Amber Archive Mar 2005: By Thread

AMBER: An error during minimization using RED tomjas.poczta.onet.pl (Mon Feb 28 2005 - 23:18:55 PST)
- Re: AMBER: An error during minimization using RED FyD (Tue Mar 01 2005 - 13:44:33 PST)
  - Re: Re: AMBER: An error during minimization using RED tomjas.poczta.onet.pl (Wed Mar 02 2005 - 01:15:15 PST)
  - Re: Re: AMBER: An error during minimization using RED tomjas.poczta.onet.pl (Wed Mar 02 2005 - 05:18:00 PST)
AMBER: problem with MD simulation Ye Mei (Tue Mar 01 2005 - 00:00:31 PST)
- RE: AMBER: problem with MD simulation Ross Walker (Tue Mar 01 2005 - 08:51:40 PST)
  - Re: RE: AMBER: problem with MD simulation Ye Mei (Fri Mar 04 2005 - 17:46:24 PST)
AMBER: NaNQ ilaria massarelli (Tue Mar 01 2005 - 00:45:10 PST)
- RE: AMBER: NaNQ Ross Walker (Tue Mar 01 2005 - 08:46:08 PST)
  - RE: AMBER: NaNQ ilaria massarelli (Wed Mar 02 2005 - 07:01:33 PST)
    - AMBER: across-correlation in ptraj Xin Hu (Wed Mar 02 2005 - 08:20:09 PST)
Re: AMBER: creating a new residue YoungJin Cho (Tue Mar 01 2005 - 07:18:16 PST)
Re: AMBER: Amber8 Solaris installation failure Joe Nolan (Tue Mar 01 2005 - 07:23:06 PST)
Re: AMBER: Controlling number of water residues... Guanglei Cui (Tue Mar 01 2005 - 07:49:57 PST)
- Re: AMBER: Controlling number of water residues... David A. Case (Tue Mar 01 2005 - 08:25:14 PST)
Re: AMBER: Amber Poisson-Boltzmann MD :Equilibration Problem David A. Case (Tue Mar 01 2005 - 08:41:08 PST)
AMBER: Dihedral Energy calculation yen li (Tue Mar 01 2005 - 10:12:56 PST)
- RE: AMBER: Dihedral Energy calculation Junmei Wang (Tue Mar 01 2005 - 10:57:49 PST)
  - RE: AMBER: Dihedral Energy calculation yen li (Wed Mar 02 2005 - 04:37:01 PST)
    - RE: AMBER: Dihedral Energy calculation Ross Walker (Wed Mar 02 2005 - 08:48:56 PST)
    - RE: AMBER: Dihedral Energy calculation yen li (Wed Mar 02 2005 - 10:03:24 PST)
    - RE: AMBER: Dihedral Energy calculation Ross Walker (Wed Mar 02 2005 - 14:37:20 PST)
- AMBER: MM-GBSA Alessio Coi (Wed Mar 02 2005 - 02:00:52 PST)
  - Re: AMBER: MM-GBSA David A. Case (Wed Mar 02 2005 - 07:44:15 PST)
- RE: AMBER: Dihedral Energy calculation yen li (Fri Mar 04 2005 - 13:29:08 PST)
AMBER: PMEMD on Opterons; building/benchmarks/recommendations Robert Duke (Tue Mar 01 2005 - 11:14:56 PST)
AMBER: Xleap execution problems on Solaris Joe Nolan (Tue Mar 01 2005 - 12:51:26 PST)
- Re: AMBER: Xleap execution problems on Solaris Scott Brozell (Tue Mar 01 2005 - 19:36:56 PST)
AMBER: RESP of negatively charged molecule Rhoad, Jonathan S. (Tue Mar 01 2005 - 13:39:05 PST)
AMBER: Sample more conformational space Bogos Agianian (Wed Mar 02 2005 - 04:52:49 PST)
- Re: AMBER: Sample more conformational space Marc Baaden (Wed Mar 02 2005 - 05:03:02 PST)
- Re: AMBER: Sample more conformational space Carlos Simmerling (Wed Mar 02 2005 - 08:35:18 PST)
AMBER: bond type for a virtual bond in a biomolecular transition state Eric Hu (Wed Mar 02 2005 - 14:54:45 PST)
- Re: AMBER: bond type for a virtual bond in a biomolecular transition state David A. Case (Wed Mar 02 2005 - 15:08:38 PST)
AMBER: Installation problem S.Sundar Raman (Wed Mar 02 2005 - 22:28:29 PST)
- Re: AMBER: Installation problem Maciej (Thu Mar 03 2005 - 01:26:30 PST)
- Re: AMBER: Installation problem David A. Case (Thu Mar 03 2005 - 08:18:47 PST)
AMBER: Amber 8 on cygwin install problem Maciej (Thu Mar 03 2005 - 02:49:17 PST)
- Re: AMBER: Amber 8 on cygwin install problem David A. Case (Thu Mar 03 2005 - 08:07:52 PST)
