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AMBER Archive (2002) - By Thread
Most recent messages2133 messages sorted by: [ author ] [ date ] [ subject ]
About this archive
Starting: Wed Jan 02 2002 - 16:22:14 CST
Ending: Tue Dec 31 2002 - 15:51:31 CST
- question Kang, Jonghoon (Wed Jan 02 2002 - 16:22:14 CST)
- linux? Shixiang Yan (Thu Jan 03 2002 - 20:17:46 CST)
- pairlist limit Laila Abou Zeid (Fri Jan 04 2002 - 08:32:57 CST)
- xleap sara nunez (Fri Jan 04 2002 - 17:28:14 CST)
- MPI (parallel) version of GIBBS Etienne ENGLER (Mon Jan 07 2002 - 06:13:45 CST)
- Re: Not able to do parallel run (again) Stéphane Teletchéa (Mon Jan 07 2002 - 11:08:17 CST)
- average position of water Hungie Hungie (Tue Jan 08 2002 - 06:28:00 CST)
- questions about resp X. Tan (Tue Jan 08 2002 - 10:31:55 CST)
- Amber on Tru64 Sebastian Jayaraj (Tue Jan 08 2002 - 13:22:43 CST)
- adiabatic map franck chevalier (Wed Jan 09 2002 - 06:41:57 CST)
- SCEE parameter Sophia Kondratova (Wed Jan 09 2002 - 10:49:36 CST)
- removing rotational motion in MD Michael G Cooney (Wed Jan 09 2002 - 11:41:26 CST)
- question: velocity units Martina Roeselova (Wed Jan 09 2002 - 11:46:00 CST)
- Amber 6 on IA64 Karen Haskell (Wed Jan 09 2002 - 15:35:02 CST)
- (no subject) amutha ramaswamy (Thu Jan 10 2002 - 04:11:15 CST)
- inquiry regarding AMBER xz27 (Thu Jan 10 2002 - 15:24:08 CST)
- seperate_solute_output Mirjam Lerch (Fri Jan 11 2002 - 03:02:31 CST)
- Re: Re:ERROR TERMINATION DUE TO SHAKE OR TORCON sxzheng (Fri Jan 11 2002 - 21:21:30 CST)
- multiple improper torsion terms Thijs Beuming (Fri Jan 11 2002 - 21:37:58 CST)
- pukering of DNA bases? A.Madhumalar (Sat Jan 12 2002 - 23:03:50 CST)
- ptraj cannot use compressed files? Michael G Cooney (Mon Jan 14 2002 - 10:17:03 CST)
- ptraj and compressed files Michael G Cooney (Mon Jan 14 2002 - 10:48:40 CST)
- (no subject) Sophia Kondratova (Mon Jan 14 2002 - 12:28:01 CST)
- how to neutralise the system? X. Tan (Mon Jan 14 2002 - 13:18:14 CST)
- resizing and recompiling sander UMEMOTO kimiko (Mon Jan 14 2002 - 19:12:02 CST)
- temperature control Jerry wu (Mon Jan 14 2002 - 21:55:16 CST)
- azobenzene parameters Uwe Richter (Tue Jan 15 2002 - 04:18:03 CST)
- minimising WATBOX216 sara nunez (Tue Jan 15 2002 - 13:11:04 CST)
- I can not see text in xleap ! S. Jang (Wed Jan 16 2002 - 00:56:04 CST)
- Amber 6.0 purchasing!! hathaimard pongkasem (Wed Jan 16 2002 - 02:14:48 CST)
- Amber 6.0 purchasing!! hathaimard pongkasem (Wed Jan 16 2002 - 02:15:03 CST)
- sander (Amber5) vs sander_classic (Amber6) Uwe Richter (Wed Jan 16 2002 - 05:33:32 CST)
- Open position: Postdoctoral Scientist Joachim Reichelt (Wed Jan 16 2002 - 09:57:07 CST)
- Parameters Marta Murcia (Wed Jan 16 2002 - 09:59:26 CST)
- Stretching Constants Daniel Flint (Thu Jan 17 2002 - 05:21:52 CST)
- Amino acid unit "NHE" problem ? S. Jang (Thu Jan 17 2002 - 06:27:19 CST)
- NAD parameters Andy Purkiss (Thu Jan 17 2002 - 13:42:21 CST)
- nmode memory requirements Michael Jakusch (Fri Jan 18 2002 - 10:15:52 CST)
- Amber6 + IBM SP3 Sanjeev B.S. (Sat Jan 19 2002 - 08:59:58 CST)
- Latest parm + getting parm98 as default in LEaP Sanjeev B.S. (Mon Jan 21 2002 - 00:43:42 CST)
- nmode vectors Thijs Beuming (Mon Jan 21 2002 - 06:24:48 CST)
- triNAG parameters?4 Andrea Bernini (Mon Jan 21 2002 - 09:13:26 CST)
- timescale of deoxyribose ring repuckering Jake Isaacs (Tue Jan 22 2002 - 10:43:40 CST)
- "flags" in .lib files Sue Heavner (Wed Jan 23 2002 - 10:22:08 CST)
- DOCK Peter Gannett (Thu Jan 24 2002 - 08:48:52 CST)
- MP_Lite Stéphane Teletchéa (Thu Jan 24 2002 - 11:44:40 CST)
- torsional fit Fabrizio Giordanetto (Fri Jan 25 2002 - 04:34:55 CST)
- group input in ANAL Elizabeth K. White (Fri Jan 25 2002 - 16:11:13 CST)
- xleap and PDB file Prabal Maiti (Tue Jan 29 2002 - 01:28:23 CST)
- restart md simulation Uwe Richter (Tue Jan 29 2002 - 03:35:50 CST)
- box_size Susanna Monti (Tue Jan 29 2002 - 04:34:22 CST)
- MacOS X David Bevan (Tue Jan 29 2002 - 10:15:12 CST)
- B-factor Michal Otyepka (Thu Jan 31 2002 - 04:45:50 CST)
- LIMIN Faliure/Energies per residue for B-DNA etc. Prabal Maiti (Thu Jan 31 2002 - 13:49:00 CST)
- question regarding ntwv. Margaret Cheung (Thu Jan 31 2002 - 19:55:58 CST)
- help on parameters. X. Tan (Mon Feb 04 2002 - 19:40:52 CST)
- quasih Sue Heavner (Wed Feb 06 2002 - 09:16:25 CST)
- ImagingAtom eric ARNOULT (Wed Feb 06 2002 - 10:07:04 CST)
- compile AMBER on cygwin? quch quch (Thu Feb 07 2002 - 13:46:43 CST)
- frcmod file format Sophia Kondratova (Mon Feb 11 2002 - 12:16:23 CST)
- parm94.dat file x357l (Tue Feb 12 2002 - 12:21:44 CST)
- IFTRES option in sander and gibbs Alexander Issanin (Tue Feb 12 2002 - 15:09:52 CST)
- belly input Prabal Maiti (Tue Feb 12 2002 - 16:26:21 CST)
- Linking to its own image Miguel Angel Rodriguez Carvajal (Thu Feb 14 2002 - 08:15:52 CST)
- RESP Crash Mike Keller (Thu Feb 14 2002 - 09:24:51 CST)
- Re: problem in running MM-PBSA script David Case (Thu Feb 14 2002 - 10:42:52 CST)
- residual dipolar coupling restraints Jake Isaacs (Thu Feb 14 2002 - 13:37:42 CST)
- memory problem on gibbs X. Tan (Thu Feb 14 2002 - 18:24:55 CST)
- flying monomers... Margaret Cheung (Fri Feb 15 2002 - 17:58:39 CST)
- MPICH/LAM on sparc Sanjeev B.S. (Sat Feb 16 2002 - 06:23:26 CST)
- Power Point slides Krishna Bisetty (Mon Feb 18 2002 - 01:11:22 CST)
- .OFF file format Dr Jan Rosenzweig (Mon Feb 18 2002 - 12:14:27 CST)
- Gibbs Question Bernd Wellenzohn (Mon Feb 18 2002 - 14:47:15 CST)
- removing rotational motion John Finke (Tue Feb 19 2002 - 03:44:08 CST)
- Re: removing rotational motion Andreas Svrcek-Seiler (Tue Feb 19 2002 - 06:27:18 CST)
- Re: removing rotational motion Raik Grunberg (Tue Feb 19 2002 - 06:30:00 CST)
- Re: removing rotational motion Raik Grunberg (Tue Feb 19 2002 - 06:30:00 CST)
- Re: removing rotational motion Jianxin Guo (Fri Feb 22 2002 - 16:32:48 CST)
- restrt problem Sanjeev B.S. (Tue Feb 19 2002 - 07:50:41 CST)
- Xleap x357l (Tue Feb 19 2002 - 10:03:11 CST)
- The link is out Stéphane Teletchéa (Tue Feb 19 2002 - 10:58:44 CST)
- ERROR from RESNBA X. Tan (Tue Feb 19 2002 - 19:39:21 CST)
- AMBER logo citation FyD (Wed Feb 20 2002 - 01:53:18 CST)
- rms and watershell (in ptraj) dkon_at_email.arizona.edu (Wed Feb 20 2002 - 18:54:58 CST)
- MPI sander Uwe Richter (Thu Feb 21 2002 - 07:13:52 CST)
- vlimit exceed Prabal Maiti (Thu Feb 21 2002 - 21:23:39 CST)
- MD with simulated annealing Giulio Rastelli (Fri Feb 22 2002 - 12:39:56 CST)
- anal input Prabal Maiti (Fri Feb 22 2002 - 18:31:58 CST)
- recursively calling sander? Jeff Ames (Mon Feb 25 2002 - 10:32:54 CST)
- redius of B-DNA duplex Hungie Hungie (Mon Feb 25 2002 - 10:49:26 CST)
- Carnal coordinate averaging Michael G Cooney (Mon Feb 25 2002 - 16:01:26 CST)
- (no subject) deepak rangaswamy (Tue Feb 26 2002 - 05:28:18 CST)
- leap:segmentation fault Sanjeev B.S. (Tue Feb 26 2002 - 10:30:45 CST)
- xleap and carbohydrates and stuff Amesh Patel (Wed Feb 27 2002 - 08:43:23 CST)
- Cholesterol PREP file samantha hughes (Wed Feb 27 2002 - 09:28:46 CST)
- (no subject) Ian Bates (Wed Feb 27 2002 - 15:23:17 CST)
- visualizaion program for NMODE! Pradipta Bandyopadhyay (Wed Feb 27 2002 - 16:48:30 CST)
- correlated motions in a protein! Pradipta Bandyopadhyay (Wed Feb 27 2002 - 17:52:55 CST)
- Persistence length Bernd Wellenzohn (Thu Feb 28 2002 - 09:39:11 CST)
- AMBER 99 John Finke (Thu Feb 28 2002 - 18:22:55 CST)
- (no subject) deepak rangaswamy (Fri Mar 01 2002 - 05:00:51 CST)
- Release of Amber, version 7 (fwd) amber mail account (Sun Mar 03 2002 - 17:13:26 CST)
- concentrated system Jerry wu (Mon Mar 04 2002 - 02:36:21 CST)
- carnal and union Pascal Bonnet (Mon Mar 04 2002 - 03:00:20 CST)
- carnal and union: solution Pascal Bonnet (Mon Mar 04 2002 - 06:33:17 CST)
- GB simulation Giulio Rastelli (Mon Mar 04 2002 - 10:32:28 CST)
- amber 60 on Unicos Cray Cezary Czaplewski (Mon Mar 04 2002 - 11:56:36 CST)
- (no subject) Campbell, Matthew P (Tue Mar 05 2002 - 11:21:07 CST)
- a question about .in files Vlad Cojocaru (Wed Mar 06 2002 - 09:00:02 CST)
- leap calculation Itziar Maestre Asenjo (Wed Mar 06 2002 - 11:43:44 CST)
- Re: leap calculation (loadamberprep) Bill Ross (Wed Mar 06 2002 - 13:22:33 CST)
- Are the programs sander and gibbs in Amber 7 parallel? ramon kleber da rocha (Wed Mar 06 2002 - 13:28:01 CST)
- converting some files Vlad Cojocaru (Thu Mar 07 2002 - 05:00:00 CST)
- dG of wild type/mutant FyD (Thu Mar 07 2002 - 05:26:31 CST)
- statistical analysis of MD trajectories Jake Isaacs (Thu Mar 07 2002 - 11:24:03 CST)
- parameter estimation Vlad Cojocaru (Thu Mar 07 2002 - 12:32:25 CST)
- choosing a forcefield nepenthes_at_vplaces.net (Thu Mar 07 2002 - 21:51:25 CST)
- high electrostatic energy thenmalar rathinavelan (Thu Mar 07 2002 - 23:13:40 CST)
- new units Vlad Cojocaru (Fri Mar 08 2002 - 08:35:46 CST)
- Europium force field parms Peter Gannett (Sun Mar 10 2002 - 14:07:44 CST)
- Re Europium force field parms Fabrice Yerly (Mon Mar 11 2002 - 01:32:59 CST)
- Re Europium force field parms Marc Baaden (Mon Mar 11 2002 - 05:52:40 CST)
- limit of written files with ptraj Carles Ferrer (Mon Mar 11 2002 - 14:54:16 CST)
- combining trajectory file Rukman Hertadi (Tue Mar 12 2002 - 03:48:49 CST)
- question on Gibbs calculation X. Tan (Tue Mar 12 2002 - 15:50:24 CST)
- help please :) Richard Kho (Fri Mar 15 2002 - 18:59:23 CST)
- Post-doctoral position Wolfe, Jennifer (Mon Mar 18 2002 - 10:33:11 CST)
- Dual AMD motherboards jim caldwell (Mon Mar 18 2002 - 17:47:12 CST)
- Dual AMD ASUS A7M266-D Solved jim caldwell (Mon Mar 18 2002 - 20:37:19 CST)
- minimization problem Uwe Richter (Tue Mar 19 2002 - 06:22:06 CST)
- carnal RST output format Pascal Bonnet (Tue Mar 19 2002 - 08:12:31 CST)
- Still no bench Stéphane Teletchéa (Tue Mar 19 2002 - 09:17:45 CST)
- creating a unit wth xleap Marcela Madrid (Tue Mar 19 2002 - 13:07:30 CST)
- Amber6 & ES40 incompatability Sanjeev B.S. (Wed Mar 20 2002 - 01:01:17 CST)
- building bcyd with tleap Itziar Maestre Asenjo (Wed Mar 20 2002 - 04:51:47 CST)
- MM-PBSA philosophy Michal Otyepka (Wed Mar 20 2002 - 06:34:24 CST)
- atom connection, .off file problem Uwe Richter (Wed Mar 20 2002 - 07:48:07 CST)
- Question about obtaining amber! Peter Fojan (Thu Mar 21 2002 - 07:19:59 CST)
- MS program ... A. Ababou (Sat Mar 23 2002 - 10:21:15 CST)
- mdcrd to arc Ian R Bates (Sat Mar 23 2002 - 10:46:21 CST)
- nmropt problem in AMBER7 Rukman Hertadi (Mon Mar 25 2002 - 03:51:22 CST)
- Resending: Medicinal and Computational Chemistry Job Market Computational Chemistry Job Market (Mon Mar 25 2002 - 14:05:03 CST)
- Re: polarizabilities Lepsa (Tue Mar 26 2002 - 03:12:09 CST)
- Hydrogen bond energy using Anal A.Madhumalar (Tue Mar 26 2002 - 04:23:34 CST)
- One question about how to use the amber Zhe SUN (Tue Mar 26 2002 - 06:49:35 CST)
- secondary structure Ian R Bates (Tue Mar 26 2002 - 13:49:48 CST)
- problems using Link John Finke (Tue Mar 26 2002 - 14:39:59 CST)
- GB model and belly dkon_at_email.arizona.edu (Tue Mar 26 2002 - 15:46:40 CST)
- More GB/Belly dkon_at_email.arizona.edu (Tue Mar 26 2002 - 16:00:23 CST)
- s-matrix format and ftnmr Shixiang Yan (Wed Mar 27 2002 - 15:49:50 CST)
- What is the atoms limit for Amber 7? William Wei (Wed Mar 27 2002 - 16:19:34 CST)
- sulfate and sulfamate parameters jeff dyason (Wed Mar 27 2002 - 22:28:55 CST)
- AMBER 5 Monica (Wed Mar 27 2002 - 22:29:12 CST)
- change topology Michal Otyepka (Thu Mar 28 2002 - 02:44:38 CST)
- Magnesium as a DNA counterion in AMBER 6.0 Mike Keller (Thu Mar 28 2002 - 09:31:29 CST)
- Amber6, GB (Memory, MATOM, nmr.h)/Folding (mutation) Wu, JianHui(IAF)(LAVAL) (Thu Mar 28 2002 - 11:56:04 CST)
- a little bit confused with leap-frog algorithm... Margaret Cheung (Thu Mar 28 2002 - 15:08:40 CST)
- Problem with atom type rhertadi_at_bio.titech.ac.jp (Thu Mar 28 2002 - 15:55:33 CST)
