AMBER Archive (2008) - Mar 2008 By DateMost recent messages
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Starting: Sat Mar 01 2008 - 10:10:10 CST
Ending: Mon Mar 31 2008 - 15:40:52 CDT
- AMBER: regarding:calculation of b factor using ptraj jani sahil (Sat Mar 01 2008 - 10:10:10 CST)
- Re: AMBER: regarding:calculation of b factor using ptraj gurpreet singh (Sun Mar 02 2008 - 11:24:29 CST)
- AMBER: questions about run MD at different pH Kailee (Mon Mar 03 2008 - 08:51:40 CST)
- AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 12:58:46 CST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation David A. Case (Mon Mar 03 2008 - 13:24:20 CST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation Vlad Cojocaru (Mon Mar 03 2008 - 13:26:50 CST)
- Re: AMBER: Writing pressure in md.out file in NVT simulation Sudha Mani Karra (Mon Mar 03 2008 - 14:56:13 CST)
- AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 15:02:54 CST)
- Re: AMBER: xleap screen output David A. Case (Mon Mar 03 2008 - 15:31:17 CST)
- Re: AMBER: xleap screen output Francesco Pietra (Mon Mar 03 2008 - 15:48:59 CST)
- Re: AMBER: xleap screen output Bill Ross (Mon Mar 03 2008 - 16:08:17 CST)
- AMBER: ACS COMP Division awards- deadline this week Carlos Simmerling (Mon Mar 03 2008 - 18:14:03 CST)
- Re: AMBER: questions about run MD at different pH David A. Case (Mon Mar 03 2008 - 23:07:00 CST)
- AMBER: Problem running implicit minimization Lili Peng (Mon Mar 03 2008 - 23:10:52 CST)
- Re: AMBER: Problem running implicit minimization David A. Case (Mon Mar 03 2008 - 23:59:00 CST)
- Re: AMBER: Problem running implicit minimization Lili Peng (Tue Mar 04 2008 - 00:17:27 CST)
- AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 02:46:38 CST)
- Re: AMBER: Problem running implicit minimization Carlos Simmerling (Tue Mar 04 2008 - 05:04:38 CST)
- Re: AMBER: questions about run MD at different pH Kailee (Tue Mar 04 2008 - 05:40:30 CST)
- Re: AMBER: missing gaff parameters Junmei Wang (Tue Mar 04 2008 - 08:53:39 CST)
- RE: AMBER: missing gaff parameters Ross Walker (Tue Mar 04 2008 - 09:39:03 CST)
- Re: AMBER: missing gaff parameters Samuele Giani (Tue Mar 04 2008 - 10:42:03 CST)
- Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 11:27:00 CST)
- Fwd: Re: AMBER: xleap screen output Francesco Pietra (Tue Mar 04 2008 - 11:33:34 CST)
- Fwd: Re: AMBER: xleap screen output SOLVED Francesco Pietra (Tue Mar 04 2008 - 14:44:15 CST)
- Re: AMBER: Problem running implicit minimization Lili Peng (Tue Mar 04 2008 - 17:25:32 CST)
- Re: Fwd: Re: AMBER: xleap screen output Bill Ross (Tue Mar 04 2008 - 11:59:58 CST)
- Re: AMBER: Problem running implicit minimization Thomas Cheatham (Tue Mar 04 2008 - 17:47:50 CST)
- Re: AMBER: Problem running implicit minimization Carlos Simmerling (Tue Mar 04 2008 - 17:39:23 CST)
- RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program Mohd Farid Ismail (Tue Mar 04 2008 - 19:09:52 CST)
- Re: AMBER: Problem running implicit minimization Lili Peng (Tue Mar 04 2008 - 19:29:36 CST)
- Re: AMBER: questions about run MD at different pH David A. Case (Tue Mar 04 2008 - 19:59:49 CST)
- AMBER: el w-end en galicia! neva_at_mmb.pcb.ub.es (Wed Mar 05 2008 - 03:05:09 CST)
- AMBER: a question about parameter b in the hyperbolic form of penalty function for RESP fit Ye Mei (Wed Mar 05 2008 - 03:30:50 CST)
- AMBER: Atom types/parameters for chromene anna.schrey_at_gmx.de (Wed Mar 05 2008 - 03:34:24 CST)
- Re: AMBER: Atom types/parameters for chromene Junmei Wang (Wed Mar 05 2008 - 10:23:19 CST)
- Re: AMBER: Atom types/parameters for chromene Francesco Pietra (Wed Mar 05 2008 - 12:07:05 CST)
- Re: AMBER: Atom types/parameters for chromene David A. Case (Wed Mar 05 2008 - 13:15:25 CST)
- AMBER: setBox command Vijay Manickam Achari (Wed Mar 05 2008 - 23:20:01 CST)
- AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Thu Mar 06 2008 - 06:23:06 CST)
- Re: AMBER: Atom types/parameters for chromene anna.schrey_at_gmx.de (Thu Mar 06 2008 - 07:35:06 CST)
- AMBER: Steve Seibold (Thu Mar 06 2008 - 12:04:01 CST)
- Re: AMBER: Thomas Steinbrecher (Thu Mar 06 2008 - 12:13:23 CST)
- Re: AMBER: setBox command Thomas Steinbrecher (Thu Mar 06 2008 - 12:06:32 CST)
- RE: AMBER: Ross Walker (Thu Mar 06 2008 - 12:37:16 CST)
- RE: AMBER: Steve Seibold (Thu Mar 06 2008 - 12:27:34 CST)
- Re: AMBER: Jianyin Shao (Thu Mar 06 2008 - 15:24:03 CST)
- AMBER: XMGRACE on Linux 64 Bit dpandit_at_brandeis.edu (Thu Mar 06 2008 - 17:15:00 CST)
- Re: AMBER: XMGRACE on Linux 64 Bit Bill Ross (Thu Mar 06 2008 - 18:12:51 CST)
- Re: AMBER: XMGRACE on Linux 64 Bit dpandit_at_brandeis.edu (Thu Mar 06 2008 - 19:50:55 CST)
- RE: AMBER: XMGRACE on Linux 64 Bit Ross Walker (Thu Mar 06 2008 - 20:30:44 CST)
- AMBER: Microcannonical MD Reference priya priya (Fri Mar 07 2008 - 07:40:34 CST)
- AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 09:36:48 CST)
- Re: AMBER: NVE energy and temperature drift David A. Case (Fri Mar 07 2008 - 10:32:51 CST)
- AMBER: Fwd: positive potential energy and large 1-4 EEL Mey Khalili (Fri Mar 07 2008 - 10:54:28 CST)
- Re: AMBER: NVE energy and temperature drift Lars Skjærven (Fri Mar 07 2008 - 11:34:33 CST)
- AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis James Thomas (Fri Mar 07 2008 - 11:30:58 CST)
- RE: AMBER: XMGRACE on Linux 64 Bit dpandit_at_brandeis.edu (Fri Mar 07 2008 - 12:40:19 CST)
- AMBER: AMBER install problem Kijeong Kwac (Fri Mar 07 2008 - 12:12:08 CST)
- Re: AMBER: XMGRACE on Linux 64 Bit David LeBard (Fri Mar 07 2008 - 12:53:47 CST)
- AMBER: RE: Request Ross Walker (Fri Mar 07 2008 - 14:38:25 CST)
- Re: AMBER: Inquiry on nmode for alculate frequencies & thermodynamics analysis David A. Case (Fri Mar 07 2008 - 15:36:33 CST)
- Re: AMBER: Microcannonical MD Reference David A. Case (Fri Mar 07 2008 - 16:47:02 CST)
- AMBER: reg molecular dynamics Uma R (Fri Mar 07 2008 - 21:17:32 CST)
- AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Sat Mar 08 2008 - 05:36:56 CST)
- AMBER: Compiler issues with Altix450 finke_at_oakland.edu (Sat Mar 08 2008 - 12:37:25 CST)
- AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 14:09:23 CST)
- Re: AMBER: Clarification on error message Thomas Steinbrecher (Sat Mar 08 2008 - 14:17:35 CST)
- RE: AMBER: Clarification on error message Campbell, Patrick (Sat Mar 08 2008 - 15:15:36 CST)
- Re: AMBER: Compiler issues with Altix450 Atro Tossavainen (Sat Mar 08 2008 - 16:19:36 CST)
- AMBER: mmpbsa INSTRNG error? Sergio Wong (Sun Mar 09 2008 - 00:06:44 CST)
- Re: AMBER: mmpbsa INSTRNG error? Gohlke_at_bioinformatik.uni-frankfurt.de (Sun Mar 09 2008 - 11:13:05 CDT)
- AMBER: Timing analysis on Ranger David LeBard (Sun Mar 09 2008 - 15:06:18 CDT)
- AMBER: Antechamber, net molecular charge gurpreet singh (Sun Mar 09 2008 - 23:51:58 CDT)
- AMBER: Benchmarks on Fujitsu PrimePower 2500? Craig Gough (Mon Mar 10 2008 - 00:36:28 CDT)
- Fwd: AMBER: Negative ligand (Peroxide) Syed Tarique Moin (Mon Mar 10 2008 - 00:59:43 CDT)
- Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Atro Tossavainen (Mon Mar 10 2008 - 03:04:20 CDT)
- Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Robert Duke (Mon Mar 10 2008 - 08:24:21 CDT)
- Re: AMBER: Benchmarks on Fujitsu PrimePower 2500? Atro Tossavainen (Mon Mar 10 2008 - 08:24:33 CDT)
- AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 08:33:55 CDT)
- Re: AMBER: Antechamber, net molecular charge Junmei Wang (Mon Mar 10 2008 - 09:39:08 CDT)
- AMBER: problem with antech amber Madjid Taghdir (Mon Mar 10 2008 - 10:07:16 CDT)