  - Re: AMBER: Amber 8 on cygwin install problem Maciej (Thu Mar 03 2005 - 22:51:32 PST)
    - Re: AMBER: Amber 8 on cygwin install problem David A. Case (Sun Mar 06 2005 - 11:23:52 PST)
AMBER: phosphorylated DNA not recognized Annette Höglund (Thu Mar 03 2005 - 06:55:18 PST)
- Re: AMBER: phosphorylated DNA not recognized FyD (Thu Mar 03 2005 - 10:59:27 PST)
AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 10:56:32 PST)
- Re: AMBER: bond connectivity among dummy atoms Ilyas Yildirim (Thu Mar 03 2005 - 11:57:48 PST)
  - Re: AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 13:25:19 PST)
    - Re: AMBER: bond connectivity among dummy atoms Ilyas Yildirim (Thu Mar 03 2005 - 13:58:38 PST)
    - Re: AMBER: bond connectivity among dummy atoms Eric Hu (Thu Mar 03 2005 - 14:12:26 PST)
AMBER: A problem about Gaussian Yanze Zhang (Thu Mar 03 2005 - 14:38:59 PST)
- Re: AMBER: A problem about Gaussian FyD (Thu Mar 03 2005 - 15:27:23 PST)
  - AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Thu Mar 03 2005 - 16:24:03 PST)
    - Re: AMBER: Dummy atoms: Changing the source code Julien Michel (Fri Mar 04 2005 - 01:44:31 PST)
    - Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Fri Mar 04 2005 - 18:56:34 PST)
    - Re: AMBER: Dummy atoms: Changing the source code David A. Case (Tue Mar 08 2005 - 11:50:58 PST)
    - Re: AMBER: Dummy atoms: Changing the source code Ilyas Yildirim (Tue Mar 08 2005 - 12:56:48 PST)
- Re: AMBER: A problem about Gaussian David A. Case (Thu Mar 03 2005 - 16:55:35 PST)
AMBER: Antechamber/Divcon assigned charges Marc Christensen (Thu Mar 03 2005 - 19:38:10 PST)
- Re: AMBER: Antechamber/Divcon assigned charges David A. Case (Thu Mar 03 2005 - 21:17:13 PST)
- RE: AMBER: Antechamber/Divcon assigned charges Junmei Wang (Thu Mar 03 2005 - 21:20:38 PST)
AMBER: atom type designation Lihua Wang (Fri Mar 04 2005 - 16:05:10 PST)
AMBER: R.E.D Wai Keat Yam (Sat Mar 05 2005 - 21:14:49 PST)
- Re: AMBER: R.E.D FyD (Sun Mar 06 2005 - 17:42:20 PST)
  - Re: AMBER: R.E.D Wai Keat Yam (Sun Mar 06 2005 - 18:31:57 PST)
Re: AMBER: R.E.D Piotr Cieplak (Sun Mar 06 2005 - 16:20:42 PST)
AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Cenk Andac (Sun Mar 06 2005 - 16:57:21 PST)
- Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) Yuuki Komata (Sun Mar 06 2005 - 17:14:18 PST)
- Re: AMBER: Citing Generalized Born Implicit solvent Model (igb=5) David A. Case (Sun Mar 06 2005 - 17:14:35 PST)
AMBER: AMBER8 Compile Error on Dual Opteron Thomas Patko (Sun Mar 06 2005 - 17:53:46 PST)
- Re: AMBER: AMBER8 Compile Error on Dual Opteron David A. Case (Sun Mar 06 2005 - 20:24:27 PST)
AMBER: amber with mpich-G2 putra abdullah (Sun Mar 06 2005 - 18:55:44 PST)
- Re: AMBER: amber with mpich-G2 Robert Duke (Sun Mar 06 2005 - 20:07:21 PST)
AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 04:28:19 PST)
- Re: AMBER: A problem about removing waters and counterions by ptraj Carlos Simmerling (Mon Mar 07 2005 - 05:29:14 PST)
  - Re: AMBER: A problem about removing waters and counterions by ptraj scopio (Mon Mar 07 2005 - 05:48:40 PST)
AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks Robert Duke (Mon Mar 07 2005 - 08:47:02 PST)
- Re: AMBER: New pmemd build utility; pathscale vs. pgi vs. ifort em64 opteron benchmarks David A. Case (Mon Mar 07 2005 - 10:36:40 PST)
AMBER: What PRESS is? hj zou (Mon Mar 07 2005 - 19:08:39 PST)