- convergence of MD simulations Sue Heavner (Sat Mar 30 2002 - 17:02:16 CST)
- does PME function without charge neutralization? Ian R Bates (Tue Apr 02 2002 - 12:30:41 CST)
- (no subject) deepak rangaswamy (Tue Apr 02 2002 - 22:52:55 CST)
- input files Monica (Wed Apr 03 2002 - 07:00:42 CST)
- Initial Amber 7 benchmark timings David Case (Wed Apr 03 2002 - 20:33:14 CST)
- amber7, PME and anisotrop press. Arvid Soederhaell (Thu Apr 04 2002 - 03:46:58 CST)
- new residues Vlad Cojocaru (Thu Apr 04 2002 - 07:03:37 CST)
- convergence of MD simulations Sue Heavner (Thu Apr 04 2002 - 16:24:05 CST)
- Sander-Gibbs Kidley N J (Mon Apr 08 2002 - 10:34:49 CDT)
- PDB file with CONECT record Prabal Maiti (Mon Apr 08 2002 - 14:06:21 CDT)
- PDB file with CONECT record (fwd) Prabal Maiti (Tue Apr 09 2002 - 20:04:50 CDT)
- Roar 2.1 with Amber7 Soonmin Jang (Tue Apr 09 2002 - 22:39:07 CDT)
- Amber7 and VMD Soonmin Jang (Wed Apr 10 2002 - 03:40:37 CDT)
- (no subject) Mark Hsieh (Wed Apr 10 2002 - 15:31:50 CDT)
- Matching Patterns Tali (Wed Apr 10 2002 - 16:57:59 CDT)
- DNA structure get distorted Monica (Thu Apr 11 2002 - 03:00:48 CDT)
- noesy intensity input in DNA Monica (Thu Apr 11 2002 - 03:03:50 CDT)
- Follow distances during MD Francois Dupradeau (Thu Apr 11 2002 - 05:19:02 CDT)
- (no subject) Mark Beardsell (Thu Apr 11 2002 - 08:36:29 CDT)
- Save from LEaP to a PDBQ file ? jeff dyason (Thu Apr 11 2002 - 22:50:32 CDT)
- Thanks FyD (Fri Apr 12 2002 - 02:04:53 CDT)
- order parameters? Arvid Soederhaell (Fri Apr 12 2002 - 07:55:33 CDT)
- Compiling Amber7 on a Beowulf Cluster - Compiling Error Peter Gannett (Fri Apr 12 2002 - 18:59:38 CDT)
- help ..problem about antechamber Yi ming Cheng (Sat Apr 13 2002 - 00:30:26 CDT)
- Vulgar Models Do Everything And Love It!!! telesales (Mon Apr 15 2002 - 19:03:45 CDT)
- Re: Help! Sander run error: Bus error David Case (Tue Apr 16 2002 - 00:32:16 CDT)
- compiling amber 6.0 in a Sun starfire ENT10000 ramon kleber da rocha (Tue Apr 16 2002 - 14:08:54 CDT)
- 4 Medicinal and Computational Chemistry Candidates medicinal and Compuatational Chemistry Resumes and Jobs (Tue Apr 16 2002 - 16:55:48 CDT)
- Recalculating energies John Finke (Tue Apr 16 2002 - 19:45:23 CDT)
- RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 05:53:27 CDT)
- Amber in a distributed environment Peter Gannett (Wed Apr 17 2002 - 07:07:56 CDT)
- RESP charges Vlad Cojocaru (Wed Apr 17 2002 - 07:36:43 CDT)
- Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 12:32:28 CDT)
- again...Minimization of pentane holding a plane of carbon atoms Hungie Hungie (Wed Apr 17 2002 - 13:03:23 CDT)
- mm pbsa: generate snapshots Mark Hsieh (Wed Apr 17 2002 - 16:52:41 CDT)
- pentane minimization Hungie Hungie (Thu Apr 18 2002 - 04:15:33 CDT)
- pentane minimization Hungie Hungie (Thu Apr 18 2002 - 04:16:46 CDT)
- DNA shifts during MD; C.O.M. removing and ptraj doesn't help... Filip Ryjacek (Thu Apr 18 2002 - 10:17:12 CDT)
- RESP cfrenz_at_aecom.yu.edu (Thu Apr 18 2002 - 10:55:55 CDT)
- pentane minimization...again Hungie Hungie (Thu Apr 18 2002 - 11:30:15 CDT)
- MPICH and AMBER 7 Mark Hsieh (Thu Apr 18 2002 - 18:12:58 CDT)
- RESP-ivary Vlad Cojocaru (Fri Apr 19 2002 - 06:26:22 CDT)
- To PROFEC users Salinthip Thipayang (Fri Apr 19 2002 - 09:13:11 CDT)
- amber7 compilation on a beowulf cluster Peter Gannett (Fri Apr 19 2002 - 14:59:56 CDT)
- RE: amber7 compilation on a beowulf cluster John Bushnell (Fri Apr 19 2002 - 16:48:00 CDT)
- RE: amber7 compilation on a beowulf cluster Bill Ross (Fri Apr 19 2002 - 17:26:19 CDT)
- Re: amber7 compilation on a beowulf cluster David Case (Fri Apr 19 2002 - 20:56:50 CDT)
- Re: amber7 compilation on a beowulf cluster Peter Gannett (Sat Apr 20 2002 - 07:14:01 CDT)
- mm_pbsa for uhbd Mark Hsieh (Fri Apr 19 2002 - 20:56:18 CDT)
- (no subject) deepak rangaswamy (Sat Apr 20 2002 - 00:22:54 CDT)
- dummy atoms. Yongjun Jiang (Sat Apr 20 2002 - 22:20:44 CDT)
- leap bugfix Bill Ross (Sun Apr 21 2002 - 16:55:34 CDT)
- RESP Vlad Cojocaru (Mon Apr 22 2002 - 05:17:17 CDT)
- amber6 with parallel Khatcharin Siriwong (Mon Apr 22 2002 - 07:48:24 CDT)
- a problem Vlad Cojocaru (Mon Apr 22 2002 - 10:56:48 CDT)
- (no subject) SPEROLEEM_at_aol.com (Mon Apr 22 2002 - 13:47:28 CDT)
- a more general question Vlad Cojocaru (Tue Apr 23 2002 - 09:20:34 CDT)
- DME and Carnal with AMBER6 Katherine W. Abold (Tue Apr 23 2002 - 09:48:04 CDT)
- RESP tutorial Michael G Cooney (Tue Apr 23 2002 - 12:15:51 CDT)
- INTPRT and PMF Sophia Kondratova (Tue Apr 23 2002 - 13:23:36 CDT)
- (no subject) Bill Ross (Tue Apr 23 2002 - 14:30:58 CDT)
- parallel sander? Mark Hsieh (Tue Apr 23 2002 - 14:31:55 CDT)
- generating left-handed A-DNA Marcela Madrid (Tue Apr 23 2002 - 19:41:08 CDT)
- sander & prmtop file generated from antechamber input ? jeff dyason (Tue Apr 23 2002 - 22:33:58 CDT)
- Re: amber7 and tip5p David Case (Wed Apr 24 2002 - 16:04:05 CDT)
- Number of WATBOX yuann (Thu Apr 25 2002 - 00:54:02 CDT)
- PMF calculations Sophia Kondratova (Thu Apr 25 2002 - 08:30:11 CDT)
- About Group in Carnal William Wei (Thu Apr 25 2002 - 10:50:08 CDT)
- sander mpich hangs Mark Hsieh (Thu Apr 25 2002 - 17:01:26 CDT)
- Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Fri Apr 26 2002 - 03:39:35 CDT)
- Re: Problems with AMBER7 and Multiple Processors on SGI servers Carlos Simmerling (Fri Apr 26 2002 - 07:05:52 CDT)
- Re: Problems with AMBER7 and Multiple Processors on SGI servers Ian bates (Fri Apr 26 2002 - 10:17:52 CDT)
- RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Tue Apr 30 2002 - 04:59:11 CDT)
- RE: Problems with AMBER7 and Multiple Processors on SGI servers Vincent BOSQUIER (Thu May 02 2002 - 03:55:45 CDT)
- max_rstack requested Albert Codony (Sun Apr 28 2002 - 17:39:58 CDT)
- parmjoin Vlad Cojocaru (Mon Apr 29 2002 - 11:53:01 CDT)
- Fail message:Segmantation fault and Bus error? William Wei (Mon Apr 29 2002 - 14:38:48 CDT)
- NTT=5? Jung-Hsing Lin (Mon Apr 29 2002 - 18:10:30 CDT)
- TIP4P parameters Ge Zhou (Mon Apr 29 2002 - 21:03:54 CDT)
- install leap not working nepenthes_at_vplaces.net (Tue Apr 30 2002 - 02:52:07 CDT)
- How to run the leap module param_at_ibab.ac.in (Tue Apr 30 2002 - 04:34:32 CDT)
- valine to alanine example Sophia Kondratova (Tue Apr 30 2002 - 10:23:21 CDT)
- heterochirical peptides ? Yuguang Mu (Tue Apr 30 2002 - 10:43:39 CDT)
- NaCl concentration Peter Gannett (Tue Apr 30 2002 - 14:34:38 CDT)
- about ew_legal.h X. Tan (Tue Apr 30 2002 - 19:12:01 CDT)
- Amber7 compilation on IBM sp3 machine Soonmin Jang (Tue Apr 30 2002 - 23:33:05 CDT)
- AMBER 7 - more problems with leap Mark Beardsell (Wed May 01 2002 - 07:17:46 CDT)
- Amber7 nmode Sue Heavner (Wed May 01 2002 - 12:23:19 CDT)
- Carnal BUG?? William Wei (Wed May 01 2002 - 22:19:03 CDT)
- RE: Carnal BUG?? --- How can I get the correct residue number? William Wei (Thu May 02 2002 - 11:09:21 CDT)
- Compilation on RedHat-7.2 with MPICH Vincent BOSQUIER (Thu May 02 2002 - 11:29:32 CDT)
- new RNA residues Vlad Cojocaru (Thu May 02 2002 - 14:07:32 CDT)
- Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 15:26:45 CDT)
- Re: How can I get the correct residue number? Bill Ross (Thu May 02 2002 - 15:38:24 CDT)
- Help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 09:40:41 CDT)
- help/suggestions needed with PROFEC Salinthip Thipayang (Fri May 03 2002 - 10:03:47 CDT)
- TI integration Joe Fernandez (Sat May 04 2002 - 08:59:57 CDT)
- Thanks to all Albert Codony (Sat May 04 2002 - 10:38:12 CDT)
- crdgrow Vlad Cojocaru (Sat May 04 2002 - 15:06:32 CDT)
- missing residues Mark Hsieh (Sun May 05 2002 - 02:15:31 CDT)
- topology file generation Sanjeev B.S. (Mon May 06 2002 - 00:36:36 CDT)
- (no subject) Sophia Kondratova (Mon May 06 2002 - 08:13:53 CDT)
- TI using sander on cluster Joe Fernandez (Mon May 06 2002 - 09:52:50 CDT)
- "Unit 5 Error" with a Linux/MPICH Amber7 Vincent BOSQUIER (Mon May 06 2002 - 10:50:07 CDT)
- Problems with parallel computing in Amber7 Vincent BOSQUIER (Tue May 14 2002 - 09:28:10 CDT)
- NMR refinement Jake Isaacs (Tue May 14 2002 - 14:16:37 CDT)
- Topology file format in AMBER 7 Joffre Heredia (Tue May 14 2002 - 16:14:55 CDT)
- RE: automated rescoring of ligands Vickie Tsui (Tue May 14 2002 - 16:23:29 CDT)
- question Masamichi Fujinami 4029 (Wed May 15 2002 - 00:49:03 CDT)
- Energy problem during dynamics with amber 7 Florence CASSET (Wed May 15 2002 - 04:48:23 CDT)
- Re: help: nmode compile question!!! Andreas Svrcek-Seiler (Wed May 15 2002 - 06:30:12 CDT)
- Sander, Setup for Parallel SMP Linux Cluster Jianhui Wu (Wed May 15 2002 - 14:02:27 CDT)
- Mutations - Molecular Dynamics William Wei (Thu May 16 2002 - 18:11:36 CDT)
- igb=2,gbsa=1,antechamber,bad atom type Jianhui Wu (Fri May 17 2002 - 14:20:14 CDT)
- Re: About the box info read error Bill Ross (Fri May 17 2002 - 15:33:51 CDT)
- Re: Anal in AMBER7 David Case (Sun May 19 2002 - 20:44:38 CDT)
- vanadium Natasja Brooijmans (Sun May 19 2002 - 21:35:27 CDT)
- about sander_classic AMBER6.0 Nikolai Smolin (Mon May 20 2002 - 08:08:14 CDT)
- helix analysis Prabal Maiti (Mon May 20 2002 - 14:20:45 CDT)
- mm_pbsa X. Tan (Mon May 20 2002 - 18:04:52 CDT)
- Energy conservation in NVE simulation ? Soonmin Jang (Tue May 21 2002 - 00:42:40 CDT)
- (no subject) Sophia Kondratova (Tue May 21 2002 - 13:37:24 CDT)
- ptraj problem Jake Isaacs (Tue May 21 2002 - 16:20:02 CDT)
- antechamber Giulio Rastelli (Wed May 22 2002 - 05:56:25 CDT)
- Re: Protonate doesn-t recognize my pdb input file Stéphane Teletchéa (Wed May 22 2002 - 06:41:08 CDT)
- again about sander_classic Amber 6.0 Nikolai Smolin (Wed May 22 2002 - 06:42:50 CDT)
- this is a test of the amber reflector. Please ignore. Marcela Marcela Madrid (Wed May 22 2002 - 08:59:24 CDT)
- still having ptraj problems Jake Isaacs (Wed May 22 2002 - 10:19:06 CDT)
- Protonate doesn-t recognize by pdb input file David Case (Wed May 22 2002 - 11:20:20 CDT)
- TIP4P water with AMBER6 Noriaki Okimoto (Wed May 22 2002 - 13:01:35 CDT)
- ambpdb in AMBER7 Matthew Lee (Wed May 22 2002 - 15:42:34 CDT)
- this is a test for amber reflector - please ignore Asif Rahaman (Wed May 22 2002 - 17:17:29 CDT)
- Problem with 2D Gibbs run Asif Rahaman (Wed May 22 2002 - 17:32:49 CDT)
- This is a test for amber reflector - please ignore Lorenzo Gontrani (Thu May 23 2002 - 03:34:38 CDT)
- CARNAL Vlad Cojocaru (Thu May 23 2002 - 05:35:29 CDT)
- charges Marcela Madrid (Thu May 23 2002 - 15:25:43 CDT)
- helix analysis (fwd) Prabal Maiti (Thu May 23 2002 - 16:30:33 CDT)
- subdomain moving as a rigid unit during MD Marcela Madrid (Fri May 24 2002 - 10:59:40 CDT)
- Re: compilation of sander on Alpha/Linux clusters jim caldwell (Fri May 24 2002 - 16:41:00 CDT)
- PME & cutoff A. Hungie (Sat May 25 2002 - 08:12:48 CDT)
- parallel sander on T3E Peter Gannett (Sat May 25 2002 - 09:46:37 CDT)
- compilation for Hitachi SR8000 A. Hungie (Sun May 26 2002 - 12:25:17 CDT)
- Charge export from Leap is rounded off jeff dyason (Sun May 26 2002 - 19:06:36 CDT)
- Linux Parallel compilation Linux Mpich PGI Fabrice Yerly (Mon May 27 2002 - 07:31:09 CDT)
- glucose Yuguang Mu (Tue May 28 2002 - 10:05:10 CDT)
- RESP charges for phosphorylated residues Uwe Richter (Tue May 28 2002 - 11:05:05 CDT)
- xleap Marcela Madrid (Tue May 28 2002 - 16:21:39 CDT)
- Cyclodextrin Toshikazu Matsuoka (Wed May 29 2002 - 01:48:19 CDT)
- minimization to fix up hydrogen positions yuann (Wed May 29 2002 - 02:33:23 CDT)
- SHAKE troubles Arvid Soederhaell (Wed May 29 2002 - 05:07:17 CDT)
- MPich error Fabrice Yerly (Wed May 29 2002 - 07:46:29 CDT)
- xLeap problem Donald Thomas (Wed May 29 2002 - 23:42:04 CDT)
- sander_classic, erratic on IBM Giovanni Fossati (Thu May 30 2002 - 01:17:07 CDT)
- GROUP Specification - Error decoding variable yuann (Thu May 30 2002 - 02:43:02 CDT)
- TIP4P SEKIJIMA Masakazu (Thu May 30 2002 - 03:43:14 CDT)
- Intel ifc Compiler Joachim Reichelt (Thu May 30 2002 - 04:23:21 CDT)