- Re: AMBER: writing out a distance between two atoms in sander Thomas Steinbrecher (Mon Mar 10 2008 - 12:17:35 CDT)
- Re: AMBER: writing out a distance between two atoms in sander Vlad Cojocaru (Mon Mar 10 2008 - 12:35:58 CDT)
- Re: AMBER: Compiler issues with Altix450 finke_at_oakland.edu (Mon Mar 10 2008 - 15:45:37 CDT)
- AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 17:57:06 CDT)
- Re: AMBER: Compiler issues with Altix450 Atro Tossavainen (Mon Mar 10 2008 - 18:13:45 CDT)
- Re: AMBER: Compiler issues with Altix450 David A. Case (Mon Mar 10 2008 - 18:29:50 CDT)
- Re: AMBER: output effective Born radii David A. Case (Mon Mar 10 2008 - 19:07:39 CDT)
- AMBER: Re: Amber: parameters for Silicon Scott Brozell (Mon Mar 10 2008 - 18:57:29 CDT)
- Re: AMBER: Fwd: positive potential energy and large 1-4 EEL David A. Case (Mon Mar 10 2008 - 19:19:51 CDT)
- Re: AMBER: AMBER install problem David A. Case (Mon Mar 10 2008 - 19:50:30 CDT)
- AMBER: SMD using amber ChengZhong Zhang (Mon Mar 10 2008 - 20:54:23 CDT)
- Re: AMBER: output effective Born radii Holly Freedman (Mon Mar 10 2008 - 21:24:32 CDT)
- Re: AMBER: AMBER install problem Atro Tossavainen (Tue Mar 11 2008 - 01:51:18 CDT)
- AMBER: convert AMBER format input files into DL_POLY format input files? Kefa Lu (Tue Mar 11 2008 - 03:27:23 CDT)
- AMBER: solvate with methanol san_amber roy (Tue Mar 11 2008 - 04:23:40 CDT)
- AMBER: Adding New Parameters and Modifying Existing Parameters serhanyigen_at_mail.ege.edu.tr (Tue Mar 11 2008 - 06:51:18 CDT)
- Re: AMBER: solvate with methanol Rita Cassia (Tue Mar 11 2008 - 07:33:46 CDT)
- AMBER: SPARC benchmarks (was re Fujitsu PRIMEPOWER) Atro Tossavainen (Tue Mar 11 2008 - 09:33:33 CDT)
- Re: AMBER: Adding New Parameters and Modifying Existing Parameters Thomas Steinbrecher (Tue Mar 11 2008 - 11:46:33 CDT)
- AMBER: question on antechamber: jaguar ouput wei zhang (Tue Mar 11 2008 - 12:01:55 CDT)
- Re: AMBER: question on antechamber: jaguar ouput Junmei Wang (Tue Mar 11 2008 - 13:22:52 CDT)
- Re: AMBER: question on antechamber: jaguar ouput Marcelo Puiatti (Tue Mar 11 2008 - 13:35:10 CDT)
- Re: AMBER: AMBER install problem David A. Case (Tue Mar 11 2008 - 19:47:58 CDT)
- AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Tue Mar 11 2008 - 22:30:14 CDT)
- Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David A. Case (Wed Mar 12 2008 - 00:43:26 CDT)
- AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 10:07:23 CDT)
- Fwd: AMBER: lastrst problem san_amber roy (Wed Mar 12 2008 - 10:19:08 CDT)
- AMBER: ptraj and non-bonded contacts Samuel Genheden (a03samge) (Wed Mar 12 2008 - 11:34:44 CDT)
- Re: AMBER: Error during compilation of Amber8, /bin/sh: ./Makelist: not found, make[1]: *** [libobj] Error 127 David Rangel (Wed Mar 12 2008 - 12:04:18 CDT)
- Re: AMBER: question on antechamber: jaguar ouput wei zhang (Wed Mar 12 2008 - 13:14:55 CDT)
- AMBER: study of protein stability in different ion using AMBER Prem Prakash Pathak (Thu Mar 13 2008 - 01:20:31 CDT)
- AMBER: distance restraint gurpreet singh (Thu Mar 13 2008 - 06:28:28 CDT)
- AMBER: [success] problem compiling Amber9 on Bull Linux Yannick Monclin (Thu Mar 13 2008 - 06:56:48 CDT)
- AMBER: Energy calculation and replica exchange in Amber9 Li Dawei (Thu Mar 13 2008 - 08:50:49 CDT)
- AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Thu Mar 13 2008 - 09:03:45 CDT)
- AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Thu Mar 13 2008 - 09:54:03 CDT)
- AMBER: Temperature Range For REMD tushar garud (Thu Mar 13 2008 - 10:20:02 CDT)
- Re: AMBER: Temperature Range For REMD Carlos Simmerling (Thu Mar 13 2008 - 10:26:44 CDT)
- AMBER: implicit energy calculations rebeca_at_mmb.pcb.ub.es (Thu Mar 13 2008 - 11:26:43 CDT)
- AMBER: RE: Re: AMBER: AMBER install problem Kijeong Kwac (Thu Mar 13 2008 - 12:35:10 CDT)