- Re: AMBER: What PRESS is? Mingyue Zheng (Mon Mar 07 2005 - 19:26:01 PST)
- RE: AMBER: What PRESS is? Ross Walker (Mon Mar 07 2005 - 20:07:37 PST)
AMBER: global pH variation in AMBER. Osman Gani (Tue Mar 08 2005 - 02:56:06 PST)
- Re: AMBER: global pH variation in AMBER. David A. Case (Tue Mar 08 2005 - 11:38:30 PST)
AMBER: Error limits of TI and MM_PBSA methods Nelson Fonseca (Tue Mar 08 2005 - 08:54:42 PST)
AMBER: Energy fluctuations David.LeBard.asu.edu (Tue Mar 08 2005 - 09:40:46 PST)
- Re: AMBER: Energy fluctuations David A. Case (Tue Mar 08 2005 - 11:36:14 PST)
AMBER: radii "leap" from which file xhu1.memphis.edu (Tue Mar 08 2005 - 11:34:48 PST)
- Re: AMBER: radii "leap" from which file David A. Case (Wed Mar 09 2005 - 17:02:43 PST)
AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Tue Mar 08 2005 - 12:37:50 PST)
- RE: AMBER: Sander questions on dual-processor Sun with MPICH Ross Walker (Tue Mar 08 2005 - 17:50:55 PST)
- Re: AMBER: Sander questions on dual-processor Sun with MPICH Robert Duke (Wed Mar 09 2005 - 05:41:08 PST)
- Re: AMBER: Sander questions on dual-processor Sun with MPICH Joe Nolan (Thu Mar 10 2005 - 08:46:23 PST)
AMBER: X Windows for LEaP on SGI Akshay Patny (Tue Mar 08 2005 - 13:07:44 PST)
- RE: AMBER: X Windows for LEaP on SGI Ross Walker (Tue Mar 08 2005 - 18:05:01 PST)
  - Re: AMBER: X Windows for LEaP on SGI Thomas Patko (Tue Mar 08 2005 - 21:44:26 PST)
AMBER: capping? Hui-Hsu Tsai (Tue Mar 08 2005 - 13:34:59 PST)
- RE: AMBER: capping? Ross Walker (Tue Mar 08 2005 - 18:09:44 PST)
  - RE: AMBER: capping? FyD (Wed Mar 09 2005 - 08:51:32 PST)
    - Re: AMBER: capping? Heiko Meyer (Wed Mar 09 2005 - 09:17:01 PST)
Re: AMBER: radii "leap" from which file Bill Ross (Tue Mar 08 2005 - 13:43:18 PST)
- Re: AMBER: radii "leap" from which file xhu1.memphis.edu (Tue Mar 08 2005 - 19:06:22 PST)
AMBER: heating Gustavo Pierdominici Sottile (Tue Mar 08 2005 - 14:20:34 PST)
- Re: AMBER: heating Ilyas Yildirim (Tue Mar 08 2005 - 15:02:17 PST)
  - AMBER: Compiling just sander Ilyas Yildirim (Thu Mar 10 2005 - 19:07:31 PST)
    - Re: AMBER: Compiling just sander david.evans.ulsop.ac.uk (Fri Mar 11 2005 - 01:24:24 PST)
  - AMBER: "The system has extended beyond" error Ilyas Yildirim (Tue Mar 29 2005 - 14:28:35 PST)
    - Re: AMBER: "The system has extended beyond" error David A. Case (Wed Mar 30 2005 - 07:08:07 PST)
    - Re: AMBER: "The system has extended beyond" error Ilyas Yildirim (Thu Mar 31 2005 - 04:26:21 PST)
Re: AMBER: heating Bill Ross (Tue Mar 08 2005 - 14:55:47 PST)
AMBER: The pressure bybaker.itsa.ucsf.edu (Tue Mar 08 2005 - 17:54:44 PST)
- RE: AMBER: The pressure Ross Walker (Tue Mar 08 2005 - 18:20:44 PST)
- Re: AMBER: The pressure bybaker.itsa.ucsf.edu (Tue Mar 08 2005 - 22:38:14 PST)
  - AMBER: Priti Hansia (Tue Mar 08 2005 - 23:38:59 PST)
    - Re: AMBER: David A. Case (Fri Mar 11 2005 - 11:02:40 PST)
    - RE: AMBER: Ross Walker (Sun Mar 13 2005 - 16:29:08 PST)
AMBER: how can I deal with the puzzle? hj zou (Tue Mar 08 2005 - 19:36:39 PST)
- Re: AMBER: how can I deal with the puzzle? Thomas E. Cheatham, III (Tue Mar 08 2005 - 19:53:48 PST)
  - Re: Re: AMBER: how can I deal with the puzzle? ZhangJian (Tue Mar 08 2005 - 23:59:42 PST)
AMBER: Problems Binding Protein to DNA Pieter Smith (Tue Mar 08 2005 - 21:21:30 PST)
- RE: AMBER: Problems Binding Protein to DNA Vineet Pande (Wed Mar 09 2005 - 03:16:44 PST)