- AMBER7 Michael Sattler (Thu May 30 2002 - 07:59:11 CDT)
- (no subject) SPEROLEEM_at_aol.com (Thu May 30 2002 - 17:51:26 CDT)
- H-bond Dmitry Pavlov (Fri May 31 2002 - 03:01:42 CDT)
- Fwd: NPT-MD Antonio J. Díaz Quintana (Fri May 31 2002 - 04:17:55 CDT)
- Problem with Gibbs 2D run Asif Rahaman (Sun Jun 02 2002 - 22:29:38 CDT)
- (no subject) Ishita sharma (Mon Jun 03 2002 - 06:07:38 CDT)
- Re: mm_pbsa in parallel system David Case (Mon Jun 03 2002 - 09:49:08 CDT)
- Parallel Amber on Solaris 2.6 Thomas A. Spraggins (Mon Jun 03 2002 - 09:49:45 CDT)
- Re: mm_pbsa in parallel system (fwd) Jianhui Wu (Mon Jun 03 2002 - 11:03:12 CDT)
- Clarification R.Sathyapriya (Tue Jun 04 2002 - 02:45:19 CDT)
- Amber PGF77 comilation error + MPICH problem Fabrice Yerly (Wed Jun 05 2002 - 03:31:26 CDT)
- Parameters for hexachloroethane Bjorn-Olav Brandsdal (Wed Jun 05 2002 - 04:13:54 CDT)
- Machine_file for Hitachi SR8000 A. Hungie (Wed Jun 05 2002 - 06:09:03 CDT)
- PME box ? Yi ming Cheng (Wed Jun 05 2002 - 07:11:15 CDT)
- reference Marcela Madrid (Wed Jun 05 2002 - 10:48:55 CDT)
- Question TL Poulos (Wed Jun 05 2002 - 10:49:10 CDT)
- Amber7, sander, restart, blast up Jianhui Wu (Wed Jun 05 2002 - 12:07:51 CDT)
- Running amber7 and nab on FreeBSD bdodson_at_scms.utmb.EDU (Wed Jun 05 2002 - 15:31:24 CDT)
- cap water eric hu (Wed Jun 05 2002 - 19:14:10 CDT)
- Intel Kernel Math Library Joffre Heredia (Thu Jun 06 2002 - 14:46:32 CDT)
- Mac OS X compiliation? Randy M. Wadkins (Thu Jun 06 2002 - 16:58:18 CDT)
- amber on MAC OSX case (Thu Jun 06 2002 - 19:22:44 CDT)
- analysis of Gibbs 2D run Asif Rahaman (Thu Jun 06 2002 - 23:46:34 CDT)
- no mdcrd, no mden file Arvid Soederhaell (Fri Jun 07 2002 - 06:43:30 CDT)
- benchmark for Amber7 A. Hungie (Fri Jun 07 2002 - 09:37:07 CDT)
- charges for peptides Marcela Madrid (Fri Jun 07 2002 - 10:14:59 CDT)
- Suggestion to Bill and Case William Wei (Fri Jun 07 2002 - 15:49:10 CDT)
- model molecules for getting charges of DNA Jiyoung Heo (Sat Jun 08 2002 - 19:20:10 CDT)
- C=C=C bending parameters Jones de Andrade (Sun Jun 09 2002 - 15:55:33 CDT)
- cold belly run error eric hu (Sun Jun 09 2002 - 17:55:47 CDT)
- (no subject) Snyder, James (Sun Jun 09 2002 - 19:45:03 CDT)
- RE: xaLeap make fails on AIX Thomas A. Spraggins (Mon Jun 10 2002 - 11:13:01 CDT)
- Re:xaLeap make fails on AIX Bill Ross (Mon Jun 10 2002 - 13:19:47 CDT)
- entropy calculation X. Tan (Mon Jun 10 2002 - 18:42:59 CDT)
- Re: Floating Invalid Bill Ross (Tue Jun 11 2002 - 00:36:16 CDT)
- Reorder water in amber7 Peter Varnai (Tue Jun 11 2002 - 03:38:32 CDT)
- Amber protein-ion problem Emma.Sigfridsson_at_astrazeneca.com (Tue Jun 11 2002 - 06:41:29 CDT)
- minimization probs Amesh Patel (Tue Jun 11 2002 - 10:57:12 CDT)
- Protonated database Andrew Petersen (Tue Jun 11 2002 - 14:12:28 CDT)
- sander input for a newbie Randy M. Wadkins (Tue Jun 11 2002 - 18:21:22 CDT)
- test of mm_pbsa Yongjun Jiang (Tue Jun 11 2002 - 22:08:23 CDT)
- igb problem in sander Emma.Sigfridsson_at_astrazeneca.com (Wed Jun 12 2002 - 04:11:20 CDT)
- vlimit exceeded A. Hungie (Wed Jun 12 2002 - 04:49:44 CDT)
- perturbed type DH not found Mao Xiang (Wed Jun 12 2002 - 05:47:19 CDT)
- Application of Amber Monica (Wed Jun 12 2002 - 10:24:49 CDT)
- sander parallel eric hu (Wed Jun 12 2002 - 16:11:24 CDT)
- Re: sander parallel Joffre Heredia (Thu Jun 13 2002 - 12:39:55 CDT)
- Re: sander parallel eric hu (Thu Jun 13 2002 - 17:05:13 CDT)
- Re: sander parallel Stéphane Teletchéa (Fri Jun 14 2002 - 03:58:53 CDT)
- free energy for binding Qing Zhang (Fri Jun 14 2002 - 17:50:54 CDT)
- how to keep aromatic ring flat Qing Zhang (Fri Jun 14 2002 - 18:00:51 CDT)
- Re: how to keep aromatic ring flat Bill Ross (Fri Jun 14 2002 - 18:34:42 CDT)
- remove COM velocity in Amber7 Peter VARNAI (Mon Jun 17 2002 - 07:16:27 CDT)
- Re: remove COM velocity in Amber7 Peter VARNAI (Thu Jun 20 2002 - 07:03:07 CDT)
- Re: sander parallel Stéphane Teletchéa (Fri Jun 14 2002 - 03:58:53 CDT)
- RE: Floating Invalid lifang xu (Wed Jun 12 2002 - 22:02:21 CDT)
- How to set the dielctric constant equals 1, when running MD simulations in real solvent water? Ling Zhang (Thu Jun 13 2002 - 15:54:53 CDT)
- The atom number mismatch in coord and topology file. Ling Zhang (Thu Jun 13 2002 - 16:41:08 CDT)
- Using TIP4P water S. Yamasaki (Thu Jun 13 2002 - 20:05:48 CDT)
- (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Fri Jun 14 2002 - 00:30:15 CDT)
- Periodic water box Rudesh Toofanny (Fri Jun 14 2002 - 07:41:01 CDT)
- The atom number mismatch in coord and topology file in AMBER6. Ling Zhang (Fri Jun 14 2002 - 09:58:45 CDT)
- tleap error for systems with 64-bit pointers Karen Haskell (Fri Jun 14 2002 - 14:55:16 CDT)
- Amber tutorial rino ragno (Sat Jun 15 2002 - 04:53:53 CDT)
- Mn parameters!!! navjot_at_bioinfo.ernet.in (Mon Jun 17 2002 - 04:19:12 CDT)
- (no subject) Christian.Pilger_at_bc.boehringer-ingelheim.com (Mon Jun 17 2002 - 05:09:11 CDT)
- WG: Christian.Pilger_at_bc.boehringer-ingelheim.com (Tue Jun 18 2002 - 00:48:01 CDT)
- question Craig A Bayse (Tue Jun 18 2002 - 17:04:47 CDT)
- propeller twist of ideal B-DNA A. Hungie (Wed Jun 19 2002 - 11:37:29 CDT)
- solvated time-averaged restraint refinement of DNA Jake Isaacs (Wed Jun 19 2002 - 11:52:35 CDT)
- parameters for Zn2+ bond to CYS- X. Tan (Wed Jun 19 2002 - 19:23:16 CDT)
- re: parameters for zn2+ bond to cys- lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 08:17:38 CDT)
- turning PME off in AMBER7 lamon_at_lav.Boehringer-Ingelheim.com (Thu Jun 20 2002 - 08:28:30 CDT)
- RESP Multiconformer Fitting Miguel de Federico (Thu Jun 20 2002 - 18:05:11 CDT)
- van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 03:54:05 CDT)
- more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 04:00:59 CDT)
- even more van der Waals explosion Arvid Soederhaell (Fri Jun 21 2002 - 04:23:17 CDT)
- j3 coupling Yuguang Mu (Fri Jun 21 2002 - 05:38:31 CDT)
- Compilation ov Amber 7 Dov Barak (Fri Jun 21 2002 - 11:40:58 CDT)
- SHAKE... Arvid Soederhaell (Mon Jun 24 2002 - 06:25:05 CDT)
- New Residue Monica (Mon Jun 24 2002 - 10:01:42 CDT)
- ptraj problem Vlad Cojocaru (Mon Jun 24 2002 - 10:54:32 CDT)
- Re: SHAKE (actually: new atom types) Bill Ross (Mon Jun 24 2002 - 14:22:02 CDT)
- antechamber charges don't sum up to zero Michael Jakusch (Mon Jun 24 2002 - 14:38:15 CDT)
- partial charges Osvaldo Santos-Filho (Mon Jun 24 2002 - 19:33:15 CDT)
- Query regarding Gamess Nitin Kumar Singh (Tue Jun 25 2002 - 10:23:09 CDT)
- plep question FyD (Wed Jun 26 2002 - 02:28:23 CDT)
- minimum image cut-off Nikolai Smolin (Wed Jun 26 2002 - 06:05:08 CDT)
- transferring structures Matt Hartings (Wed Jun 26 2002 - 12:24:23 CDT)
- Using a trucated octahedral box in Amber6 Ling Zhang (Wed Jun 26 2002 - 20:28:46 CDT)
- Problem in amber Monica (Thu Jun 27 2002 - 00:28:21 CDT)
- xleap problem FyD (Thu Jun 27 2002 - 03:20:53 CDT)
- a problem with AMBER7 Vlad Cojocaru (Thu Jun 27 2002 - 05:12:58 CDT)
- dummy torsional parameters Giulio Rastelli (Thu Jun 27 2002 - 05:31:50 CDT)
- problems compiling Amber 7 ramon kleber da rocha (Thu Jun 27 2002 - 12:18:50 CDT)
- mopac David.Rilett_at_astrazeneca.com (Thu Jun 27 2002 - 12:50:41 CDT)
- Re: mopac David A. Case (Thu Jun 27 2002 - 13:34:34 CDT)
- Re: mopac Pascal Bonnet (Fri Jun 28 2002 - 03:49:11 CDT)
- van der Waals, hydrogen bond energy Qing Zhang (Fri Jun 28 2002 - 17:57:10 CDT)
- Re: van der Waals, hydrogen bond energy Carlos Simmerling (Fri Jun 28 2002 - 18:41:11 CDT)
- Re: van der Waals, hydrogen bond energy jim caldwell (Fri Jun 28 2002 - 19:24:21 CDT)
- Re: van der Waals, hydrogen bond energy Andreas Svrcek-Seiler (Sat Jun 29 2002 - 07:29:38 CDT)
- Re: mopac Pascal Bonnet (Fri Jun 28 2002 - 03:49:11 CDT)
- Re: mopac David A. Case (Thu Jun 27 2002 - 13:34:34 CDT)
- iwrap set in sander of Amber6 Ling Zhang (Thu Jun 27 2002 - 15:43:41 CDT)
- Re: Fwd: Re: probelms in install of amber (fwd) Marcelo Roitburd (Thu Jun 27 2002 - 15:59:35 CDT)
- xmkmf: not found Bill Ross (Thu Jun 27 2002 - 17:29:08 CDT)
- box size & 1st equilibrium yuann (Fri Jun 28 2002 - 01:16:51 CDT)
- EWALD BOMB (The system has extended beyond ...) Michael Jakusch (Fri Jun 28 2002 - 04:17:20 CDT)
- error in rMD Monica (Fri Jun 28 2002 - 08:35:34 CDT)
- The crystal water is solute or solvent during solvation Ling Zhang (Fri Jun 28 2002 - 13:58:08 CDT)
- Zn/Mg Counterion placement around DNA mdk7p_at_cms.mail.virginia.edu (Fri Jun 28 2002 - 14:46:11 CDT)
- Interaction table from minimization kiyean.nam_at_pharma.novartis.com (Fri Jun 28 2002 - 16:40:59 CDT)
- How to decrease the solvated system in Amber6? Ling Zhang (Mon Jul 01 2002 - 11:28:51 CDT)
- torsion angle constrains Marcela Madrid (Tue Jul 02 2002 - 16:22:09 CDT)
- parameter file for MgGTP Holger Sondermann (Tue Jul 02 2002 - 20:34:24 CDT)
- BR parameters in AMBER Esther Kellenberger (Wed Jul 03 2002 - 09:24:26 CDT)
- (no subject) Narang Manpreet Kaur (Wed Jul 03 2002 - 10:08:40 CDT)
- docking in xleap Bill Ross (Wed Jul 03 2002 - 23:25:50 CDT)
- Origin300, Linux Cluster Jianhui Wu (Thu Jul 04 2002 - 11:04:07 CDT)
- problem in compiling amber7 in IBMSP3 cluster A.Madhumalar (Thu Jul 04 2002 - 11:29:50 CDT)
- create new atom problem on xleap yuann (Thu Jul 04 2002 - 15:04:01 CDT)
- TEST Sarangan Ravichandran (Fri Jul 05 2002 - 07:43:37 CDT)
- Distance dependent vaccum energy minimization in AMBER7 Sarangan Ravichandran (Fri Jul 05 2002 - 10:29:40 CDT)
- simulation management tools Tom Bishop (Fri Jul 05 2002 - 10:58:59 CDT)
- anal in AMBER7 gives inconsistent results with itself Prabal Maiti (Fri Jul 05 2002 - 18:00:55 CDT)
- installing MPICH for AMBER on Linux CLuster root (Mon Jul 08 2002 - 05:02:52 CDT)
- md equilibration in chloroform Sophia Kondratova (Mon Jul 08 2002 - 08:38:27 CDT)
- RDC restraints Richard Stefl (Mon Jul 08 2002 - 10:01:39 CDT)
- Pictausch?? nicolescholiz1_at_web.de (Mon Jul 08 2002 - 18:14:10 CDT)
- eedmeth variable in AMBER7 Sarangan Ravichandran (Tue Jul 09 2002 - 09:30:28 CDT)
- Amber 7 Installation Rajesh Korde (Tue Jul 09 2002 - 11:45:36 CDT)
- Net Charge is Different In The Sander Output!! Sarangan Ravichandran (Tue Jul 09 2002 - 20:19:00 CDT)
- MAX_RSTACK Jithesh (Wed Jul 10 2002 - 01:24:42 CDT)
- Announcement: Optimally Partitioned Electric Properties - OPEP Chris Chipot (Wed Jul 10 2002 - 03:06:48 CDT)
- Problem getting sander started Thomas Steinbrecher (Wed Jul 10 2002 - 07:24:00 CDT)
- new problems compiling amber 7 ramon kleber da rocha (Wed Jul 10 2002 - 08:11:52 CDT)
- Not able to image a snapshot. Stéphane Teletchéa (Wed Jul 10 2002 - 10:28:12 CDT)
- simulated annealing example Snyder, James (Wed Jul 10 2002 - 15:42:43 CDT)
- time scale to see the ion effect on DNA A.Madhumalar (Thu Jul 11 2002 - 01:40:52 CDT)
- counter-ions in FEP Christophe L M J Verlinde (Thu Jul 11 2002 - 11:37:41 CDT)
- new problems compiling amber 7 ramon kleber da rocha (Thu Jul 11 2002 - 12:30:07 CDT)
- China International Biology Projects Fair Genefax (Fri Jul 12 2002 - 00:40:19 CDT)
- looking for frcmod in AMBER Tutorials yuann (Fri Jul 12 2002 - 04:19:45 CDT)
- Question about error message about "lastist" and "virtual box" Masaki Tomimoto (Fri Jul 12 2002 - 10:19:12 CDT)
- anal in AMBER7 gives inconsistent results with itself (fwd) Prabal Maiti (Fri Jul 12 2002 - 12:38:19 CDT)
- This one with anal in amber6 Prabal Maiti (Fri Jul 12 2002 - 13:09:39 CDT)
- are there inconsistencies in anal? David A. Case (Fri Jul 12 2002 - 13:58:02 CDT)
- LEaP gives "no sp2 improper torsion term" warnings David A. Case (Fri Jul 12 2002 - 15:25:35 CDT)
- Decrease the solvated system by removing the outside crystal water Ling Zhang (Mon Jul 15 2002 - 11:58:34 CDT)
- Problem with LEAP Miguel de Federico (Tue Jul 16 2002 - 05:53:37 CDT)
- antechamber created prep file--Problem in xleap Sarangan Ravichandran (Tue Jul 16 2002 - 08:54:45 CDT)