- Re: AMBER: ptraj, hbond and non-bonded contacts Thomas Cheatham III (Thu Mar 13 2008 - 12:49:14 CDT)
- Re: AMBER: implicit energy calculations Thomas Cheatham III (Thu Mar 13 2008 - 12:47:04 CDT)
- Re: AMBER: distance restraint David A. Case (Thu Mar 13 2008 - 15:40:07 CDT)
- AMBER: force field oguz gurbulak (Thu Mar 13 2008 - 17:00:58 CDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ) Lwin, ThuZar (Thu Mar 13 2008 - 19:13:57 CDT)
- AMBER: How to calculate deformability by PTRAJ ? sychen (Thu Mar 13 2008 - 20:44:36 CDT)
- Re: AMBER: ptraj, hbond and non-bonded contacts Jojart Balazs (Fri Mar 14 2008 - 03:19:37 CDT)
- AMBER: Torsion potential in GAFF / "statistic value of parm94" Alexander Metz (Fri Mar 14 2008 - 07:53:10 CDT)
- AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Lwin, ThuZar (Fri Mar 14 2008 - 10:32:25 CDT)
- RE: AMBER: protonated histidine ( charges in parm file versus all_amino03.lib ). Ross Walker (Fri Mar 14 2008 - 11:30:13 CDT)
- AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 13:44:44 CDT)
- Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 14:01:06 CDT)
- Re: AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 14:13:02 CDT)
- Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 14:31:03 CDT)
- Re: AMBER: Heating POL3 Box Troubles Paul Johns (Fri Mar 14 2008 - 16:01:22 CDT)
- Re: AMBER: Heating POL3 Box Troubles Thomas Steinbrecher (Fri Mar 14 2008 - 16:22:21 CDT)
- Re: AMBER: can't make antechamber work for regular nucleotides Junmei Wang (Fri Mar 14 2008 - 21:10:41 CDT)
- Re: AMBER: Torsion potential in GAFF / "statistic value of parm94" Junmei Wang (Fri Mar 14 2008 - 22:01:20 CDT)
- Re: AMBER: Heating POL3 Box Troubles David A. Case (Fri Mar 14 2008 - 22:40:35 CDT)
- Re: AMBER: Heating POL3 Box Troubles David A. Case (Fri Mar 14 2008 - 23:41:09 CDT)
- Re: AMBER: problem with antech amber David A. Case (Sat Mar 15 2008 - 00:09:00 CDT)
- Re: AMBER: study of protein stability in different ion using AMBER David A. Case (Sat Mar 15 2008 - 00:48:13 CDT)
- AMBER: Negative ligand Syed Tarique Moin (Sat Mar 15 2008 - 04:12:09 CDT)
- SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 05:43:21 CDT)
- Re: SV: AMBER: ptraj, hbond and non-bonded contacts Vlad Cojocaru (Mon Mar 17 2008 - 06:00:41 CDT)
- SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 06:02:59 CDT)
- SV: SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 07:00:52 CDT)
- Re: AMBER: can't make antechamber work for regular nucleotides Mey Khalili (Mon Mar 17 2008 - 08:59:01 CDT)
- Re: SV: AMBER: ptraj, hbond and non-bonded contacts Thomas Cheatham III (Mon Mar 17 2008 - 11:51:54 CDT)
- AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 13:20:21 CDT)
- Re: AMBER: mm_pbsa positive ELE Ray Luo (Mon Mar 17 2008 - 13:33:11 CDT)
- AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Fri Mar 14 2008 - 12:44:56 CDT)
- RE: AMBER: mm_pbsa positive ELE Qi Yan (Mon Mar 17 2008 - 14:23:52 CDT)
- Re: AMBER: Heating POL3 Box Troubles Paul Johns (Mon Mar 17 2008 - 15:07:02 CDT)
- Re: AMBER: mm_pbsa positive ELE Ray Luo (Mon Mar 17 2008 - 15:14:57 CDT)
- SV: SV: AMBER: ptraj, hbond and non-bonded contacts Samuel Genheden (a03samge) (Mon Mar 17 2008 - 15:41:31 CDT)
- Re: AMBER: compiling AMBER9 with bintraj option on AMD64 David A. Case (Mon Mar 17 2008 - 18:48:00 CDT)
- AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 19:20:30 CDT)
- RE: AMBER: What's making my system lose total energy? Ross Walker (Mon Mar 17 2008 - 21:54:19 CDT)
- Re: AMBER: What's making my system lose total energy? Thomas Cheatham (Mon Mar 17 2008 - 22:36:30 CDT)
- Re: AMBER: What's making my system lose total energy? David Cerutti (Mon Mar 17 2008 - 22:52:10 CDT)
- Re: AMBER: Heating POL3 Box Troubles David A. Case (Tue Mar 18 2008 - 00:30:48 CDT)