AMBER: amber on sgi mathew k varghese (Wed Mar 09 2005 - 03:23:12 PST)
- Re: AMBER: amber on sgi Robert Duke (Wed Mar 09 2005 - 05:32:29 PST)
- Re: AMBER: amber on sgi Karol Miaskiewicz (Wed Mar 09 2005 - 05:37:31 PST)
- Re: AMBER: amber on sgi Bill Ross (Wed Mar 09 2005 - 07:35:21 PST)
  - Re: AMBER: amber on sgi Melinda Layten (Wed Mar 09 2005 - 08:52:28 PST)
AMBER: For further question about Targeted MD ZhangJian (Wed Mar 09 2005 - 04:48:44 PST)
- AMBER: problem with running AMBER with lam-mpi though PBS script Ru-Zhen Li (Wed Mar 09 2005 - 06:01:24 PST)
  - Re: AMBER: problem with running AMBER with lam-mpi though PBS script Karol Miaskiewicz (Wed Mar 09 2005 - 05:57:46 PST)
    - Re: AMBER: problem with running AMBER with lam-mpi though PBS script Ru-Zhen Li (Wed Mar 09 2005 - 17:48:56 PST)
AMBER: vlimit in heating Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 06:13:20 PST)
- Re: AMBER: vlimit in heating David A. Case (Wed Mar 09 2005 - 08:10:42 PST)
Re: AMBER: vlimit in heating Bill Ross (Wed Mar 09 2005 - 07:44:06 PST)
AMBER: solvatebox problem in the antechamber tutorial Heiko Meyer (Wed Mar 09 2005 - 08:29:00 PST)
- Re: AMBER: solvatebox problem in the antechamber tutorial David A. Case (Wed Mar 09 2005 - 16:18:19 PST)
AMBER: vlimit heat Gustavo Pierdominici Sottile (Wed Mar 09 2005 - 09:36:30 PST)
AMBER: Re: Amber 8 dual-Xeon compile problem keiodai.shohoku.ac.jp (Wed Mar 09 2005 - 20:14:33 PST)
AMBER: how to excite a single residue ? Priti Hansia (Wed Mar 09 2005 - 20:28:24 PST)
- Re: AMBER: how to excite a single residue ? Pradipta Bandyopadhyay (Wed Mar 09 2005 - 21:24:34 PST)
AMBER: PTRAJ $ Antechamber Andrew Box (Wed Mar 09 2005 - 22:47:29 PST)
- Re: AMBER: PTRAJ $ Antechamber David A. Case (Sat Mar 12 2005 - 14:17:49 PST)
AMBER: Sander error Vojtìch Klusák (Thu Mar 10 2005 - 04:03:21 PST)
- Re: AMBER: Sander error Viktor Hornak (Fri Mar 11 2005 - 08:36:38 PST)
Re: AMBER: PTRAJ $ Antechamber Bill Ross (Thu Mar 10 2005 - 09:22:39 PST)
AMBER: expected error in mean (Amber 8 TI tutorial) Eric Hu (Thu Mar 10 2005 - 15:38:13 PST)
- Re: AMBER: expected error in mean (Amber 8 TI tutorial) David A. Case (Sat Mar 12 2005 - 14:18:40 PST)
AMBER: Re: inconsistent ordering in an improper dihedral of TRP Sanghyun Park (Thu Mar 10 2005 - 19:08:25 PST)
AMBER: IDIEL in sander sebnem (Thu Mar 10 2005 - 23:14:50 PST)
- Re: AMBER: IDIEL in sander David A. Case (Sat Mar 12 2005 - 14:10:09 PST)
AMBER: vlimit Gustavo Pierdominici Sottile (Fri Mar 11 2005 - 04:33:36 PST)
AMBER: Holes in water Lukasz Bielecki (Fri Mar 11 2005 - 06:13:40 PST)
- Re :AMBER: Holes in water Pascal Auffinger (Fri Mar 11 2005 - 07:26:31 PST)
  - Re: Re :AMBER: Holes in water Bill Ross (Sat Mar 12 2005 - 11:15:43 PST)
AMBER: problem with nmode using ntrun=5 Phineus Markwick (Fri Mar 11 2005 - 06:38:34 PST)
Re: AMBER: Re: inconsistent ordering in an improper dihedral of TRP Bill Ross (Fri Mar 11 2005 - 07:46:40 PST)
Re: Re :AMBER: Holes in water Bill Ross (Fri Mar 11 2005 - 07:59:03 PST)
- Re: Re :AMBER: Holes in water Lukasz Bielecki (Sat Mar 12 2005 - 08:52:31 PST)
  - Re: Re :AMBER: Holes in water Carlos Simmerling (Sat Mar 12 2005 - 10:32:06 PST)
- Re: Re :AMBER: Holes in water Bill Ross (Sat Mar 12 2005 - 10:13:06 PST)
  - Re: Re :AMBER: Holes in water Carlos Simmerling (Sat Mar 12 2005 - 10:46:24 PST)
    - Re: Re :AMBER: Holes in water Thomas E. Cheatham, III (Sat Mar 12 2005 - 14:20:32 PST)