- antechamber created prep file--Problem in xleap--additional info Sarangan Ravichandran (Tue Jul 16 2002 - 09:06:31 CDT)
- Minimization in GB-SA-E-Spikes, LINMIN Sarangan Ravichandran (Tue Jul 16 2002 - 10:02:58 CDT)
- PME in gibbs module X. Tan (Tue Jul 16 2002 - 15:29:27 CDT)
- PTRAJ: radial distribution function A. Hungie (Wed Jul 17 2002 - 10:58:14 CDT)
- building general solvent boxes with leap Xavier Deupi (Wed Jul 17 2002 - 12:19:28 CDT)
- Re: amber on sp3 David A. Case (Wed Jul 17 2002 - 14:14:44 CDT)
- prmtop file question. Carlos Andres Ramirez-Mondragon (Wed Jul 17 2002 - 16:15:59 CDT)
- GENERALIZED BORN model on a protein with Fe Mahadevan Seetharaman (Thu Jul 18 2002 - 09:55:01 CDT)
- Defining Restraints in Sander Asif Rahaman (Thu Jul 18 2002 - 15:21:59 CDT)
- about solvateOct Nikolai Smolin (Fri Jul 19 2002 - 03:22:20 CDT)
- correction about solvateOct Nikolai Smolin (Fri Jul 19 2002 - 04:09:58 CDT)
- electrostatics truncation in AMBER Therese Malliavin (Fri Jul 19 2002 - 08:21:59 CDT)
- Questions about xleap and mm_pbsa] Salinthip Thipayang (Fri Jul 19 2002 - 12:49:08 CDT)
- AMBER7 and Movie Y Fang (Fri Jul 19 2002 - 16:03:22 CDT)
- Including explicit waters in GB dynamics Kristina Furse (Sat Jul 20 2002 - 19:30:43 CDT)
- Format in a trajectory files is suddenly changed Masaki Tomimoto (Mon Jul 22 2002 - 11:54:44 CDT)
- Benchmark Stéphane Teletchéa (Mon Jul 22 2002 - 11:55:14 CDT)
- C sp2 connected to OS Bimo Ario Tejo (Mon Jul 22 2002 - 12:37:27 CDT)
- problem with make_crd_hg, mm_pbsa Jianhui Wu (Mon Jul 22 2002 - 13:28:29 CDT)
- Summary: make_crd_hp, mm_pbsa Jianhui Wu (Mon Jul 22 2002 - 16:45:32 CDT)
- (no subject) deepak rangaswamy (Tue Jul 23 2002 - 02:01:41 CDT)
- Questions about xleap and mm_pbsa (cont.2) Salinthip Thipayang (Tue Jul 23 2002 - 10:21:23 CDT)
- problem compiling roar (mop7mm) on alpha hagop demirdjian (Tue Jul 23 2002 - 10:35:11 CDT)
- CA-OS parameter Bimo Ario Tejo (Tue Jul 23 2002 - 11:07:19 CDT)
- "crd" file created with VMD Soonmin Jang (Tue Jul 23 2002 - 11:23:56 CDT)
- Re: Questions about xleap ... Bill Ross (Tue Jul 23 2002 - 14:03:52 CDT)
- Segmentation fault Bimo Ario Tejo (Tue Jul 23 2002 - 14:44:58 CDT)
- problemas running amber7 tests on a SP2 machine ramon kleber da rocha (Tue Jul 23 2002 - 15:33:28 CDT)
- several questions David Keller (Tue Jul 23 2002 - 17:24:04 CDT)
- "crd" file created with VMD Soonmin Jang (Tue Jul 23 2002 - 19:47:04 CDT)
- Trajectory files Miguel de Federico (Wed Jul 24 2002 - 07:10:51 CDT)
- gaff and parm99 Pascal Bonnet (Wed Jul 24 2002 - 08:11:36 CDT)
- Octane Box (equilibrated) samantha hughes (Wed Jul 24 2002 - 10:27:53 CDT)
- CCL4 solvent box Bimo Ario Tejo (Wed Jul 24 2002 - 10:40:10 CDT)
- am1-bcc charges, antechamber Sophia Kondratova (Wed Jul 24 2002 - 14:02:02 CDT)
- Re: am1-bcc charges, antechamber David A. Case (Wed Jul 24 2002 - 14:58:25 CDT)
- Re: am1-bcc charges, antechamber M. L. Dodson (Wed Jul 24 2002 - 15:24:23 CDT)
- Re: am1-bcc charges, antechamber Laurent Chiche (Thu Jul 25 2002 - 04:17:58 CDT)
- Re: am1-bcc charges, antechamber Giulio Rastelli (Thu Jul 25 2002 - 05:53:46 CDT)
- Re: am1-bcc charges, antechamber M. L. Dodson (Thu Jul 25 2002 - 07:32:05 CDT)
- mol2 with antechamber Giulio Rastelli (Fri Jul 26 2002 - 05:57:22 CDT)
- Re: mol2 with antechamber David A. Case (Fri Jul 26 2002 - 10:54:08 CDT)
- Re: am1-bcc charges, antechamber M. L. Dodson (Wed Jul 24 2002 - 15:24:23 CDT)
- Re: am1-bcc charges, antechamber David A. Case (Wed Jul 24 2002 - 14:58:25 CDT)
- SS bond Masaki Tomimoto (Wed Jul 24 2002 - 14:04:21 CDT)
- makeDIP_RST.dna McAteer, Kathleen (Wed Jul 24 2002 - 14:24:42 CDT)
- CCl4 solvent box Bimo Ario Tejo (Wed Jul 24 2002 - 14:55:04 CDT)
- increase lastist Marcela Madrid (Wed Jul 24 2002 - 15:41:45 CDT)
- Umbrella sampling in AMBER Pratul Agarwal (Wed Jul 24 2002 - 15:53:54 CDT)
- Gibbs tutorial problem yuann (Wed Jul 24 2002 - 19:40:50 CDT)
- (no subject) deepak rangaswamy (Wed Jul 24 2002 - 22:57:14 CDT)
- Pressure probs in MD suvendu lomash (Thu Jul 25 2002 - 02:49:28 CDT)
- sulfonic group generated with antechamber Michael Jakusch (Thu Jul 25 2002 - 07:23:30 CDT)
- Purine to Pyrimidine mutation Bernd Wellenzohn (Thu Jul 25 2002 - 07:29:27 CDT)
- creating a solvent box Bimo Ario Tejo (Thu Jul 25 2002 - 07:32:17 CDT)
- "amber mail" jim caldwell (Thu Jul 25 2002 - 11:11:01 CDT)
- acetyl groups on protein fragments Elizabeth K. White (Thu Jul 25 2002 - 13:55:04 CDT)
- New Promotion Products at American Disc Corporation Service (Thu Jul 25 2002 - 14:56:47 CDT)
- Water molecule numbering Masaki Tomimoto (Thu Jul 25 2002 - 17:28:25 CDT)
- ptraj Joseph Nachman (Fri Jul 26 2002 - 14:43:36 CDT)
- periodic box Jiyoung Heo (Fri Jul 26 2002 - 17:00:28 CDT)
- sander crash K.Seshadri (Mon Jul 29 2002 - 03:40:57 CDT)
- parallel jobs die with no error message from sander lamon_at_lav.Boehringer-Ingelheim.com (Mon Jul 29 2002 - 12:48:20 CDT)
- Re: parallel jobs die with no error message from sander Scott Brozell (Mon Jul 29 2002 - 17:43:51 CDT)
- Re: parallel jobs die with no error message from sander Joffre Heredia (Mon Jul 29 2002 - 23:06:33 CDT)
- Re: parallel jobs die with no error message from sander jim caldwell (Mon Jul 29 2002 - 15:08:50 CDT)
- Re: parallel jobs die with no error message from sander Joffre Heredia (Tue Jul 30 2002 - 12:46:37 CDT)
- Error decoding variable Rukman Hertadi (Wed Jul 31 2002 - 05:52:02 CDT)
- Re: Error decoding variable Carlos Simmerling (Wed Jul 31 2002 - 07:37:46 CDT)
- Re: Error decoding variable jim caldwell (Wed Jul 31 2002 - 09:43:56 CDT)
- Re: Error decoding variable Carlos Simmerling (Wed Jul 31 2002 - 10:41:04 CDT)
- Re: Error decoding variable Rukman Hertadi (Wed Jul 31 2002 - 20:50:27 CDT)
- Re: parallel jobs die with no error message from sander jim caldwell (Mon Jul 29 2002 - 15:08:50 CDT)
- Re: SANDER documentation for nmropt David A. Case (Mon Jul 29 2002 - 19:27:52 CDT)
- a water jumps Masaki Tomimoto (Mon Jul 29 2002 - 22:47:21 CDT)
- NON-BONDED INTERACTION Rosalia Pascual (Tue Jul 30 2002 - 09:41:49 CDT)
- sander mpirun hangs with 4 CPU, but not with 2 Thomas Steinbrecher (Tue Jul 30 2002 - 10:09:03 CDT)
- AMBER Machine Questions DTphonehome33_at_aol.com (Tue Jul 30 2002 - 12:00:33 CDT)
- AM1-BCC sensitivity to AM1 charges Matthew Lee (Tue Jul 30 2002 - 12:31:43 CDT)
- Energies/coordinate files from mm_pbsa problem Peter Gannett (Tue Jul 30 2002 - 13:25:29 CDT)
- 'triangular' bond or angle Mahadevan Seetharaman (Tue Jul 30 2002 - 15:53:20 CDT)
- building ss DNA/RNA Cozmuta (Tue Jul 30 2002 - 16:47:45 CDT)
- tests for amber Cozmuta (Tue Jul 30 2002 - 18:47:18 CDT)
- structure Cozmuta (Tue Jul 30 2002 - 22:34:44 CDT)
- dielectric constant for partialy solvated MD Miyashita, Osamu (Wed Jul 31 2002 - 13:55:58 CDT)
- problem with amber7 mpi Bimo Ario Tejo (Thu Aug 01 2002 - 05:50:32 CDT)
- Potential Energy and RMS-Deviation Issues mdk7p_at_cms.mail.virginia.edu (Thu Aug 01 2002 - 10:01:07 CDT)
- distance restraint stuff Layi Adekoya (Thu Aug 01 2002 - 10:24:50 CDT)
- file Cozmuta (Thu Aug 01 2002 - 12:24:13 CDT)
- proton_info/PS Cozmuta (Thu Aug 01 2002 - 12:29:02 CDT)
- Using the new2oldparm command dianah_at_unm.edu (Thu Aug 01 2002 - 15:18:32 CDT)
- MD on cytochrome Mahadevan Seetharaman (Thu Aug 01 2002 - 16:15:52 CDT)
- Solvated DNA using Amber 7 Nicholson, James D Mr ARO (Thu Aug 01 2002 - 16:32:13 CDT)
- reorder water with nmropt Peter Varnai (Fri Aug 02 2002 - 07:24:59 CDT)
- look for benchmark with myrinet vs. 100-BT Jianhui Wu (Fri Aug 02 2002 - 12:15:29 CDT)
- FWD: RE: Including explicit waters in GB dynamics Kristina Furse (Fri Aug 02 2002 - 15:32:52 CDT)
- igb=2 in amber7 Randy M. Wadkins (Fri Aug 02 2002 - 17:28:48 CDT)
- water box-nonperiodic Cozmuta (Fri Aug 02 2002 - 22:14:35 CDT)
- PROTON_INFO Cozmuta (Fri Aug 02 2002 - 22:25:37 CDT)
- Benchmarks Sanjeev B.S. (Sat Aug 03 2002 - 00:48:09 CDT)
- Please give me a hand on understanding AMBER/MPI and locmem. Margaret Cheung (Sat Aug 03 2002 - 01:49:46 CDT)
- Generalized Born and OPLS potential Soonmin Jang (Sat Aug 03 2002 - 03:05:27 CDT)
- problems with parallel sander on linux clusters? David Case (Sun Aug 04 2002 - 13:34:20 CDT)
- (no subject) sepideh ameli (Sun Aug 04 2002 - 14:01:20 CDT)
- Import of CHARMM force field and GB potential parameters into Amber7 Soonmin Jang (Sun Aug 04 2002 - 21:19:20 CDT)
- MD in alcohol Marc DOBLER (Sun Aug 04 2002 - 21:33:52 CDT)
- Information request - where to buy software Claire Edmonds (Mon Aug 05 2002 - 08:23:59 CDT)
- Amber 7 timings? Jim (Mon Aug 05 2002 - 09:53:25 CDT)
- "number of processors must be a power of two" Jim (Tue Aug 06 2002 - 09:50:53 CDT)
- Re: "number of processors must be a power of two" Sanjeev B.S. (Tue Aug 06 2002 - 11:17:35 CDT)
- Re: "number of processors must be a power of two" David A. Case (Tue Aug 06 2002 - 11:40:33 CDT)
- Re: "number of processors must be a power of two" Jim (Tue Aug 06 2002 - 12:29:48 CDT)
- Re: "number of processors must be a power of two" Michael Crowley (Tue Aug 06 2002 - 12:31:50 CDT)
- Amber trajectory movies in Powerpoint mdk7p_at_cms.mail.virginia.edu (Tue Aug 06 2002 - 10:53:39 CDT)
- creating a solvent box Bimo Ario Tejo (Tue Aug 06 2002 - 12:23:13 CDT)
- am1-bcc charges Sophia Kondratova (Tue Aug 06 2002 - 13:26:22 CDT)
- Re: am1-bcc charges David A. Case (Tue Aug 06 2002 - 14:32:12 CDT)
- Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 14:50:04 CDT)
- Re: Leap error: PDB file with more than 10000 residues David A. Case (Tue Aug 06 2002 - 16:13:30 CDT)
- Re: Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 16:47:00 CDT)
- Re: Leap error: PDB file with more than 10000 residues jim caldwell (Tue Aug 06 2002 - 16:57:34 CDT)
- Leap error: PDB file with more than 10000 residues Pratul Agarwal (Tue Aug 06 2002 - 14:50:04 CDT)
- Re: am1-bcc charges David A. Case (Tue Aug 06 2002 - 14:32:12 CDT)
- check-up question Cozmuta (Tue Aug 06 2002 - 14:13:31 CDT)
- charges Cozmuta (Tue Aug 06 2002 - 18:24:14 CDT)
- (no subject) Giulio Rastelli (Wed Aug 07 2002 - 04:07:21 CDT)
- SHAKE problem Rosalia Pascual (Wed Aug 07 2002 - 10:13:12 CDT)
- Amber+Mosix Jianhui Wu (Wed Aug 07 2002 - 15:40:15 CDT)
- mpich, I/O, Master node, filesystem Jianhui Wu (Wed Aug 07 2002 - 23:24:13 CDT)
- Compiling Amber7 for a multiprocessor SUN Ultra-Sparc system. jeff dyason (Wed Aug 07 2002 - 23:45:49 CDT)
- nmode segmentation fault zhongh_at_umich.edu (Thu Aug 08 2002 - 08:56:08 CDT)
- Gentoo vs. Redhat Linux, shared/distributed filesystem Jianhui Wu (Thu Aug 08 2002 - 14:44:53 CDT)
- protonation pH dependent Cozmuta (Thu Aug 08 2002 - 16:14:46 CDT)
- LINMIN failure during minimization Giulio Rastelli (Fri Aug 09 2002 - 03:46:18 CDT)
- namelist error with sander Andreas Kerzmann (Fri Aug 09 2002 - 03:47:53 CDT)
- problems runing gibbs on a IBM SP2 machine ramon kleber da rocha (Fri Aug 09 2002 - 09:48:11 CDT)
- FW: Compiling on HP-UX 11.00 Hagedorn, Dan N (Fri Aug 09 2002 - 13:45:00 CDT)
- Amber/Gentoo linux Jianhui Wu (Fri Aug 09 2002 - 14:53:16 CDT)
- Nanotubes with AMBER Stefan Andreev Andreev (Sun Aug 11 2002 - 18:59:26 CDT)
- literature for NVE Khatcharin Siriwong (Mon Aug 12 2002 - 04:07:05 CDT)
- Constant pressure MD problems (sander) Pratul Agarwal (Mon Aug 12 2002 - 09:45:15 CDT)
- Memory and swap in sander William Wei (Mon Aug 12 2002 - 10:11:35 CDT)
- chesey@panther.gsu.edu Michael G Cooney (Mon Aug 12 2002 - 14:03:37 CDT)
- misdirected message Michael G Cooney (Mon Aug 12 2002 - 14:35:35 CDT)
- Format of prep input files dianah_at_unm.edu (Tue Aug 13 2002 - 12:42:11 CDT)
- sander minimizations failing John Bushnell (Tue Aug 13 2002 - 19:03:12 CDT)
- minimization in amber7 for nonperiodic systems David Case (Wed Aug 14 2002 - 00:47:43 CDT)
- dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Wed Aug 14 2002 - 03:37:50 CDT)