- AMBER: a minor bug in RESP Ye Mei (Tue Mar 18 2008 - 02:05:34 CDT)
- Re: AMBER: compiling AMBER9 with bintraj option on AMD64 Vlad Cojocaru (Tue Mar 18 2008 - 04:32:13 CDT)
- AMBER: problem with distance restrain aneesh cna (Tue Mar 18 2008 - 05:16:09 CDT)
- AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 09:09:34 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 09:29:38 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 10:29:39 CDT)
- Re: Fwd: AMBER: lastrst problem David A. Case (Tue Mar 18 2008 - 10:37:48 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 11:21:21 CDT)
- RE: AMBER: protonated histidine ( charges in parm file versus all_a mino03.lib ). . . Lwin, ThuZar (Tue Mar 18 2008 - 11:45:49 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 11:39:01 CDT)
- AMBER: Problems with neglected restaints anna.schrey_at_gmx.de (Tue Mar 18 2008 - 11:40:20 CDT)
- Re: AMBER: Problems with neglected restaints Carlos Simmerling (Tue Mar 18 2008 - 12:05:11 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 12:07:54 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Tue Mar 18 2008 - 12:12:03 CDT)
- Re: AMBER: Problems with neglected restaints David A. Case (Tue Mar 18 2008 - 12:15:56 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Tue Mar 18 2008 - 12:24:10 CDT)
- Re: AMBER: What's making my system lose total energy? David Cerutti (Tue Mar 18 2008 - 13:43:42 CDT)
- Re: AMBER: problem with distance restrain David A. Case (Tue Mar 18 2008 - 14:00:11 CDT)
- Re: AMBER: can't make antechamber work for regular nucleotides Junmei Wang (Tue Mar 18 2008 - 16:08:46 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 07:14:38 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 07:14:38 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Wed Mar 19 2008 - 07:47:04 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 08:13:01 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Wed Mar 19 2008 - 08:25:11 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 08:35:55 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Wed Mar 19 2008 - 08:49:23 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Wed Mar 19 2008 - 08:57:55 CDT)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? David A. Case (Wed Mar 19 2008 - 10:42:13 CDT)
- AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 11:09:05 CDT)
- Re: Fwd: AMBER: lastrst problem san_amber roy (Wed Mar 19 2008 - 11:07:26 CDT)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Wed Mar 19 2008 - 11:49:45 CDT)
- AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Wed Mar 19 2008 - 11:28:35 CDT)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Francesco Pietra (Wed Mar 19 2008 - 12:26:24 CDT)
- AMBER: MNDO parameters for Mg+2 E.M. (Wed Mar 19 2008 - 12:28:09 CDT)
- RE: AMBER: MNDO parameters for Mg+2 Ross Walker (Wed Mar 19 2008 - 13:10:18 CDT)
- AMBER: standard residues Holly Freedman (Wed Mar 19 2008 - 15:03:02 CDT)
- Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 15:25:25 CDT)
- Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 15:43:50 CDT)
- Re: AMBER: Amber9 Installation Problem Cenk Andac (Wed Mar 19 2008 - 15:55:23 CDT)
- Re: AMBER: Inquiry on analyzing the amplitude from nmdout results David A. Case (Wed Mar 19 2008 - 16:46:10 CDT)
- Re: AMBER: Heating POL3 Box Troubles Paul Johns (Wed Mar 19 2008 - 14:22:50 CDT)
- Re: AMBER: Heating POL3 Box Troubles David A. Case (Wed Mar 19 2008 - 16:57:54 CDT)
- Re: AMBER: Inquiry on analyzing the amplitude from nmdout results James Thomas (Wed Mar 19 2008 - 17:00:35 CDT)
- Re: AMBER: Inquiry on analyzing the amplitude from nmdout results David A. Case (Wed Mar 19 2008 - 17:49:21 CDT)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? David A. Case (Wed Mar 19 2008 - 17:54:24 CDT)