AMBER: problem with nmode using ntrun=5 (2) Phineus Markwick (Fri Mar 11 2005 - 08:39:43 PST)
AMBER: ptraj xueping (Fri Mar 11 2005 - 20:56:29 PST)
- Re: AMBER: ptraj scopio (Fri Mar 11 2005 - 21:44:04 PST)
- Re: AMBER: ptraj xueping (Fri Mar 11 2005 - 23:08:37 PST)
AMBER: Amber PBMD:Energy fluctuation Praveena Gopal (Sat Mar 12 2005 - 01:48:03 PST)
Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 04:28:34 PST)
- Re: AMBER: Cu++ and RED FyD (Sat Mar 12 2005 - 09:35:53 PST)
- Re:Re: AMBER: Cu++ and RED Cenk Andac (Sat Mar 12 2005 - 10:39:10 PST)
  - Re: AMBER: Cu++ and RED FyD (Sat Mar 12 2005 - 14:00:56 PST)
AMBER: spherical boundary condition Hui-Hsu Tsai (Sat Mar 12 2005 - 11:05:52 PST)
- Re: AMBER: spherical boundary condition David A. Case (Sat Mar 12 2005 - 18:51:58 PST)
- Re: AMBER: spherical boundary condition protege.snu.ac.kr (Mon Mar 14 2005 - 09:43:14 PST)
- Re: AMBER: spherical boundary condition protege.snu.ac.kr (Mon Mar 14 2005 - 09:43:14 PST)
  - Re: AMBER: spherical boundary condition Andreas Svrcek-Seiler (Mon Mar 14 2005 - 10:36:06 PST)
    - Re: AMBER: spherical boundary condition Hui-Hsu Tsai (Mon Mar 14 2005 - 10:59:01 PST)
AMBER: mesure dihedral angle during MD julien (Sun Mar 13 2005 - 08:52:01 PST)
- Re: AMBER: mesure dihedral angle during MD Guanglei Cui (Sun Mar 13 2005 - 10:10:46 PST)
AMBER: gyration radius julien (Sun Mar 13 2005 - 08:49:50 PST)
- Re: AMBER: gyration radius Guanglei Cui (Sun Mar 13 2005 - 10:18:18 PST)
Re: AMBER: gyration radius Bill Ross (Sun Mar 13 2005 - 11:36:15 PST)
AMBER: leap warnings mathew k varghese (Sun Mar 13 2005 - 22:34:32 PST)
- RE: AMBER: leap warnings Ross Walker (Sun Mar 13 2005 - 22:56:17 PST)
AMBER: surfen and surfoff Giulio Rastelli (Mon Mar 14 2005 - 08:21:22 PST)
AMBER: RDF input preparation problem Maciej (Sun Mar 13 2005 - 20:12:22 PST)
AMBER: Xserve and amber Markus W. Germann (Mon Mar 14 2005 - 08:55:53 PST)
- Re: AMBER: Xserve and amber Mengjuei Hsieh (Mon Mar 14 2005 - 17:51:12 PST)
AMBER: Geometrical distortion because of charge? peng79.email.unc.edu (Mon Mar 14 2005 - 10:21:28 PST)
AMBER: Question about radial command in ptraj opitz.che.udel.edu (Mon Mar 14 2005 - 11:19:11 PST)
Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 11:48:17 PST)
- Re: AMBER: Question about radial command in ptraj opitz.che.udel.edu (Mon Mar 14 2005 - 12:04:55 PST)
- Re: AMBER: Question about radial command in ptraj Bill Ross (Mon Mar 14 2005 - 13:09:08 PST)
AMBER: antechamber and multiplicity Cenk Andac (Mon Mar 14 2005 - 11:57:27 PST)
AMBER: determining solvent/ion densities Joseph W.Toporowski (Mon Mar 14 2005 - 15:35:25 PST)
AMBER: Hydrogen bonding question opitz.che.udel.edu (Tue Mar 15 2005 - 06:57:45 PST)
- Re: AMBER: Hydrogen bonding question Carlos Simmerling (Tue Mar 15 2005 - 07:21:37 PST)
- Re: AMBER: Hydrogen bonding question David A. Case (Tue Mar 15 2005 - 07:23:30 PST)
- Re: AMBER: Hydrogen bonding question opitz.che.udel.edu (Tue Mar 15 2005 - 07:34:53 PST)
  - Re: AMBER: Hydrogen bonding question Carlos Simmerling (Tue Mar 15 2005 - 07:48:41 PST)
  - Re: AMBER: Hydrogen bonding question Thomas E. Cheatham, III (Tue Mar 15 2005 - 07:59:00 PST)
AMBER: Problem saving file in xleap aanzellotti.mail2.vcu.edu (Tue Mar 15 2005 - 09:03:12 PST)
- RE: AMBER: Problem saving file in xleap Ross Walker (Tue Mar 15 2005 - 10:02:32 PST)
  - RE: AMBER: Problem saving file in xleap aanzellotti.mail2.vcu.edu (Thu Mar 17 2005 - 08:45:07 PST)
AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 11:45:47 PST)
- Re: AMBER: Sander: idecomp Jack Lei (Tue Mar 15 2005 - 15:57:21 PST)
  - Re: AMBER: Sander: idecomp lei jia (Tue Mar 15 2005 - 18:25:24 PST)
    - Re: Re: AMBER: Sander: idecomp Xiao He (Mon Mar 28 2005 - 05:44:53 PST)
AMBER: frcmod.mod_phipsi.2 bybaker.itsa.ucsf.edu (Tue Mar 15 2005 - 12:04:31 PST)
- RE: AMBER: frcmod.mod_phipsi.2 Junmei Wang (Tue Mar 15 2005 - 12:22:29 PST)
- Re: AMBER: frcmod.mod_phipsi.2 Carlos Simmerling (Tue Mar 15 2005 - 14:52:53 PST)
AMBER: in vacuo parameters Stern, Julie (Tue Mar 15 2005 - 15:14:44 PST)
- Re: AMBER: in vacuo parameters Carlos Simmerling (Tue Mar 15 2005 - 15:29:31 PST)
AMBER: restraintmask dimension Piero Altoè (Wed Mar 16 2005 - 03:42:12 PST)
- Re: AMBER: restraintmask dimension Viktor Hornak (Wed Mar 16 2005 - 05:46:27 PST)
AMBER: Bio-Image summer school in Paris this year Marc Baaden (Wed Mar 16 2005 - 03:44:47 PST)
AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 06:08:42 PST)
- Re: AMBER: Velocity Info Guanglei Cui (Wed Mar 16 2005 - 06:55:07 PST)
  - Re: AMBER: Velocity Info Vineet Pande (Wed Mar 16 2005 - 08:02:04 PST)
    - Re: AMBER: Velocity Info Guanglei Cui (Wed Mar 16 2005 - 08:29:35 PST)
AMBER: "personality" of Amber force field Hui-Hsu Tsai (Wed Mar 16 2005 - 08:01:00 PST)
- Re:AMBER: "personality" of Amber force field Asim Okur (Fri Mar 18 2005 - 13:01:19 PST)
  - Re:AMBER: "personality" of Amber force field Hui-Hsu Tsai (Fri Mar 18 2005 - 13:22:11 PST)
    - Re: AMBER: "personality" of Amber force field Adrian E. Roitberg (Fri Mar 18 2005 - 13:24:50 PST)
    - Re: AMBER: "personality" of Amber force field Hui-Hsu Tsai (Fri Mar 18 2005 - 15:05:07 PST)
    - Re: AMBER: "personality" of Amber force field Ray Luo (Thu Mar 17 2005 - 14:17:03 PST)
AMBER: question about amber parameter file format etc. jz7.duke.edu (Wed Mar 16 2005 - 09:37:29 PST)
- RE: AMBER: question about amber parameter file format etc. Vineet Pande (Wed Mar 16 2005 - 10:06:53 PST)
AMBER: periodicity problem Stern, Julie (Wed Mar 16 2005 - 13:02:28 PST)
- Re: AMBER: periodicity problem Ilyas Yildirim (Wed Mar 16 2005 - 13:25:39 PST)
AMBER: Zn complex parametrization question Ashutosh Suhas Jogalekar (Wed Mar 16 2005 - 13:27:38 PST)
Re: AMBER: periodicity problem Bill Ross (Wed Mar 16 2005 - 14:23:03 PST)
AMBER: sander.QMMM and fcap Claudio Morgado (Thu Mar 17 2005 - 05:56:34 PST)
- Re: AMBER: sander.QMMM and fcap David A. Case (Thu Mar 17 2005 - 08:00:04 PST)
AMBER: van der Waals interactions (PTRAJ) Vineet Pande (Thu Mar 17 2005 - 06:07:12 PST)
AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 06:50:03 PST)
- Re: AMBER: Minimization of avg structure-SANDER Bomb David A. Case (Thu Mar 17 2005 - 08:51:59 PST)
  - Re: AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 10:45:01 PST)
    - Re: AMBER: Minimization of avg structure-SANDER Bomb David A. Case (Thu Mar 17 2005 - 10:54:18 PST)
    - Re: AMBER: Minimization of avg structure-SANDER Bomb Vineet Pande (Thu Mar 17 2005 - 12:11:10 PST)
- Re: AMBER: Minimization of avg structure-SANDER Bomb Thomas E. Cheatham, III (Thu Mar 17 2005 - 11:01:33 PST)
AMBER: Bus error - ambpdb David C. Chan (Thu Mar 17 2005 - 06:54:17 PST)
- Re: AMBER: Bus error - ambpdb David A. Case (Thu Mar 17 2005 - 08:54:28 PST)
AMBER: compiler for amber8 on opteron Marc Petitmermet (Thu Mar 17 2005 - 07:56:37 PST)