- GB in Amber7 Jithesh (Wed Aug 14 2002 - 03:37:54 CDT)
- problem reading rstrnt file with pgf77 compiled sander Michael Petersen (Wed Aug 14 2002 - 05:13:24 CDT)
- Carnal stream problem Vlad Cojocaru (Wed Aug 14 2002 - 09:45:04 CDT)
- Running amber7 on Param10000 Sanjeev B.S. (Wed Aug 14 2002 - 10:38:34 CDT)
- Q: waters in NPT & periodic boundary condition Masaki Tomimoto (Wed Aug 14 2002 - 11:06:15 CDT)
- a question about carnal Vlad Cojocaru (Wed Aug 14 2002 - 11:39:36 CDT)
- E going up and down??? Jiyoung Heo (Wed Aug 14 2002 - 16:13:44 CDT)
- Can we get trajectories coordinates after FIT in Carnal? William Wei (Wed Aug 14 2002 - 16:52:34 CDT)
- mpi version of sander in Amber 6.0 with constraints Stefan Andreev Andreev (Wed Aug 14 2002 - 17:13:26 CDT)
- PMF with sander module mer_at_gordon.chem.wayne.edu (Wed Aug 14 2002 - 18:23:25 CDT)
- problem with amber7 compiling on SGI Chris Switzer (Wed Aug 14 2002 - 20:26:54 CDT)
- force field name A. Hungie (Thu Aug 15 2002 - 08:50:48 CDT)
- sander on NEC-SX5 C. Klein (Thu Aug 15 2002 - 11:12:24 CDT)
- trajectory file limit??? Vlad Cojocaru (Thu Aug 15 2002 - 11:43:54 CDT)
- Re: Help needed about mm_pbsa Holger Gohlke (Thu Aug 15 2002 - 12:04:03 CDT)
- Order of a protein, bound waters and ligand in saveamberparm Masaki Tomimoto (Thu Aug 15 2002 - 15:25:45 CDT)
- GB in amber6 Prabal Maiti (Thu Aug 15 2002 - 19:26:22 CDT)
- add DUMMY atom into coordinate file yuann (Fri Aug 16 2002 - 04:12:04 CDT)
- Re: problem reading rstrnt file with pgf77 Michael Petersen (Fri Aug 16 2002 - 08:23:48 CDT)
- dihedral parameter for conjugated double bonds in GAFF Giulio Rastelli (Fri Aug 16 2002 - 11:37:03 CDT)
- Etot drops after restarting MD in sander Pratul Agarwal (Fri Aug 16 2002 - 13:18:58 CDT)
- antechamber's prepc option Matthew Lee (Fri Aug 16 2002 - 14:20:59 CDT)
- a couple missing gaff angle terms Matthew Lee (Fri Aug 16 2002 - 16:55:44 CDT)
- average of LES copies mer_at_chem.wayne.edu (Sun Aug 18 2002 - 20:00:22 CDT)
- Antibody residue numbering Mark Hsieh (Mon Aug 19 2002 - 15:56:00 CDT)
- mail host switchover jim caldwell (Mon Aug 19 2002 - 16:58:11 CDT)
- Im lost Sankha Subhra Som (Tue Aug 20 2002 - 00:16:00 CDT)
- PC (principal component) analysis Soonmin Jang (Tue Aug 20 2002 - 03:02:24 CDT)
- segmentation fault Vlad Cojocaru (Tue Aug 20 2002 - 16:21:30 CDT)
- Nitro parameters Jerry Matthew Parks (Wed Aug 21 2002 - 16:28:48 CDT)
- RMSD by residue (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:49:39 CDT)
- Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:02 CDT)
- adding_hydrogens_to_pdb (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:07 CDT)
- ewald bomb in md equilibration (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:14 CDT)
- why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:27 CDT)
- ambpdb problem (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:32 CDT)
- Gibbs (FEP) (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:36 CDT)
- QUICK HELP! Parameters for neutral amino acids (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:43 CDT)
- amber7, gaff and minimization (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:50 CDT)
- regarding RESP run from gamess output (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:55 CDT)
- why is mm_pbsa broken ? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:50:59 CDT)
- Re: Can we get trajectories coordinates after FIT in Carnal? (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:03 CDT)
- How to make mpeg files from amber trajectories (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:07 CDT)
- Carnal RMSDs (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:12 CDT)
- Re: Etot drops after restarting MD in sander (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:16 CDT)
- turning off ewald (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:21 CDT)
- a more general question about ff (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:25 CDT)
- leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:29 CDT)
- Torsion restraint between center of mass groups Pratul Agarwal (Mon Aug 26 2002 - 16:51:33 CDT)
- a more general question (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:41 CDT)
- leaprc file (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:44 CDT)
- Re: Extra points (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:49 CDT)
- Scaling of Sander on Linux Clusters (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:51:57 CDT)
- Re: "number of processors must be a power of two" (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:01 CDT)
- Using GBSA for a DNA-PROTEIN complex (fwd) amber_at_heimdal.compchem.ucsf.edu (Mon Aug 26 2002 - 16:52:06 CDT)
- test James W. Caldwell (Mon Aug 26 2002 - 17:04:35 CDT)
- mail reflector James W. Caldwell (Mon Aug 26 2002 - 17:35:53 CDT)
- ewald bomb in md equilibration Sophia Kondratova (Mon Aug 26 2002 - 17:54:37 CDT)
- Re: Carnal RMSDs Bill Ross (Mon Aug 26 2002 - 18:56:50 CDT)
- Interface and Amber 7.0 Nigel D Priestley (Mon Aug 26 2002 - 21:45:55 CDT)
- question Sankha Subhra Som (Tue Aug 27 2002 - 01:24:32 CDT)
- amber7: ES40s Sanjeev B.S. (Tue Aug 27 2002 - 08:08:49 CDT)
- difference 94 99 force field Vlad Cojocaru (Tue Aug 27 2002 - 08:34:11 CDT)
- Re: how to make mpeg files from amber trajectories Anke Eisenmann (Tue Aug 27 2002 - 09:41:01 CDT)
- problem in MD Xiang Mao (Tue Aug 27 2002 - 19:05:11 CDT)
- What's this "interface" the tutorial talks about? Andreas Kerzmann (Wed Aug 28 2002 - 07:41:01 CDT)
- iwrap and image Sophia Kondratova (Wed Aug 28 2002 - 07:55:36 CDT)
- Fw: amber problem Carlos Simmerling (Wed Aug 28 2002 - 12:10:26 CDT)
- [Re: can carnal do the job as anal to break down the energy?] Holger Gohlke (Wed Aug 28 2002 - 13:36:51 CDT)
- gibbs sara nunez (Wed Aug 28 2002 - 14:52:56 CDT)
- [Re: can carnal do the job as anal to break down the energy?] Bill Ross (Wed Aug 28 2002 - 15:35:40 CDT)
- a missing variable Vlad Cojocaru (Wed Aug 28 2002 - 15:43:04 CDT)
- sorry!!!!maybe another stupid question Vlad Cojocaru (Wed Aug 28 2002 - 17:48:03 CDT)
- Tutorial Error Message Joel Konkle-Parker (Wed Aug 28 2002 - 18:19:48 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 05:14:06 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 07:20:52 CDT)
- pbc in amber Xiang Mao (Thu Aug 29 2002 - 08:00:04 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Thu Aug 29 2002 - 12:02:23 CDT)
- image command Sophia Kondratova (Thu Aug 29 2002 - 12:46:01 CDT)
- PyMOL + AMBER Trajectories DeLano, Warren (Thu Aug 29 2002 - 13:27:01 CDT)
- ES40 hangs amber7 jobs. Sanjeev B.S. (Thu Aug 29 2002 - 22:09:13 CDT)
- dump coordinate into mdcrd A. Hungie (Fri Aug 30 2002 - 03:03:17 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 05:08:15 CDT)
- example gibbs file for the methane tutorial Andreas Kerzmann (Fri Aug 30 2002 - 05:18:06 CDT)
- NTX value giudice (Fri Aug 30 2002 - 05:31:19 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Aug 30 2002 - 05:59:25 CDT)
- sander7 on IBM 7040-681 under AIX 5.1 Peter Varnai (Fri Aug 30 2002 - 08:01:07 CDT)
- ewald bomb Vlad Cojocaru (Fri Aug 30 2002 - 08:38:49 CDT)
- Vanderbilt Biomolecular Modeling Symposium Jarrod Smith (Fri Aug 30 2002 - 13:00:40 CDT)
- Binding site volume/Sander MD Jianhui Wu (Fri Aug 30 2002 - 16:20:09 CDT)
- GBSA with IGB=2, setting the PBradii bondi Sarangan Ravichandran (Fri Aug 30 2002 - 16:55:28 CDT)
- mpirun Ioana Cozmuta (Sun Sep 01 2002 - 13:32:08 CDT)
- additional info Ioana Cozmuta (Sun Sep 01 2002 - 13:44:32 CDT)
- mm_pbsa positive binding energies Mathy Froeyen (Mon Sep 02 2002 - 04:11:34 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 05:12:42 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 02 2002 - 06:25:18 CDT)
- carnal averaging Vlad Cojocaru (Mon Sep 02 2002 - 06:43:33 CDT)
- atoms coming too close during MD (with SHAKE on) Pratul Agarwal (Mon Sep 02 2002 - 20:01:18 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 03 2002 - 06:57:12 CDT)
- compile Moil-View, GL header files Jianhui Wu (Tue Sep 03 2002 - 10:20:09 CDT)
- protein minimization m.elizabeth sophia (Tue Sep 03 2002 - 11:01:35 CDT)
- question Ioana Cozmuta (Tue Sep 03 2002 - 12:46:04 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Wed Sep 04 2002 - 05:40:26 CDT)
- Escaping Atoms ch cureton (Wed Sep 04 2002 - 05:43:03 CDT)
- old prmtop Thomas Steinbrecher (Wed Sep 04 2002 - 10:56:47 CDT)
- how to detect bad contact? X. Tan (Wed Sep 04 2002 - 14:14:40 CDT)
- cut-off question Ioana Cozmuta (Wed Sep 04 2002 - 14:43:38 CDT)
- DNA Tutorial Script Joel Konkle-Parker (Wed Sep 04 2002 - 18:18:16 CDT)
- average structure Raja Swaminathan (Thu Sep 05 2002 - 12:16:03 CDT)
- bondbydistance eric hu (Thu Sep 05 2002 - 18:20:43 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 06 2002 - 06:13:47 CDT)
- group selection for all heavy atoms ? Raik Grunberg (Fri Sep 06 2002 - 11:23:33 CDT)
- compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 15:46:43 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 17:01:27 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 18:11:55 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC John Bushnell (Fri Sep 06 2002 - 18:43:12 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC James W. Caldwell (Fri Sep 06 2002 - 19:56:42 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 19:16:40 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC ramon kleber da rocha (Fri Sep 06 2002 - 18:11:55 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC Florian Barth (Fri Sep 06 2002 - 17:13:31 CDT)
- Re: compiling amber on a linux box using DMEM-ALLOC Scott Brozell (Fri Sep 06 2002 - 17:01:27 CDT)
- cut-off question Cozmuta (Fri Sep 06 2002 - 17:49:21 CDT)
- about amber and charmm, thanks Zhang Jian (Sun Sep 08 2002 - 04:10:57 CDT)
- who to address this to?... Jessica Swanson (Sun Sep 08 2002 - 17:59:23 CDT)
- Distace dependent dielectric constant Lorenzo Gontrani (Mon Sep 09 2002 - 03:33:43 CDT)
- parameterization of a new class of compounds (nucleic acid base analogues) Vlad Cojocaru (Mon Sep 09 2002 - 04:40:05 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Mon Sep 09 2002 - 06:04:45 CDT)
- amber7 compilation on irix6.4 mp K.Seshadri (Mon Sep 09 2002 - 12:44:13 CDT)
- How to check whether the trajectory file matches the coordinates file or not? Ling Zhang (Mon Sep 09 2002 - 13:31:13 CDT)
- why are the results so large difference calculating by mm_pbsa and mm_gbsa? Yongjun Jiang (Tue Sep 10 2002 - 02:18:46 CDT)
- Strange MD simulation results with GB solvation at high temp. Soonmin Jang (Tue Sep 10 2002 - 05:09:06 CDT)
- nmode compile question? Yongjun Jiang (Tue Sep 10 2002 - 07:46:18 CDT)
- GBSA and surface crystal waters Raik Grunberg (Tue Sep 10 2002 - 09:44:20 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Tue Sep 10 2002 - 10:57:00 CDT)
- rdparm Joffre Heredia (Tue Sep 10 2002 - 13:07:26 CDT)
- loadpdb error messages Joel Konkle-Parker (Tue Sep 10 2002 - 17:58:07 CDT)
- Polarizability, a general question Michal Otyepka (Wed Sep 11 2002 - 03:56:32 CDT)
- memory allocation in mm_pbsa Giulio Rastelli (Wed Sep 11 2002 - 05:41:04 CDT)
- just a test Vlad Cojocaru (Wed Sep 11 2002 - 08:39:59 CDT)
- Problems during equilibration Pratul Agarwal (Wed Sep 11 2002 - 14:38:36 CDT)
- Dual Processor AMD vs. Single Processor DeLano, Warren (Wed Sep 11 2002 - 19:34:47 CDT)
- why are the results so large difference calculating by mm_pbsaandmm_gbsa? Yongjun Jiang (Thu Sep 12 2002 - 02:25:32 CDT)
- Qustion about calculation of pressure Nikolai Smolin (Thu Sep 12 2002 - 05:01:44 CDT)
- sorry this is just a test Vlad Cojocaru (Thu Sep 12 2002 - 10:23:24 CDT)
- leap and topology file Marcela Madrid (Thu Sep 12 2002 - 11:12:20 CDT)
- sander.LES questions Peter Varnai (Thu Sep 12 2002 - 11:27:12 CDT)
- large energy fluctration eric hu (Thu Sep 12 2002 - 13:05:10 CDT)
