003 - 09:32:21 CST)
- morse potential hagop demirdjian (Mon Jan 20 2003 - 10:22:03 CST)
- script for Potential/kinectic energy Layi Adekoya (Mon Jan 20 2003 - 10:30:09 CST)
- scripts for compiling UHBD/MEAD with amber 7.0 eric hu (Mon Jan 20 2003 - 11:54:37 CST)
- SASA and H-bond over trajectories Bimo Ario Tejo (Mon Jan 20 2003 - 22:59:12 CST)
- Amber tutorial crown-ether Dvira Segal (Tue Jan 21 2003 - 08:06:55 CST)
- (no subject) Anke Eisenmann (Tue Jan 21 2003 - 08:07:25 CST)
- 'hot-solvent' and 'cold solute' problem Stefan Jungblut (Tue Jan 21 2003 - 09:36:37 CST)
- shake and H-O-H angle Luis Gracia (Tue Jan 21 2003 - 10:57:16 CST)
- Probelm with the generation of topology file Jash, Panchatapa (Tue Jan 21 2003 - 12:01:45 CST)
- reduce the disk space eric hu (Tue Jan 21 2003 - 12:48:14 CST)
- average structure generated by carnal eric hu (Tue Jan 21 2003 - 12:53:49 CST)
- shake and belly GUILLERMINA L ESTIU (Tue Jan 21 2003 - 15:38:59 CST)
- problems in equilibrating NaCl solution Seongeun Yang (Tue Jan 21 2003 - 16:48:04 CST)
- How to control box size pu xuemei (Wed Jan 22 2003 - 06:58:53 CST)
- SCSL Joffre Heredia (Wed Jan 22 2003 - 14:23:12 CST)
- Gibbs tutorial question Patricia Burgess (Wed Jan 22 2003 - 14:27:34 CST)
- question on ptraj Ioana Cozmuta (Wed Jan 22 2003 - 15:01:26 CST)
- MM_PBSA for Linux Ramón Garduño-Juárez (Wed Jan 22 2003 - 18:53:55 CST)
- LAM-MPI, Oscar and Amber compile Machine.g77_lam-mpi Dr Chris L. Brown (Wed Jan 22 2003 - 21:10:34 CST)
- Dummy-parameters in Amber? meiselba (Thu Jan 23 2003 - 04:39:17 CST)
- conformational sampling Robert G. Endres (Thu Jan 23 2003 - 08:17:57 CST)
- Proper torsion parameters missing? Heike Meiselbach (Thu Jan 23 2003 - 13:05:05 CST)
- Polymers Ndubuisi Emmanuel Okoro (Thu Jan 23 2003 - 21:12:10 CST)
- Chloroform Parameters N. Jiten Singh (Thu Jan 23 2003 - 23:27:24 CST)
- How much is minimum distance pu xuemei (Fri Jan 24 2003 - 01:11:29 CST)
- Shake problem in organic solvent yuan bo (Fri Jan 24 2003 - 06:03:48 CST)
- RESP-group constraint Artur Galstyan (Fri Jan 24 2003 - 08:38:53 CST)
- Nmode query kinsellg (Fri Jan 24 2003 - 09:00:40 CST)
- Amber Web page. caldwell_at_heimdal.compchem.ucsf.edu (Fri Jan 24 2003 - 10:45:00 CST)
- Zn2+ parameters Xiang, Tian-Xiang (Fri Jan 24 2003 - 15:42:07 CST)
- terminal phosphate group in RNA David A. Case (Fri Jan 24 2003 - 18:03:06 CST)
- posphinic acid parameters Alfonso Garcia Sosa (Sun Jan 26 2003 - 10:28:11 CST)
- polarization + ewald GUILBAUD Philippe 153683 (Mon Jan 27 2003 - 05:21:44 CST)
- structure image Xiang, Tian-Xiang (Mon Jan 27 2003 - 09:31:46 CST)
- gibbs run Xiang, Tian-Xiang (Mon Jan 27 2003 - 11:05:06 CST)
- lastrst Steve Seibold (Mon Jan 27 2003 - 11:46:57 CST)
- crystal structure of DNA/RNA homopolymers Ioana Cozmuta (Mon Jan 27 2003 - 13:34:13 CST)
- compiling amber on myrinet Scott E. Boesch (Mon Jan 27 2003 - 14:12:31 CST)
- freeware to visualize RMSD matrices creatde with Carnal Vlad Cojocaru (Mon Jan 27 2003 - 16:41:00 CST)
- xleap in Amber7 arubin_at_unmc.edu (Mon Jan 27 2003 - 18:54:46 CST)
- xleap in Amber7 arubin_at_unmc.edu (Mon Jan 27 2003 - 18:56:16 CST)
- Question: about restarting Energy vannajan_at_chiangmai.ac.th (Mon Jan 27 2003 - 19:53:30 CST)
- single point mutations to investigate the conformational change Sichun Yang (Mon Jan 27 2003 - 21:43:29 CST)
- Intramolecular H-bonds in charge fitting Lepsa (Tue Jan 28 2003 - 03:05:58 CST)
- script for H-bonds extracting Bimo Ario Tejo (Tue Jan 28 2003 - 04:00:52 CST)
- 2drms command in ptraj Vlad Cojocaru (Tue Jan 28 2003 - 06:52:17 CST)
- mm-pbsa error message Thomas Steinbrecher (Tue Jan 28 2003 - 09:02:04 CST)
- one question Fan Gao (Tue Jan 28 2003 - 10:14:56 CST)
- gibbs calculation Xiang, Tian-Xiang (Tue Jan 28 2003 - 13:03:44 CST)
- MM_PBSA Lepsa (Wed Jan 29 2003 - 07:12:34 CST)
- naphthalene, anthracene force field yuann (Wed Jan 29 2003 - 08:58:47 CST)
- antechamber and gamess Arvid Soederhaell (Wed Jan 29 2003 - 09:08:00 CST)
- antechamber and gamess David A. Case (Wed Jan 29 2003 - 10:16:03 CST)
- mm_pbsa and ALA scan Ahammadunny Pathiaseril (Wed Jan 29 2003 - 10:24:06 CST)
- Polymers Ndubuisi Emmanuel Okoro (Wed Jan 29 2003 - 15:40:53 CST)
- Request johneluwa_at_eircom.net (Wed Jan 29 2003 - 20:42:28 CST)
- new amino acid residues Nick Polfer (Thu Jan 30 2003 - 06:58:41 CST)
- mm-pbsa problem & possible solution Thomas Steinbrecher (Thu Jan 30 2003 - 09:51:57 CST)
- Quasi-harmonic analysis Pratul Agarwal (Thu Jan 30 2003 - 17:48:22 CST)
- ptraj on Methane in water box Dvira Segal (Fri Jan 31 2003 - 04:45:03 CST)
- AMBER7 & mpich FyD (Fri Jan 31 2003 - 08:05:41 CST)
- roar-cp : input for QM part ; output for CM2 charges hagop demirdjian (Fri Jan 31 2003 - 09:38:29 CST)
- Domain/Helix movement/MD Jianhui Wu (Fri Jan 31 2003 - 10:35:18 CST)
- Gibbs, ewald and ifc David Smith (Fri Jan 31 2003 - 16:16:14 CST)
- question about ligand Lishan Yao (Fri Jan 31 2003 - 16:43:39 CST)
- Gibbs dummy atom Paula Petrone (Fri Jan 31 2003 - 17:49:52 CST)
Last message date: Fri Feb 06 2004 - 10:15:04 CST
Archived on: Thu May 05 2005 - 14:17:43 CDT
232 messages sorted by:
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