- Re: AMBER: Amber9 Installation Problem David A. Case (Wed Mar 19 2008 - 20:37:57 CDT)
- Re: AMBER: What's making my system lose total energy? David A. Case (Wed Mar 19 2008 - 20:46:31 CDT)
- AMBER: Water Topology Ivelin Georgiev (Wed Mar 19 2008 - 23:12:28 CDT)
- RE: AMBER: Water Topology Ross Walker (Wed Mar 19 2008 - 23:49:43 CDT)
- AMBER: potential of mean force: Unit of PMF energies and min path Catein Catherine (Thu Mar 20 2008 - 00:26:43 CDT)
- AMBER: Happy holi Bertrand P. S. Russell (Thu Mar 20 2008 - 04:03:22 CDT)
- AMBER: problem with distance restraints aneesh cna (Thu Mar 20 2008 - 05:13:31 CDT)
- Re: AMBER: Water Topology Ivelin Georgiev (Thu Mar 20 2008 - 08:44:51 CDT)
- Re: AMBER: replica exchange : problem with sander Carlos Simmerling (Thu Mar 20 2008 - 09:47:32 CDT)
- RE: AMBER: Water Topology Ross Walker (Thu Mar 20 2008 - 10:08:46 CDT)
- Re: AMBER: replica exchange : problem with sander Guillaume Renvez (Thu Mar 20 2008 - 10:02:29 CDT)
- AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 10:17:32 CDT)
- Re: AMBER: INPCRD error on open Carlos Simmerling (Thu Mar 20 2008 - 10:22:56 CDT)
- Re: AMBER: INPCRD error on open Cyril Bauvais (Thu Mar 20 2008 - 11:04:31 CDT)
- RE: AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 12:02:12 CDT)
- Re: AMBER: INPCRD error on open Carlos Simmerling (Thu Mar 20 2008 - 12:10:23 CDT)
- RE: AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 13:37:45 CDT)
- RE: AMBER: INPCRD error on open Campbell, Patrick (Thu Mar 20 2008 - 13:35:37 CDT)
- Re: AMBER: Problems with neglected restaints anna.schrey_at_gmx.de (Thu Mar 20 2008 - 14:43:20 CDT)
- Re: AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Thu Mar 20 2008 - 17:43:48 CDT)
- Re: AMBER: Amber9 Installation Problem trudy_at_uoguelph.ca (Thu Mar 20 2008 - 17:51:08 CDT)
- Re: AMBER: Amber9 Installation Problem David A. Case (Thu Mar 20 2008 - 18:23:53 CDT)
- AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 01:58:19 CDT)
- Re: AMBER: Charge scheme for simulating protonated adenine FyD (Fri Mar 21 2008 - 02:43:51 CDT)
- Re: AMBER: Charge scheme for simulating protonated adenine rpaduri_at_chem.wayne.edu (Fri Mar 21 2008 - 10:29:18 CDT)
- Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 11:32:06 CDT)
- Re: AMBER: Charge scheme for simulating protonated adenine prateeksha s (Fri Mar 21 2008 - 11:32:14 CDT)
- Re: AMBER: problem with distance restraints David A. Case (Fri Mar 21 2008 - 12:56:28 CDT)
- AMBER: equilibration of peptide tushar garud (Fri Mar 21 2008 - 23:02:25 CDT)
- AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 10:40:16 CDT)
- RE: AMBER: cntrl namelist error Ross Walker (Sat Mar 22 2008 - 11:01:47 CDT)
- Re: AMBER: cntrl namelist error David A. Case (Sat Mar 22 2008 - 11:11:52 CDT)
- RE: AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 11:11:39 CDT)
- RE: AMBER: cntrl namelist error Campbell, Patrick (Sat Mar 22 2008 - 11:22:18 CDT)
- Re: AMBER: standard residues David A. Case (Sat Mar 22 2008 - 11:30:03 CDT)
- Re: AMBER: equilibration of peptide David A. Case (Sat Mar 22 2008 - 12:51:47 CDT)
- Re: AMBER: standard residues Holly Freedman (Sat Mar 22 2008 - 17:27:07 CDT)
- AMBER: RE: Force Field Parameterizing Shultz, Jack (Mon Mar 24 2008 - 10:31:32 CDT)
- AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 10:51:51 CDT)
- Re: AMBER: hybrid remd imaging Carlos Simmerling (Mon Mar 24 2008 - 10:59:24 CDT)
- Re: AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 11:21:41 CDT)
- Re: AMBER: hybrid remd imaging Geoff Wood (Mon Mar 24 2008 - 11:16:25 CDT)
- AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Mon Mar 24 2008 - 15:01:35 CDT)
- Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Da-Wei Li (Mon Mar 24 2008 - 15:12:42 CDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Mon Mar 24 2008 - 15:50:40 CDT)
- AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 06:53:21 CDT)
- AMBER: addions and addions2 dpandit_at_brandeis.edu (Tue Mar 25 2008 - 09:38:22 CDT)
- Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Andrew Borgert (Tue Mar 25 2008 - 10:11:20 CDT)
- Re: AMBER: RE: Force Field Parameterizing David A. Case (Tue Mar 25 2008 - 10:23:34 CDT)
- AMBER: anion and cation simulaton gurpreet singh (Tue Mar 25 2008 - 11:22:29 CDT)
- AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 11:17:43 CDT)
- Re: AMBER: Nmode segmentation fault David A. Case (Tue Mar 25 2008 - 11:34:37 CDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Tue Mar 25 2008 - 12:00:35 CDT)
- Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Da-Wei Li (Tue Mar 25 2008 - 12:08:29 CDT)
- Re: AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 12:22:43 CDT)
- Re: AMBER: addions and addions2 Bill Ross (Tue Mar 25 2008 - 12:34:52 CDT)
- AMBER: Convert dcd to mdcrd Seth Lilavivat (Tue Mar 25 2008 - 13:13:22 CDT)
- Re: AMBER: Nmode segmentation fault David A. Case (Tue Mar 25 2008 - 13:44:51 CDT)
- Re: AMBER: help regarding warning message David A. Case (Tue Mar 25 2008 - 13:51:07 CDT)
- Re: AMBER: Nmode segmentation fault James Thomas (Tue Mar 25 2008 - 14:00:44 CDT)
- AMBER: RE: Force Field Parameterizing FyD (Tue Mar 25 2008 - 14:42:03 CDT)
- Re: AMBER: anion and cation simulaton FyD (Tue Mar 25 2008 - 14:54:56 CDT)
- Re: AMBER: help regarding warning message snoze pa (Tue Mar 25 2008 - 15:23:55 CDT)
- AMBER: umbrella sampling for proton transfer cniu_at_ualberta.ca (Tue Mar 25 2008 - 19:30:33 CDT)
- Re: AMBER: umbrella sampling for proton transfer Thomas Steinbrecher (Tue Mar 25 2008 - 20:11:58 CDT)
- AMBER: NTR Restraints Daniel Smith (Tue Mar 25 2008 - 20:17:27 CDT)
- Re: AMBER: Convert dcd to mdcrd Vlad Cojocaru (Wed Mar 26 2008 - 04:02:38 CDT)
- AMBER: FAD and NAD parameters Thomas Leonard (Wed Mar 26 2008 - 04:26:52 CDT)
- Re: AMBER: FAD and NAD parameters FyD (Wed Mar 26 2008 - 05:57:27 CDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Qi Yan (Wed Mar 26 2008 - 09:42:54 CDT)
- Re: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Steven Winfield (Wed Mar 26 2008 - 10:22:26 CDT)
- Re: AMBER: OPLS force field David A. Case (Wed Mar 26 2008 - 11:08:57 CDT)
- AMBER: OPLS force field aneesh cna (Wed Mar 26 2008 - 10:48:19 CDT)
- AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Wed Mar 26 2008 - 12:32:54 CDT)
- AMBER: residual dipolar couplings - alignment tensor energy Douglas Kojetin (Wed Mar 26 2008 - 14:46:48 CDT)
- AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 15:35:32 CDT)
- Re: AMBER: RMSD of two different molecules Da-Wei Li (Wed Mar 26 2008 - 15:39:19 CDT)
- AMBER: how to link two different atoms in xLeap snoze pa (Wed Mar 26 2008 - 15:56:12 CDT)
- Re: AMBER: RMSD of two different molecules JunJun Liu (Wed Mar 26 2008 - 16:54:11 CDT)
- Re: AMBER: mm-pbsa multiple trajectory approach? Chris Moth (Wed Mar 26 2008 - 17:21:25 CDT)
- RE: AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-) Chris Moth (Wed Mar 26 2008 - 17:27:35 CDT)
- AMBER: Error with a binary restart file Kijeong Kwac (Wed Mar 26 2008 - 18:07:51 CDT)
- Re: AMBER: Error with a binary restart file David A. Case (Wed Mar 26 2008 - 20:11:58 CDT)
- AMBER: PF6 parameters aneesh cna (Wed Mar 26 2008 - 23:43:58 CDT)
- Re: AMBER: how to link two different atoms in xLeap David A. Case (Wed Mar 26 2008 - 23:52:18 CDT)
- AMBER: Error- MM_PBSA calculation vikky 99 (Thu Mar 27 2008 - 03:47:53 CDT)
- AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 05:13:00 CDT)
- Re: AMBER: FW: MD run time inquiry Carlos Simmerling (Thu Mar 27 2008 - 05:41:02 CDT)