- the amino group of 2amino purine has strange behaviour Vlad Cojocaru (Thu Sep 12 2002 - 13:42:10 CDT)
- Changing MAXINT Joel Konkle-Parker (Thu Sep 12 2002 - 18:21:13 CDT)
- binding site volume Shixiang Yan (Thu Sep 12 2002 - 18:38:41 CDT)
- problems on IBM AIX Giovanni Fossati (Thu Sep 12 2002 - 20:43:52 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 08:10:40 CDT)
- MDaemon Warning - Virus Found postmaster_at_96com.com (Fri Sep 13 2002 - 08:13:22 CDT)
- Beowulf killing jobs Peter Gannett (Fri Sep 13 2002 - 16:03:19 CDT)
- Help using moilview to make animations of trajectories Nicholson, James D Mr ARO (Fri Sep 13 2002 - 17:15:33 CDT)
- D-tryptophan Perdita Barran (Sat Sep 14 2002 - 09:16:45 CDT)
- amber K.Veluraja (Mon Sep 16 2002 - 00:14:04 CDT)
- amber question yao yong (Mon Sep 16 2002 - 06:03:16 CDT)
- example 1 problems Alicia Hopkins (Mon Sep 16 2002 - 10:57:23 CDT)
- assistance required amit kumar (Mon Sep 16 2002 - 11:25:05 CDT)
- SETVEL, incorrect number of arguments? Giovanni Fossati (Mon Sep 16 2002 - 17:43:30 CDT)
- non-bonded metal ion in complex yuann (Tue Sep 17 2002 - 01:28:45 CDT)
- question about nmode again. Yongjun Jiang (Tue Sep 17 2002 - 02:15:54 CDT)
- mm_pbsa question. wentaofu (Tue Sep 17 2002 - 10:35:59 CDT)
- Density during equilibration (sander) Pratul Agarwal (Tue Sep 17 2002 - 11:56:10 CDT)
- Z DNA Sue Heavner (Tue Sep 17 2002 - 14:55:04 CDT)
- Carnal+HBond confusion Sanjeev B.S. (Wed Sep 18 2002 - 23:18:36 CDT)
- bug in New2oldparm Pascal Bonnet (Thu Sep 19 2002 - 05:35:46 CDT)
- new2oldparm format (2) Pascal Bonnet (Thu Sep 19 2002 - 05:43:39 CDT)
- a freeware to display RMSD matrices Vlad Cojocaru (Thu Sep 19 2002 - 07:44:53 CDT)
- offset of temperature when running MD with CAP and no periodic conditions Therese Malliavin (Thu Sep 19 2002 - 10:44:24 CDT)
- compiling without ISTAR2 Prem Raj (Thu Sep 19 2002 - 12:27:48 CDT)
- image X. Tan (Thu Sep 19 2002 - 12:32:15 CDT)
- Question about Counterions Markus Drumm (Thu Sep 19 2002 - 12:38:24 CDT)
- BLOWUP after 100 ns??? Randy M. Wadkins (Thu Sep 19 2002 - 15:51:28 CDT)
- npairs Prem Raj (Thu Sep 19 2002 - 17:22:42 CDT)
- Dynamic Movement of Molecule Yuuki Komata (Fri Sep 20 2002 - 03:03:48 CDT)
- Re: Parameters for AMBER David A. Case (Fri Sep 20 2002 - 08:53:18 CDT)
- mol2 file format in the future of amber M. L. Dodson (Fri Sep 20 2002 - 09:41:02 CDT)
- (no subject) Prem Raj (Fri Sep 20 2002 - 11:42:14 CDT)
- vlimit and vmax Prem Raj (Fri Sep 20 2002 - 12:27:07 CDT)
- mm_pbsa Sue Heavner (Fri Sep 20 2002 - 15:00:36 CDT)
- Periodicity Question DeLano, Warren (Fri Sep 20 2002 - 19:29:49 CDT)
- Re: Do I have to rerun 1ns MD?? Holger Gohlke (Sun Sep 22 2002 - 14:30:40 CDT)
- Re: betaP,SURFOFF inconsistency Holger Gohlke (Sun Sep 22 2002 - 15:20:03 CDT)
- ptraj-6.4/LES Peter Varnai (Mon Sep 23 2002 - 04:18:25 CDT)
- Fw: Do I have to rerun 1ns MD?? Lepsa (Mon Sep 23 2002 - 10:50:26 CDT)
- mm_pbsa output error Michael Murray (Mon Sep 23 2002 - 12:26:11 CDT)
- antechamber best practices/charge equivalence w/ AM1-BCC Tom Bishop (Mon Sep 23 2002 - 16:28:57 CDT)
- watershell in ptraj Michael Trieb (Tue Sep 24 2002 - 04:03:49 CDT)
- Mopac509mn/linux James W. Caldwell (Tue Sep 24 2002 - 10:00:20 CDT)
- ambpdb? Arvid Soederhaell (Wed Sep 25 2002 - 02:38:34 CDT)
- ptraj - BONDS_WITHOUT_HYDROGEN Sophia Kondratova (Wed Sep 25 2002 - 11:54:48 CDT)
- (no subject) Apostoluk, Wlodzimierz K (Wed Sep 25 2002 - 14:09:53 CDT)
- compiling amber 7 with Intel Fortran Compiler 6.0 ramon kleber da rocha (Wed Sep 25 2002 - 14:23:21 CDT)
- sander_classic: Recompile without ISTAR2 Mahadevan Seetharaman (Wed Sep 25 2002 - 14:53:59 CDT)
- ISTAR2 - oops, just found the answer... Mahadevan Seetharaman (Wed Sep 25 2002 - 14:55:46 CDT)
- compiling amber 7 with Intel Fortran Compiler 6.0 (fwd) John Bushnell (Wed Sep 25 2002 - 15:10:50 CDT)
- RMSD for heavy atoms only Pratul Agarwal (Wed Sep 25 2002 - 15:54:45 CDT)
- Question about Antechamber Masaki Tomimoto (Wed Sep 25 2002 - 16:37:55 CDT)
- mm_pbsa and statistic program Pascal Bonnet (Thu Sep 26 2002 - 05:50:52 CDT)
- different counterions for special type of DNA Vlad Cojocaru (Thu Sep 26 2002 - 07:59:31 CDT)
- Re: GB tutorial David A. Case (Thu Sep 26 2002 - 10:31:19 CDT)
- Torsion driving ch cureton (Thu Sep 26 2002 - 11:00:34 CDT)
- Question on Antechamber paper Nicholson, James D Mr ARO (Thu Sep 26 2002 - 12:18:17 CDT)
- Amber Reflector James W. Caldwell (Thu Sep 26 2002 - 12:47:58 CDT)
- Constant pressure equilibration in a system with a solvent cap dianah_at_unm.edu (Thu Sep 26 2002 - 20:04:38 CDT)
- Re: Constant pressure equilibration in a system with a solvent cap James W. Caldwell (Fri Sep 27 2002 - 08:54:46 CDT)
- Re: Constant pressure equilibration in a system with a solvent cap David A. Case (Fri Sep 27 2002 - 10:26:09 CDT)
- Re: Constant pressure equilibration in a system with a solvent cap David Smith (Fri Sep 27 2002 - 11:11:19 CDT)
- nmanal help request Peter Fojan (Fri Sep 27 2002 - 08:59:11 CDT)
- MM-PBSA basics Michael Ford (Fri Sep 27 2002 - 14:53:01 CDT)
- MD Primers Joel Konkle-Parker (Fri Sep 27 2002 - 14:54:03 CDT)
- Is H-bonding really there? suvendu lomash (Fri Sep 27 2002 - 14:59:48 CDT)
- Re: Is H-bonding really there? Thomas Cheatham (Fri Sep 27 2002 - 15:53:24 CDT)
- Re: Is H-bonding really there? Pratul Agarwal (Fri Sep 27 2002 - 15:58:25 CDT)
- Re: Is H-bonding really there? Ioana Cozmuta (Fri Sep 27 2002 - 17:04:37 CDT)
- Re: Is H-bonding really there? Ioana Cozmuta (Tue Oct 01 2002 - 16:44:55 CDT)
- Anal Error : Group Lifeng Tian (Fri Sep 27 2002 - 17:35:23 CDT)
- Request for help with Antechamber Nicholson, James D Mr ARO (Fri Sep 27 2002 - 18:58:58 CDT)
- question about using 10-12 in amber7/sander. Margaret Cheung (Sat Sep 28 2002 - 14:53:56 CDT)
- parameters for sugars A.Madhumalar (Sun Sep 29 2002 - 11:30:36 CDT)
- groups in targeted md Christoph Brockmann (Mon Sep 30 2002 - 08:15:10 CDT)
- Amber 7 and 6 topology files. Miguel de Federico (Mon Sep 30 2002 - 10:08:36 CDT)
- BondEn shoots in solvent minimization suvendu lomash (Mon Sep 30 2002 - 10:50:39 CDT)
- write problem on IBM-AIX Giovanni Fossati (Mon Sep 30 2002 - 10:51:54 CDT)
- Image charges with the solvate cap command dkeller_at_unm.edu (Mon Sep 30 2002 - 10:52:11 CDT)
- Problems with poly(A)-poly(T) tutorial... Andrei Leitão (Mon Sep 30 2002 - 14:55:53 CDT)
- Partial charge generation RESP/antechamber James W. Caldwell (Mon Sep 30 2002 - 17:27:37 CDT)
- divalent cations parameters Apostoluk, Wlodzimierz K (Mon Sep 30 2002 - 17:38:11 CDT)
- Questions on crosslinking residues Nicholson, James D Mr ARO (Tue Oct 01 2002 - 16:59:19 CDT)
- antechamber web page Ioana Cozmuta (Tue Oct 01 2002 - 17:33:36 CDT)
- tutorial on plastocyanin Ioana Cozmuta (Wed Oct 02 2002 - 01:04:37 CDT)
- restart without velocities Michal Otyepka (Wed Oct 02 2002 - 02:39:02 CDT)
- Sander multiprocessors running problem with MPI William Wei (Wed Oct 02 2002 - 13:09:49 CDT)
- xleap XENVIRONMENT Mark C. Ballew (Wed Oct 02 2002 - 17:34:09 CDT)
- RESP gaussian job crashing Nicholson, James D Mr ARO (Wed Oct 02 2002 - 20:22:59 CDT)
- regarding resp-doubts thenmalar rathinavelan (Thu Oct 03 2002 - 03:21:51 CDT)
- about AMBER parallel edition Shimono Fumihiro (Thu Oct 03 2002 - 06:07:36 CDT)
- atomicfluct Bimo Ario Tejo (Thu Oct 03 2002 - 06:40:47 CDT)
- MM-GBSA and counterions Michael Ford (Thu Oct 03 2002 - 14:27:27 CDT)
- EGB = NaNQ Pratul Agarwal (Thu Oct 03 2002 - 16:05:55 CDT)
- compiling SGI/mpi Ioana Cozmuta (Thu Oct 03 2002 - 20:16:38 CDT)
- RE:SAMUEL METU sam_008_at_www.com (Thu Oct 03 2002 - 20:46:50 CDT)
- RMSD calculation question Soonmin Jang (Fri Oct 04 2002 - 02:02:37 CDT)
- Re: About the Memory allocation in MM_PBSA and SANDER Alan Leo (Fri Oct 04 2002 - 07:46:15 CDT)
- Different numbers on different architectures. David Smith (Fri Oct 04 2002 - 08:33:24 CDT)
- NTX / IREST inconsistency Bimo Ario Tejo (Fri Oct 04 2002 - 10:11:59 CDT)
- (no subject) Ioana Cozmuta (Fri Oct 04 2002 - 19:12:44 CDT)
- what are "end group interactions"? C. Klein (Mon Oct 07 2002 - 03:43:00 CDT)
- How to generate PNA structure? A. Hungie (Mon Oct 07 2002 - 03:51:53 CDT)
- xleap on a SGI Fuel Giulio Rastelli (Mon Oct 07 2002 - 09:50:39 CDT)
- MACHINE file for Tru64 ES45 CUI, Guanglei (Mon Oct 07 2002 - 14:20:19 CDT)
- geometry optimization/turning off Elec and Vdw terms Tom Bishop (Mon Oct 07 2002 - 15:17:52 CDT)
- AMBER6 on cluster Mako Furukawa (Mon Oct 07 2002 - 19:12:28 CDT)
- 2D RMSd Luo Liu (Tue Oct 08 2002 - 03:32:34 CDT)
- do I need to mutate H1 atoms to HC in a "not really" perturbed part of a molecule ? hagop demirdjian (Tue Oct 08 2002 - 09:51:50 CDT)
- crdgrow Ioana Cozmuta (Tue Oct 08 2002 - 12:19:23 CDT)
- rdparm Ioana Cozmuta (Tue Oct 08 2002 - 12:33:41 CDT)
- (no subject) kbyun_at_wesleyan.edu (Tue Oct 08 2002 - 13:10:53 CDT)
- LINMIN FAILURE hung_at_atc.atccu.chula.ac.th (Tue Oct 08 2002 - 19:41:00 CDT)
- nmr and positional restraint in input Peter Varnai (Wed Oct 09 2002 - 12:44:03 CDT)
- reaction field energy of a ligand in MM-PBSA Giulio Rastelli (Wed Oct 09 2002 - 13:04:10 CDT)
- about dummy parameter of multiplicity sxzheng (Thu Oct 10 2002 - 02:55:15 CDT)
- MM-PBSA tutorial Giulio Rastelli (Thu Oct 10 2002 - 09:22:59 CDT)
- trouble with snapshots GC option of MM_PBSA Michael Ford (Thu Oct 10 2002 - 09:23:24 CDT)
- solved: nmr and positional restraint in input Peter Varnai (Thu Oct 10 2002 - 10:26:27 CDT)
- [Fwd: Re: trouble with snapshots GC option of MM_PBSA] Holger Gohlke (Thu Oct 10 2002 - 11:15:39 CDT)
- IBELLY and NMROPT in sander Tom Bishop (Thu Oct 10 2002 - 11:54:43 CDT)
- Dielectric constant for interior of proteins Pratul Agarwal (Thu Oct 10 2002 - 12:53:59 CDT)
- How to do 2dRMS in ptraj Ying Zhao (Thu Oct 10 2002 - 14:33:43 CDT)
- question about antibodies Ioana Cozmuta (Thu Oct 10 2002 - 15:05:25 CDT)
- Some error message on Leap Sichun Yang (Thu Oct 10 2002 - 15:15:43 CDT)
- docking in amber? Sichun Yang (Thu Oct 10 2002 - 18:44:45 CDT)
- problem in sander Ioana Cozmuta (Thu Oct 10 2002 - 21:11:06 CDT)
- volume of ucell too big!! sxzheng (Fri Oct 11 2002 - 10:06:52 CDT)
- period boundary Shunzhou Wan (Fri Oct 11 2002 - 10:50:39 CDT)
- DNA Tutorial: min_ntr.in Joel Konkle-Parker (Fri Oct 11 2002 - 17:28:47 CDT)
- perturbation of gln to glu M. L. Dodson (Sun Oct 13 2002 - 19:02:00 CDT)
- MM-PBSA and Insight's version of Delphi Emma.Sigfridsson_at_astrazeneca.com (Mon Oct 14 2002 - 02:47:21 CDT)
- pressure variation coupled with taup value Vlad Cojocaru (Mon Oct 14 2002 - 04:36:42 CDT)
- loss of disulfide bonds Nicolas Le Novere (Mon Oct 14 2002 - 10:31:23 CDT)
- Re: loss of disulfide bonds Holger Gohlke (Mon Oct 14 2002 - 10:51:01 CDT)
- Re: loss of disulfide bonds David A. Case (Mon Oct 14 2002 - 11:04:30 CDT)
- Re: loss of disulfide bonds Natasja Brooijmans (Mon Oct 14 2002 - 11:46:54 CDT)
- Re: loss of disulfide bonds Carlos Simmerling (Mon Oct 14 2002 - 11:49:15 CDT)
- Re: loss of disulfide bonds James W. Caldwell (Mon Oct 14 2002 - 12:28:15 CDT)
- CH2Cl2 box Eric ARNOULT (Mon Oct 14 2002 - 12:51:21 CDT)
- Potential bug in gbsa.h of sander-7 Vlad (Mon Oct 14 2002 - 19:35:58 CDT)
- Compiler & Hardware requirement of AMBER7 ? yuann (Mon Oct 14 2002 - 23:08:12 CDT)
- Computational alchemy Aldo Jongejan (Tue Oct 15 2002 - 05:52:12 CDT)
- new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan (Tue Oct 15 2002 - 06:13:49 CDT)
- new telescopes-Maksutov-Cassegrain, reflector, refractor wang lan (Tue Oct 15 2002 - 06:42:50 CDT)
- Error in Antechamber program in ammber7 Narang Manpreet Kaur (Tue Oct 15 2002 - 09:49:52 CDT)
- Bug in reading binary restart file with BOX parameters Vlad (Tue Oct 15 2002 - 21:58:54 CDT)
- dummy parameters Pierre Mignon (Wed Oct 16 2002 - 02:10:46 CDT)
