AMBER Archive (2002) - By ThreadMost recent messages
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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)
- 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)
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