- FW: AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 07:14:16 CDT)
- Re: AMBER: hybrid remd imaging Geoff Wood (Thu Mar 27 2008 - 07:56:30 CDT)
- Re: FW: AMBER: FW: MD run time inquiry Carlos Simmerling (Thu Mar 27 2008 - 08:15:09 CDT)
- FW: FW: AMBER: FW: MD run time inquiry Campbell, Patrick (Thu Mar 27 2008 - 08:55:28 CDT)
- Re: AMBER: NTR Restraints David A. Case (Thu Mar 27 2008 - 15:17:31 CDT)
- AMBER: Protein rotating out of box Lars Skjærven (Thu Mar 27 2008 - 16:34:48 CDT)
- RE: AMBER: PF6 parameters caoch (Thu Mar 27 2008 - 23:28:03 CDT)
- AMBER: measuring contacts: error "glibc detected" rebeca_at_mmb.pcb.ub.es (Fri Mar 28 2008 - 07:26:42 CDT)
- AMBER: GAFF Eric Germaneau (Fri Mar 28 2008 - 07:38:41 CDT)
- AMBER: REMD simulation error Guillaume Renvez (Fri Mar 28 2008 - 09:01:20 CDT)
- Re: AMBER: mm-pbsa multiple trajectory approach? Seth Lilavivat (Fri Mar 28 2008 - 10:28:31 CDT)
- AMBER: problem with nmod yuri pomè (Fri Mar 28 2008 - 11:42:54 CDT)
- AMBER: AMBER 9 testing Taufik Al-Sarraj (Fri Mar 28 2008 - 19:18:30 CDT)
- Re: AMBER: AMBER 9 testing David A. Case (Fri Mar 28 2008 - 19:10:02 CDT)
- Re: AMBER: problem with nmod David A. Case (Fri Mar 28 2008 - 19:19:40 CDT)
- Re: AMBER: AMBER 9 testing Taufik Al-Sarraj (Fri Mar 28 2008 - 23:13:31 CDT)
- AMBER: Amber Workshop Chih-Ying Lin (Sat Mar 29 2008 - 00:58:14 CDT)
- AMBER: meet problem in adding ions and waterbox Qiang Li (Sun Mar 30 2008 - 00:43:54 CDT)
- AMBER: Regarding SHAKE gurpreet singh (Sun Mar 30 2008 - 05:38:48 CDT)
- Re: AMBER: AMBER 9 testing David A. Case (Sun Mar 30 2008 - 11:23:15 CDT)
- Re: AMBER: meet problem in adding ions and waterbox Emilio Xavier Esposito (Sun Mar 30 2008 - 12:26:45 CDT)
- AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water Markus Kaukonen (Mon Mar 31 2008 - 01:34:48 CDT)
- AMBER: Free energy landscape? HOWTO? Yi-Ming Cheng (Mon Mar 31 2008 - 03:12:05 CDT)
- AMBER: TI: perturbation method fatima.chami_at_durham.ac.uk (Mon Mar 31 2008 - 03:40:40 CDT)
- AMBER: energy problems in simulation with restraints Daniel Cappel (Mon Mar 31 2008 - 04:39:13 CDT)
- AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 04:28:31 CDT)
- Re: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 05:31:39 CDT)
- RE: AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 06:00:52 CDT)
- AMBER: installation amber9 Geoff Wood (Mon Mar 31 2008 - 06:02:01 CDT)
- RE: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 06:19:49 CDT)
- RE: AMBER: Select specific residues (leap) Marta Rossini (Mon Mar 31 2008 - 07:57:04 CDT)
- Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER? Edyta Malolepsza (Mon Mar 31 2008 - 08:05:42 CDT)
- RE: AMBER: Select specific residues (leap) FyD (Mon Mar 31 2008 - 08:32:30 CDT)
- Re: AMBER: energy problems in simulation with restraints David A. Case (Mon Mar 31 2008 - 10:35:58 CDT)
- Re: AMBER: TI: perturbation method Thomas Steinbrecher (Mon Mar 31 2008 - 11:32:21 CDT)
- AMBER: multiple dihedral restraints using group mkseo (Mon Mar 31 2008 - 12:11:30 CDT)
- Re: AMBER: installation amber9 David A. Case (Mon Mar 31 2008 - 12:51:45 CDT)
- AMBER: memory limitation of Amber 9 yavuzturkm_at_prc.boun.edu.tr (Mon Mar 31 2008 - 13:49:40 CDT)
- AMBER: nmode James Thomas (Mon Mar 31 2008 - 13:48:43 CDT)
- Re: AMBER: nmode David A. Case (Mon Mar 31 2008 - 14:25:52 CDT)
- AMBER: running minimisation on cis-azobenzene Chih-Ying Lin (Mon Mar 31 2008 - 14:45:20 CDT)
- Re: AMBER: running minimisation on cis-azobenzene Thomas Steinbrecher (Mon Mar 31 2008 - 15:14:17 CDT)
- AMBER: Amber Workshop Chih-Ying Lin (Mon Mar 31 2008 - 15:40:52 CDT)
Last message date: Wed Dec 31 2008 - 22:47:27 CST
Archived on: Thu Jan 08 2009 - 16:01:47 CST
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