- How to specify the counterion positions using xleap? A.Madhumalar (Wed Oct 16 2002 - 07:54:41 CDT)
- Re: How to specify the counterion positions using xleap? David A. Case (Wed Oct 16 2002 - 10:09:21 CDT)
- Re: How to specify the counterion positions using xleap? James W. Caldwell (Wed Oct 16 2002 - 10:28:06 CDT)
- Re: How to specify the counterion positions using xleap? Ioana Cozmuta (Wed Oct 16 2002 - 12:45:06 CDT)
- Can I use belly and ntr at the same time? sxzheng (Wed Oct 16 2002 - 10:21:10 CDT)
- Molecular Dynamic procedure... Andrei Leitão (Wed Oct 16 2002 - 10:48:10 CDT)
- How to convert oldparmtop to newparmtop? A.Madhumalar (Wed Oct 16 2002 - 12:18:35 CDT)
- error message Vlad Cojocaru (Wed Oct 16 2002 - 12:25:01 CDT)
- more information about the previous email Vlad Cojocaru (Wed Oct 16 2002 - 12:26:43 CDT)
- restraining atoms Ioana Cozmuta (Wed Oct 16 2002 - 12:56:10 CDT)
- Re: restraining atoms Lepsa (Thu Oct 17 2002 - 01:56:17 CDT)
- Re: restraining atoms Ioana Cozmuta (Thu Oct 17 2002 - 12:54:37 CDT)
- Solvent exposed surface area over a trajectory Rebecca Perlow (Thu Oct 17 2002 - 13:20:03 CDT)
- Re: Solvent exposed surface area over a trajectory Michael Ford (Thu Oct 17 2002 - 14:09:17 CDT)
- Re: Solvent exposed surface area over a trajectory Sanjeev B.S. (Thu Oct 17 2002 - 14:18:56 CDT)
- Re: Solvent exposed surface area over a trajectory Natasja Brooijmans (Thu Oct 17 2002 - 14:35:34 CDT)
- Re: restraining atoms Ioana Cozmuta (Thu Oct 17 2002 - 12:54:37 CDT)
- Re: restraining atoms Lepsa (Thu Oct 17 2002 - 01:56:17 CDT)
- IGB =4 with GAFF and bugfix24 incomplete? Tom Bishop (Wed Oct 16 2002 - 13:12:37 CDT)
- syntax Ioana Cozmuta (Wed Oct 16 2002 - 13:14:54 CDT)
- Sir, Venkanna Belde (Thu Oct 17 2002 - 04:33:18 CDT)
- Imaging & fitting in carnal Sanjeev B.S. (Thu Oct 17 2002 - 06:01:55 CDT)
- Truncated Octahedron Box giudice (Thu Oct 17 2002 - 08:06:28 CDT)
- a leap question Vlad Cojocaru (Thu Oct 17 2002 - 08:20:23 CDT)
- dummy torsional parameters again. X. Tan (Thu Oct 17 2002 - 11:52:05 CDT)
- sander6 running and crashing at PSC? CUI, Guanglei (Thu Oct 17 2002 - 12:17:40 CDT)
- Reference for GB model 2 Jianhui Wu (Thu Oct 17 2002 - 14:26:18 CDT)
- Sander segmentation fault Joel Konkle-Parker (Thu Oct 17 2002 - 14:28:48 CDT)
- Reference, GB 2, Amber7 Jianhui Wu (Thu Oct 17 2002 - 14:34:12 CDT)
- time averaged restraint parameters Jake Isaacs (Thu Oct 17 2002 - 15:09:59 CDT)
- Carnal table output Christoph Brockmann (Fri Oct 18 2002 - 03:48:37 CDT)
- targeted MD Giulio Rastelli (Fri Oct 18 2002 - 09:28:48 CDT)
- Not able to use xleap ... Stéphane Teletchéa (Fri Oct 18 2002 - 10:58:21 CDT)
- Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 11:26:47 CDT)
- Re: Not able to use xleap ... David A. Case (Fri Oct 18 2002 - 11:38:23 CDT)
- Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 12:14:24 CDT)
- RE: Not able to use xleap ... Ross Walker (Sat Oct 19 2002 - 04:51:30 CDT)
- Re: Not able to use xleap ... Stéphane Teletchéa (Mon Oct 21 2002 - 02:08:12 CDT)
- Re: Not able to use xleap ... CUI, Guanglei (Mon Oct 21 2002 - 08:43:51 CDT)
- Re: Not able to use xleap ... Stéphane Teletchéa (Mon Oct 21 2002 - 10:02:25 CDT)
- Re: Not able to use xleap ... CUI, Guanglei (Mon Oct 21 2002 - 10:33:23 CDT)
- Re: Not able to use xleap ... Stéphane Teletchéa (Fri Oct 18 2002 - 12:24:38 CDT)
- Re: Not able to use xleap ... CUI, Guanglei (Fri Oct 18 2002 - 12:14:24 CDT)
- allocation memory error Ioana Cozmuta (Fri Oct 18 2002 - 14:50:22 CDT)
- Amber 4 question Tod Pascal (Fri Oct 18 2002 - 17:42:40 CDT)
- number of H-bonds Bimo Ario Tejo (Sat Oct 19 2002 - 23:54:44 CDT)
- How to define a sphere to minimize? Guillermo Mulliert Carlín (Mon Oct 21 2002 - 01:46:57 CDT)
- Re: reg: MAC OS David A. Case (Mon Oct 21 2002 - 11:11:56 CDT)
- question on ouput of sander Sichun Yang (Mon Oct 21 2002 - 13:19:17 CDT)
- sander7: MPI_COMM_RANK problem Matteo Dal Peraro (Mon Oct 21 2002 - 14:17:14 CDT)
- scaling of amber with number of atoms Marcela Madrid (Mon Oct 21 2002 - 14:23:59 CDT)
- problem with gibbs !!!! Asif Rahaman (Mon Oct 21 2002 - 21:18:10 CDT)
- MM-PGBSA Question!! Bernd Wellenzohn (Tue Oct 22 2002 - 07:46:29 CDT)
- Amber Crd format Tod Pascal (Tue Oct 22 2002 - 13:21:05 CDT)
- mm_pbsa-amber7 Sue Heavner (Tue Oct 22 2002 - 14:06:01 CDT)
- replacing fft routines Florian Barth (Tue Oct 22 2002 - 15:08:14 CDT)
- Dummy atoms... Miguel de Federico (Wed Oct 23 2002 - 02:44:34 CDT)
- Re: Patching AMBER7 with #24 Lepsa (Wed Oct 23 2002 - 02:49:07 CDT)
- Amber6 and MPI Yu Chen (Wed Oct 23 2002 - 13:10:30 CDT)
- Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 16:50:56 CDT)
- Re: Antechamber generating bad charges w/ gaussian 98. James W. Caldwell (Wed Oct 23 2002 - 18:16:05 CDT)
- RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 21:00:47 CDT)
- RE: Antechamber generating bad charges w/ gaussian 98. Nicholson, James D Mr ARO (Wed Oct 23 2002 - 21:12:32 CDT)
- min output Ioana Cozmuta (Wed Oct 23 2002 - 18:26:44 CDT)
- SDS forcefield? Arvid Soederhaell (Thu Oct 24 2002 - 04:25:58 CDT)
- carnal output trajectory Vlad Cojocaru (Thu Oct 24 2002 - 15:07:35 CDT)
- residue cross-correlation Bimo Ario Tejo (Thu Oct 24 2002 - 16:15:50 CDT)
- Re: HIS residues Ioana Cozmuta (Thu Oct 24 2002 - 16:51:40 CDT)
- carnal output trajectory Vlad Cojocaru (Fri Oct 25 2002 - 04:50:55 CDT)
- Re:SURFTEN for GB Lepsa (Fri Oct 25 2002 - 08:51:30 CDT)
- once again: residue cross-correlation Bimo Ario Tejo (Fri Oct 25 2002 - 09:39:40 CDT)
- time correlation function Bimo Ario Tejo (Fri Oct 25 2002 - 09:47:28 CDT)
- specification for memory requirement yuann (Fri Oct 25 2002 - 19:37:13 CDT)
- 2nd restart CUI, Guanglei (Sun Oct 27 2002 - 11:02:30 CST)
- total energies during MM-PBSA Giulio Rastelli (Sun Oct 27 2002 - 12:20:19 CST)
- Amber vijay dasa (Mon Oct 28 2002 - 00:51:02 CST)
- Hello Amber, vijay dasa (Mon Oct 28 2002 - 04:20:24 CST)
- Targeted MD Giulio Rastelli (Mon Oct 28 2002 - 15:44:05 CST)
- quasih Pratul Agarwal (Mon Oct 28 2002 - 16:25:02 CST)
- 64-bit Compilation SUN's forte compiler Fernando Martin (Mon Oct 28 2002 - 17:15:52 CST)
- LEaP: The parm and coord files disagree on the number of atoms Miguel de Federico (Tue Oct 29 2002 - 02:24:58 CST)
- FEP - ligand to nothing (or water)?? Aldo Jongejan (Tue Oct 29 2002 - 03:50:54 CST)
- mm_pbsa curious output of coordinates and resulting errors... Michael Ford (Tue Oct 29 2002 - 16:01:43 CST)
- mm_pbsa error message (warning?) Michael Ford (Tue Oct 29 2002 - 16:47:02 CST)
- Problems with tes.antechamber Chen, Ya (Tue Oct 29 2002 - 19:21:59 CST)
- Resp Multiconformational charge fitting! Marco Aurélio Correia Preto (Wed Oct 30 2002 - 05:50:52 CST)
- carnal output trajectory Vlad Cojocaru (Wed Oct 30 2002 - 07:25:36 CST)
- Sander Recompilation for the Biotin-Streptavidin Tutorial? Thomas Steinbrecher (Wed Oct 30 2002 - 09:46:30 CST)
- Charges derivation question! Marco Aurélio Correia Preto (Wed Oct 30 2002 - 10:39:24 CST)
- Re: RESP-group constraint Marco Preto (Wed Oct 30 2002 - 10:50:21 CST)
- IDECOMP Mark Hsieh (Wed Oct 30 2002 - 12:11:02 CST)
- question on belly and restraint Sichun Yang (Wed Oct 30 2002 - 14:54:37 CST)
- How to choose the box and cap size sxzheng (Thu Oct 31 2002 - 00:42:27 CST)
- *.top file: "PARM-F-UHOSED, try again" david (Thu Oct 31 2002 - 11:17:18 CST)
- carnal Ioana Cozmuta (Thu Oct 31 2002 - 12:30:35 CST)
- xleap and modified sugar residues Michael Ford (Thu Oct 31 2002 - 13:22:17 CST)
- NAV detected a virus in a document YOU sent to webmaster@nctimes.com. Mercury (Thu Oct 31 2002 - 21:12:51 CST)
- flag TREE_CHAIN_CLASSIFICATION in topology file from amber7 Pascal Bonnet (Fri Nov 01 2002 - 03:08:20 CST)
- molsurf reference Giulio Rastelli (Fri Nov 01 2002 - 06:17:35 CST)
- problem about cut and cap sxzheng (Sun Nov 03 2002 - 06:40:25 CST)
- periodic box Craig A Bayse (Mon Nov 04 2002 - 10:49:53 CST)
- P4_GLOBMEMSIZE problem Jean-Christophe Ducom (Mon Nov 04 2002 - 11:33:19 CST)
- Visualizing AMBER coordinates trajectory in VMD Pratul Agarwal (Mon Nov 04 2002 - 14:54:57 CST)
- restart Ioana Cozmuta (Mon Nov 04 2002 - 14:57:16 CST)
- RUNMIN hung_at_atc.atccu.chula.ac.th (Mon Nov 04 2002 - 19:04:23 CST)
- procheck hung_at_atc.atccu.chula.ac.th (Tue Nov 05 2002 - 00:53:56 CST)
- pseudoatoms and NMR restraints david (Tue Nov 05 2002 - 03:46:42 CST)
- Snapshot stuff Layi Adekoya (Tue Nov 05 2002 - 08:32:11 CST)
- Re: equilibrium problem about cut and belly David A. Case (Tue Nov 05 2002 - 10:14:51 CST)
- entropy calcs in mm_pbsa giulio_at_unimo.it (Tue Nov 05 2002 - 14:21:00 CST)
- torsion restraints in GIBBS Jose Ramon Blas (Tue Nov 05 2002 - 18:35:44 CST)
- amber on RH8 chernhoe (Wed Nov 06 2002 - 01:23:18 CST)
- Bugfixes William Wei (Wed Nov 06 2002 - 03:50:35 CST)
- average and runningaverage in ptraj Vlad Cojocaru (Wed Nov 06 2002 - 09:40:51 CST)
- time-averaged restraint developer Jake Isaacs (Wed Nov 06 2002 - 16:20:11 CST)
- restrt format problem Marcela Madrid (Wed Nov 06 2002 - 16:48:02 CST)
- nbflag Ioana Cozmuta (Wed Nov 06 2002 - 21:19:26 CST)
- nbflag Ioana Cozmuta (Wed Nov 06 2002 - 21:45:02 CST)
- surface Ioana Cozmuta (Thu Nov 07 2002 - 15:03:56 CST)
- averaging with ptraj and carnal Vlad Cojocaru (Fri Nov 08 2002 - 06:31:03 CST)
- ramdomized start velocities Arvid Soederhaell (Fri Nov 08 2002 - 06:35:23 CST)
- Sander: check COM velocity, temp: 0.000000 0.00(Removed) Miguel de Federico de la Rúa (Fri Nov 08 2002 - 08:08:38 CST)
- more about averaging Vlad Cojocaru (Fri Nov 08 2002 - 08:12:00 CST)
- residue cross-correlation Bimo Ario Tejo (Fri Nov 08 2002 - 09:00:01 CST)
- Roar capabilities M. L. Dodson (Fri Nov 08 2002 - 11:37:48 CST)
- residue cross-correlation Bimo Ario Tejo (Fri Nov 08 2002 - 12:57:48 CST)
- Problem in run Monica (Fri Nov 08 2002 - 22:41:52 CST)
- MEP g98_option FyD (Sat Nov 09 2002 - 00:35:22 CST)
- Forwarded mail.... Narang Manpreet Kaur (Sat Nov 09 2002 - 03:56:37 CST)
- drifting from average structure Vlad Cojocaru (Sat Nov 09 2002 - 10:17:38 CST)
- carnal7 produces memory fault and a core Giulio Rastelli (Sat Nov 09 2002 - 10:21:10 CST)
- belly and EWALD in amber7 Zhang Jian (Sat Nov 09 2002 - 21:04:14 CST)
- Re: belly and ivcap conflict in gibbs David A. Case (Sun Nov 10 2002 - 16:35:16 CST)
- .top files read into xLeap? Arvid Soederhaell (Mon Nov 11 2002 - 04:24:00 CST)
- nonpeoridic boundary + mm/gbsa Yongjun Jiang (Mon Nov 11 2002 - 06:49:03 CST)
- saveAmberParm of leap Sichun Yang (Mon Nov 11 2002 - 13:27:16 CST)
- problem in PME Monica (Tue Nov 12 2002 - 07:42:21 CST)
- re: the removal of global motion Shixiang Yan (Tue Nov 12 2002 - 10:44:38 CST)
- NMR restraints on a 10-mer DNA in Sander Jo.Vinje_at_kj.uib.no (Tue Nov 12 2002 - 11:34:55 CST)
- Amber7/CYGWIN compiling James W. Caldwell (Tue Nov 12 2002 - 15:09:33 CST)
- help! Non bond list overflow! Zhang Jian (Wed Nov 13 2002 - 04:56:39 CST)
- help on VMD movie Zhang Jian (Wed Nov 13 2002 - 06:44:36 CST)
- Ewald Monica (Wed Nov 13 2002 - 09:20:23 CST)
- CMM method Ioana Cozmuta (Wed Nov 13 2002 - 16:57:10 CST)
- input format for gibbs restraints Jose Ramon Blas (Wed Nov 13 2002 - 20:59:43 CST)
- (no subject) Monica (Thu Nov 14 2002 - 00:26:57 CST)
- restart mm_pbsa Layi Adekoya (Thu Nov 14 2002 - 07:02:51 CST)
- Amber on PC-Linux Philippe Aplincourt (Thu Nov 14 2002 - 09:22:20 CST)
- error in reading .crd file with GIBBS hagop demirdjian (Thu Nov 14 2002 - 09:40:32 CST)
- Linmin question... Andrei Leitão (Thu Nov 14 2002 - 12:10:21 CST)
- Linmin question... Andrei Leitão (Thu Nov 14 2002 - 12:13:01 CST)
- Amber Perl module Tod Pascal (Thu Nov 14 2002 - 15:33:01 CST)
- simulating dna Tod Pascal (Fri Nov 15 2002 - 19:23:54 CST)
- polarizabitlity X. Tan (Fri Nov 15 2002 - 19:41:37 CST)
- Conterions Monica (Sat Nov 16 2002 - 02:10:15 CST)
- (no subject) Narang Manpreet Kaur (Sat Nov 16 2002 - 04:17:02 CST)
- Are posters to the Amber list being spammed? Nicholson, James D Mr ARO (Sun Nov 17 2002 - 19:48:15 CST)
- choose dt in gibbs sxzheng (Sun Nov 17 2002 - 21:06:34 CST)
- NATOM mismatch in coord and topology files. Narang Manpreet Kaur (Mon Nov 18 2002 - 00:49:46 CST)
- creating a pdb trajectory with carnal Vlad Cojocaru (Mon Nov 18 2002 - 09:29:21 CST)
- makeDIST_RST? Sichun Yang (Mon Nov 18 2002 - 17:44:09 CST)
- Re: EWALD crash David A. Case (Mon Nov 18 2002 - 18:27:37 CST)
- defining groups on dif. sets in carnal Vlad Cojocaru (Tue Nov 19 2002 - 04:59:06 CST)
- limit of RMSD value Bimo Ario Tejo (Tue Nov 19 2002 - 07:57:40 CST)
- FEP/Gibbs question meiselba (Tue Nov 19 2002 - 09:29:07 CST)
- GIBBS - Error message. Miguel de Federico (Tue Nov 19 2002 - 10:00:25 CST)
- Frictional forces in gB Kristina Furse (Tue Nov 19 2002 - 17:41:32 CST)
- Nz-Acetyllysine parameters Luis Gracia (Tue Nov 19 2002 - 18:08:13 CST)
- intdiel & extdiel Fredrick Robin Devadoss (Wed Nov 20 2002 - 05:23:59 CST)
- Bulk Email Sending & Bullet Proof Web Hosting pposton (Wed Nov 20 2002 - 16:25:53 CST)
- P.3 in antechamber Giulio Rastelli (Thu Nov 21 2002 - 05:02:16 CST)
- PARMSET sara nunez (Thu Nov 21 2002 - 08:08:12 CST)
- ion distances Marcela Madrid (Thu Nov 21 2002 - 14:59:12 CST)
- targeted MD for more than 2 groups Sichun Yang (Thu Nov 21 2002 - 15:20:44 CST)
- Restraint Ambiguities Neema Salimi (Thu Nov 21 2002 - 16:56:44 CST)
- Error running AMBER6 on Beowulf cluster arubin_at_unmc.edu (Thu Nov 21 2002 - 17:10:39 CST)
- Equilibration output Amber7 Fredrick Robin Devadoss (Fri Nov 22 2002 - 03:42:32 CST)
- problem in restrt Marcela Madrid (Fri Nov 22 2002 - 10:37:53 CST)
- restarting simulation Marcela Madrid (Fri Nov 22 2002 - 14:06:42 CST)
- solvateOct Kristina Furse (Fri Nov 22 2002 - 15:36:33 CST)
- leap for peptide Sichun Yang (Fri Nov 22 2002 - 16:33:51 CST)
- ntx=7, irest=0 Marcela Madrid (Fri Nov 22 2002 - 17:56:00 CST)
- pdb file Ioana Cozmuta (Fri Nov 22 2002 - 18:41:01 CST)
- (no subject) Narang Manpreet Kaur (Sat Nov 23 2002 - 04:40:12 CST)
- Calculating atomic charges for AMBER with Gaussian98W Thomas Steinbrecher (Sat Nov 23 2002 - 07:52:47 CST)
- Hydrophobic protein in water Luo Liu (Sun Nov 24 2002 - 16:52:20 CST)
- atom type not recognized by GB eric hu (Sun Nov 24 2002 - 19:05:59 CST)
- Re: atom type not recognized by GB David A. Case (Sun Nov 24 2002 - 19:50:01 CST)
- Re: atom type not recognized by GB eric hu (Sun Nov 24 2002 - 20:30:17 CST)
- Please help. Energy suddenly increase. Protein jump out Lich Nguyen (Wed Nov 27 2002 - 01:42:29 CST)
- Re: Please help. Energy suddenly increase. Protein jump out David A. Case (Wed Nov 27 2002 - 10:26:55 CST)
- RE: Please help. Energy suddenly increase. Protein jump out Yong Duan (Wed Nov 27 2002 - 12:42:39 CST)
- Re: Please help. Energy suddenly increase. Protein jump out Carlos Simmerling (Wed Nov 27 2002 - 15:35:15 CST)
- RE: Please help. Energy suddenly increase. Protein jump out Yong Duan (Wed Nov 27 2002 - 16:52:54 CST)
- Re: atom type not recognized by GB David A. Case (Sun Nov 24 2002 - 19:50:01 CST)
- Inquiry software_at_kagaku.com (Sun Nov 24 2002 - 21:44:51 CST)
- (no subject) CHAUMONT Alain (Mon Nov 25 2002 - 09:32:50 CST)
- using SHAKE for solvent only hagop demirdjian (Mon Nov 25 2002 - 09:42:57 CST)
- external electric field Ioana Cozmuta (Mon Nov 25 2002 - 17:18:38 CST)
- a second question Ioana Cozmuta (Mon Nov 25 2002 - 18:20:52 CST)
- GIBBS - ERROR: Restraint read error from RSTIN; Check format: Miguel de Federico (Tue Nov 26 2002 - 03:14:19 CST)
- Error in Equilibration Fredrick Robin Devadoss (Tue Nov 26 2002 - 04:14:12 CST)
- restrain a residue as center of mass eric hu (Tue Nov 26 2002 - 17:36:19 CST)
- the tree name? Sichun Yang (Tue Nov 26 2002 - 21:29:27 CST)
- How Amber calculates electrostatic energy? Daniel Svozil (Wed Nov 27 2002 - 08:47:11 CST)
- esp.sh problem FyD (Wed Nov 27 2002 - 11:17:40 CST)
- external electric field/another try Ioana Cozmuta (Wed Nov 27 2002 - 16:13:08 CST)
- C60 parameter vannajan_at_chiangmai.ac.th (Thu Nov 28 2002 - 02:47:47 CST)
- Problem Monica (Fri Nov 29 2002 - 00:35:19 CST)
- parmchk -p option Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 04:09:09 CST)
- parameters for cyclic nucleotides Thomas.Fox_at_bc.boehringer-ingelheim.com (Fri Nov 29 2002 - 04:11:43 CST)
- (no subject) Narang Manpreet Kaur (Fri Nov 29 2002 - 04:54:03 CST)
- Break down energy contributions Numan Oezguen (Fri Nov 29 2002 - 15:06:36 CST)
- carnal amber 7.0 Vlad Cojocaru (Mon Dec 02 2002 - 02:35:34 CST)
- combinig two trajectory files. Yongjun Jiang (Mon Dec 02 2002 - 06:18:29 CST)
- err in specifying disulphide bridge using xleap! A.Madhumalar (Mon Dec 02 2002 - 10:25:30 CST)
- LEAP - Introducing dummy atoms Miguel de Federico (Mon Dec 02 2002 - 10:42:49 CST)
- penalty function in NMR refinement Mahadevan Seetharaman (Mon Dec 02 2002 - 11:09:05 CST)
- Biphasic box (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:13:10 CST)
- test mail Jim Caldwell (Tue Dec 03 2002 - 16:48:07 CST)
- freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:10 CST)
- Re: CCL:freeware for RNA modeling on Linux (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:21 CST)
- Constraints in Amber (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:30 CST)
- gB vs. explicit (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:57:53 CST)
- Amber Trajectories + VMD (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:00 CST)
- Energy decomposition with ANAL (fwd) amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 16:58:05 CST)
- Reflector problems amber_at_heimdal.compchem.ucsf.edu (Tue Dec 03 2002 - 17:05:02 CST)
- corrupted trajectory Guanglei Cui (Tue Dec 03 2002 - 17:07:46 CST)
- increasing the number of processors Ioana Cozmuta (Tue Dec 03 2002 - 18:17:58 CST)
- increasing the number of processors (fwd) Ioana Cozmuta (Tue Dec 03 2002 - 18:19:24 CST)
- Re: corrupted trajectory CUI, Guanglei (Tue Dec 03 2002 - 20:04:13 CST)
- restrained MD Vlad Cojocaru (Wed Dec 04 2002 - 12:18:54 CST)
- DIANA like files Vlad Cojocaru (Wed Dec 04 2002 - 14:24:12 CST)
- Amber 7 bugfix 27 !! urgent William Wei (Wed Dec 04 2002 - 14:45:13 CST)
- MDaemon Warning - Virus Found postmaster_at_bydnet.com.pl (Wed Dec 04 2002 - 21:49:28 CST)
- not compiled with -DHAS_10_12!! William Wei (Thu Dec 05 2002 - 10:29:22 CST)
- md failure: deep energetics problem eric hu (Thu Dec 05 2002 - 12:42:42 CST)
- About counterions Andrei Leitão (Thu Dec 05 2002 - 13:10:30 CST)
- Cap-atom-pointer in GIBBS Jose Ramon Blas (Thu Dec 05 2002 - 13:50:45 CST)
- ptraj rmsd calculation Thomas Steinbrecher (Thu Dec 05 2002 - 14:15:40 CST)
- Overwrite files Joffre Heredia (Thu Dec 05 2002 - 14:25:33 CST)
- timings? Arvid Soederhaell (Fri Dec 06 2002 - 02:51:10 CST)
- positional restraints Vlad Cojocaru (Fri Dec 06 2002 - 06:55:05 CST)
- Re: Energy decomposition with ANAL Numan Oezguen (Fri Dec 06 2002 - 11:08:20 CST)
- default GB radii Robert G. Endres (Fri Dec 06 2002 - 15:00:31 CST)
- carnal Ioana Cozmuta (Fri Dec 06 2002 - 17:47:56 CST)
- (no subject) Jennifer Hawkings (Sat Dec 07 2002 - 16:48:46 CST)
- CHARMm NPT input files Mahadevan Seetharaman (Sat Dec 07 2002 - 17:39:07 CST)
- NMR restrains Marcela Madrid (Mon Dec 09 2002 - 14:33:31 CST)
- running sander_classic for amber6 using different version of mpi Asif Rahaman (Mon Dec 09 2002 - 17:01:35 CST)
- difference in energy in amber6 and amber7 Prabal Maiti (Mon Dec 09 2002 - 20:07:15 CST)
- Question to perturbation charge meiselba (Tue Dec 10 2002 - 07:35:38 CST)
- bad protein structure eric hu (Tue Dec 10 2002 - 19:30:52 CST)
- Re: CCL:Amber7 and partial charges David Case (Wed Dec 11 2002 - 12:07:10 CST)
- MM-PBSA: .crg file for Delphi Thomas Steinbrecher (Wed Dec 11 2002 - 12:08:40 CST)
- Question on 2 stage RESP fit Ambarish Nag (Thu Dec 12 2002 - 00:39:08 CST)
- Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Thu Dec 12 2002 - 10:10:29 CST)
- MXVAR Guanglei Cui (Thu Dec 12 2002 - 10:34:17 CST)
- ambpdb Vlad Cojocaru (Thu Dec 12 2002 - 16:01:23 CST)
- Business Cooperation (Inheritance Claim) Mr. Daniel Osondu (Fri Dec 13 2002 - 01:50:38 CST)
- GIBBS - end-of-file during read Miguel de Federico (Fri Dec 13 2002 - 04:12:48 CST)
- plotting electrostatic potential surface Ioana Cozmuta (Fri Dec 13 2002 - 17:18:17 CST)
- solvating a protein with large cavity Tom Bishop (Sat Dec 14 2002 - 09:42:38 CST)
- FEP/Gibbs question to valine alanine tutorial meiselba (Sat Dec 14 2002 - 10:58:12 CST)
- a question about force field in AMBER jzhou (Sat Dec 14 2002 - 19:55:15 CST)
- disulfide bond link between two chains pu xuemei (Mon Dec 16 2002 - 06:50:35 CST)
- Fw: Valine to alanine Gibbs tutorial Lepsa (Mon Dec 16 2002 - 07:20:26 CST)
- sander (CAP) chokes on efc (Itanium2/Linux) Tadashi Takemori (Tue Dec 17 2002 - 01:11:14 CST)
- RST file for nonstandard residue vannajan_at_chiangmai.ac.th (Tue Dec 17 2002 - 03:07:04 CST)
- GIBBS - Routine TORCON (internal constraints) failed Miguel de Federico (Tue Dec 17 2002 - 09:29:04 CST)
- Chains, LEaP and ambpdb Luis Gracia (Tue Dec 17 2002 - 13:47:59 CST)
- water box, Ioana Cozmuta (Tue Dec 17 2002 - 17:18:31 CST)
- solvatebox Luis Gracia (Tue Dec 17 2002 - 18:52:07 CST)
- Studying in Australia John Pritchard (Tue Dec 17 2002 - 22:36:07 CST)
- amber trajectory Ioana Cozmuta (Tue Dec 17 2002 - 23:16:14 CST)
- message during minimization Ioana Cozmuta (Tue Dec 17 2002 - 23:31:52 CST)
- Re: message during minimization darden (Wed Dec 18 2002 - 10:24:48 CST)
- Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 17:09:05 CST)
- Re: message during minimization darden (Wed Dec 18 2002 - 18:32:21 CST)
- Re: message during minimization Ioana Cozmuta (Wed Dec 18 2002 - 20:02:26 CST)
- Re: message during minimization David A. Case (Thu Dec 19 2002 - 10:05:00 CST)
- chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 12:07:07 CST)
- Re: chirality.c failure - diagnosis, but no cure... Michael Ford (Thu Dec 19 2002 - 17:25:21 CST)
- Re: message during minimization darden (Wed Dec 18 2002 - 18:32:21 CST)
- SUMMARY: solvating a protein with large cavity Tom Bishop (Wed Dec 18 2002 - 09:03:27 CST)
- MPI_BCAST error Nathan A. Baker (Wed Dec 18 2002 - 09:51:02 CST)
- off-to-mol2 Anke Eisenmann (Wed Dec 18 2002 - 10:49:22 CST)
- mm_pbsa error message! William Wei (Wed Dec 18 2002 - 11:17:16 CST)
- About heating... Andrei Leitão (Wed Dec 18 2002 - 12:23:43 CST)
- antechamber Carsten Detering (Wed Dec 18 2002 - 13:38:16 CST)
- roar-cp problems M. L. Dodson (Wed Dec 18 2002 - 15:00:37 CST)
- antechamber Carsten Detering (Wed Dec 18 2002 - 16:32:44 CST)
- atomicfluct in ptraj Kristina Furse (Wed Dec 18 2002 - 17:16:29 CST)
- water/nonTIP3P Ioana Cozmuta (Wed Dec 18 2002 - 19:33:23 CST)
- ntwv saves v(t) or v(t+dt/2) ? hagop demirdjian (Thu Dec 19 2002 - 10:04:55 CST)
- RESTARTED DUE TO LINMIN FAILURE William Wei (Thu Dec 19 2002 - 13:33:07 CST)
- Nmode Pratul Agarwal (Thu Dec 19 2002 - 15:07:47 CST)
- selection of residues Ioana Cozmuta (Fri Dec 20 2002 - 18:51:52 CST)
- cap option Ioana Cozmuta (Sun Dec 22 2002 - 19:21:01 CST)
- beginners question dynamic group (Sun Dec 22 2002 - 23:17:52 CST)
- targeted MD sample eric hu (Thu Dec 26 2002 - 14:25:36 CST)
- Molecular dynamic protocol... Andrei Leitão (Fri Dec 27 2002 - 12:40:26 CST)
- cannot deal with large trajectory? yuann (Sat Dec 28 2002 - 21:17:23 CST)
- Trajectory file converted in pdb file Yongjun Jiang (Sun Dec 29 2002 - 19:13:38 CST)
- Sander rfree error kxg2248_at_njit.edu (Mon Dec 30 2002 - 16:58:19 CST)
- new on the Amber web pages... David A. Case (Tue Dec 31 2002 - 15:51:31 CST)
Last message date: Tue Dec 31 2002 - 15:51:31 CST
Archived on: Thu May 05 2005 - 14:17:25 CDT
2133 messages sorted by: [ author ] [ date ] [ subject ]
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