- Re: AMBER: compiler for amber8 on opteron Noriyuki Yamaotsu (Thu Mar 17 2005 - 17:50:24 PST)
  - Re: AMBER: compiler for amber8 on opteron Marc Petitmermet (Fri Mar 18 2005 - 00:22:42 PST)
    - Re: AMBER: compiler for amber8 on opteron Robert Duke (Fri Mar 18 2005 - 05:11:22 PST)
AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Thu Mar 17 2005 - 08:09:06 PST)
- Re: AMBER: Making topology files of big moleucles in antechamber Melinda Layten (Thu Mar 17 2005 - 11:48:39 PST)
  - Re: AMBER: Making topology files of big moleucles in antechamber Hwankyu Lee (Fri Mar 18 2005 - 08:48:02 PST)
AMBER: add waters to a system + leap problem with solvateOct command Fabien Cailliez (Thu Mar 17 2005 - 10:30:24 PST)
AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 11:21:37 PST)
- Re: AMBER: Trajectory problems Melinda Layten (Thu Mar 17 2005 - 11:34:50 PST)
AMBER: building helix bundle Yanze Zhang (Thu Mar 17 2005 - 13:30:54 PST)
AMBER: Trajectory problems Steve Seibold (Thu Mar 17 2005 - 13:44:23 PST)
- Re: AMBER: Trajectory problems Asim Okur (Thu Mar 17 2005 - 15:14:28 PST)
AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 14:50:09 PST)
- Re: AMBER: Separating solvent and solute energy in the microcanonical mode Carlos Simmerling (Thu Mar 17 2005 - 15:05:17 PST)
  - Re: AMBER: Separating solvent and solute energy in the microcanonical mode Mey Khalili (Thu Mar 17 2005 - 15:11:48 PST)
    - Re: AMBER: Separating solvent and solute energy in the microcanonical mode Carlos Simmerling (Thu Mar 17 2005 - 15:33:43 PST)
AMBER: ptraj: determining solvent/ion densities Joseph W.Toporowski (Thu Mar 17 2005 - 17:40:38 PST)
AMBER: re Updating Tutorials Vidana.Epa.csiro.au (Thu Mar 17 2005 - 19:17:50 PST)
AMBER: Replica Exchange crashing Hayden Eastwood (Fri Mar 18 2005 - 04:39:48 PST)
- Re: AMBER: Replica Exchange crashing Viktor Hornak (Fri Mar 18 2005 - 04:51:48 PST)
- Re: AMBER: Replica Exchange crashing Carlos Simmerling (Fri Mar 18 2005 - 05:11:13 PST)
AMBER: layer Gustavo Pierdominici Sottile (Fri Mar 18 2005 - 06:42:53 PST)
- Re: AMBER: layer Guanglei Cui (Fri Mar 18 2005 - 07:13:32 PST)
- Re: AMBER: layer Carlos Simmerling (Fri Mar 18 2005 - 08:01:45 PST)
AMBER: lmanal input file problem Phineus Markwick (Fri Mar 18 2005 - 08:00:18 PST)
- Re: AMBER: lmanal input file problem David A. Case (Fri Mar 18 2005 - 12:10:00 PST)
AMBER: parameter meaning Wei Wang (Fri Mar 18 2005 - 10:33:15 PST)
AMBER: Problems with Iodine David.Maxwell.di.mdacc.tmc.edu (Fri Mar 18 2005 - 13:03:38 PST)
- Re: AMBER: Problems with Iodine Carlos Simmerling (Fri Mar 18 2005 - 13:22:47 PST)
AMBER: question about periodicity of torsion parameter jz7.duke.edu (Fri Mar 18 2005 - 14:08:50 PST)
- Re: AMBER: question about periodicity of torsion parameter Carlos Simmerling (Fri Mar 18 2005 - 14:51:40 PST)
AMBER: PMEMD with big systems Florian Barth (Fri Mar 18 2005 - 15:25:41 PST)
- Re: AMBER: PMEMD with big systems Robert Duke (Fri Mar 18 2005 - 16:12:24 PST)
  - Re: AMBER: PMEMD with big systems Florian Barth (Wed Mar 23 2005 - 12:48:10 PST)
AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation Eric Hu (Fri Mar 18 2005 - 15:35:39 PST)
- Re: AMBER: substrate exit from protein in Amber 8.0 TI vdw simulation David A. Case (Mon Mar 21 2005 - 10:27:40 PST)
AMBER: igb=10 some vdW terms disappear? Wells, David H (Sun Mar 20 2005 - 23:54:23 PST)
- Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Mon Mar 21 2005 - 09:15:24 PST)
- Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Tue Mar 22 2005 - 13:54:57 PST)
  - Re: AMBER: igb=10 some vdW terms disappear? Ray Luo (Tue Mar 22 2005 - 14:59:00 PST)
- Re: AMBER: igb=10 some vdW terms disappear? Wells, David H (Wed Mar 23 2005 - 10:40:53 PST)
AMBER: Making prepin file for individual residues of huge molecule. Hwankyu Lee (Mon Mar 21 2005 - 07:00:11 PST)
- Re: AMBER: Making prepin file for individual residues of huge molecule. David A. Case (Mon Mar 21 2005 - 08:27:23 PST)
AMBER: mm-pbsa with multiple-processors Eric Hu (Mon Mar 21 2005 - 14:21:16 PST)
- Re: AMBER: mm-pbsa with multiple-processors FyD (Mon Mar 21 2005 - 14:39:54 PST)
- Re: AMBER: mm-pbsa with multiple-processors Piotr Cieplak (Mon Mar 21 2005 - 16:17:30 PST)
AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 16:12:26 PST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Mon Mar 21 2005 - 16:54:52 PST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Mon Mar 21 2005 - 19:39:42 PST)
  - RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Ross Walker (Tue Mar 22 2005 - 10:05:15 PST)
- RE: AMBER: Dual Xeon EM64T Intel Fortran Compile Problem Shekter, Lee (Wed Mar 23 2005 - 08:29:57 PST)
AMBER: TMD force constant Phineus Markwick (Tue Mar 22 2005 - 05:14:53 PST)
- Re: AMBER: TMD force constant Viktor Hornak (Tue Mar 22 2005 - 05:42:37 PST)
- Re: AMBER: TMD force constant Carlos Simmerling (Tue Mar 22 2005 - 05:57:01 PST)
Re: AMBER: MD: Water network analysis + visualization sanjeev.mbu.iisc.ernet.in (Tue Mar 22 2005 - 05:58:24 PST)
AMBER: nonbonded interaction Svetlana Kirillova (Tue Mar 22 2005 - 08:37:54 PST)
- Re: AMBER: nonbonded interaction David A. Case (Tue Mar 22 2005 - 21:38:08 PST)
  - AMBER: align snapshots to a reference Wen Li (Tue Mar 29 2005 - 13:38:36 PST)
    - Re: AMBER: align snapshots to a reference Carlos Simmerling (Tue Mar 29 2005 - 14:15:29 PST)
    - Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 07:43:21 PST)
    - Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 08:08:01 PST)
    - Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 08:14:44 PST)
    - Re: AMBER: align snapshots to a reference Thomas E. Cheatham, III (Wed Mar 30 2005 - 08:23:21 PST)
    - Re: AMBER: align snapshots to a reference Wen Li (Wed Mar 30 2005 - 11:52:34 PST)
    - Re: AMBER: align snapshots to a reference Carlos Simmerling (Wed Mar 30 2005 - 08:28:13 PST)
AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 09:32:06 PST)
- RE: AMBER: ANAL module/AMBER8 Vineet Pande (Tue Mar 22 2005 - 10:11:22 PST)
AMBER: Amber8 Parallel installation troubles Joe Nolan (Tue Mar 22 2005 - 11:03:05 PST)
- RE: AMBER: Amber8 Parallel installation troubles Ross Walker (Tue Mar 22 2005 - 11:20:22 PST)
  - Re: AMBER: Amber8 Parallel installation troubles Atro Tossavainen (Tue Mar 22 2005 - 23:43:18 PST)
- Re: AMBER: Amber8 Parallel installation troubles Wei Zhang (Tue Mar 22 2005 - 15:39:06 PST)
AMBER: wierd behavior of addions jz7.duke.edu (Tue Mar 22 2005 - 11:22:54 PST)
- RE: AMBER: wierd behavior of addions Ross Walker (Tue Mar 22 2005 - 11:45:32 PST)
- RE: AMBER: wierd behavior of addions Bill Ross (Tue Mar 22 2005 - 13:23:52 PST)
AMBER: Methionine with both C-ter and N-ter jz7.duke.edu (Tue Mar 22 2005 - 14:17:18 PST)
- Re: AMBER: Methionine with both C-ter and N-ter FyD (Tue Mar 22 2005 - 16:26:35 PST)
AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Tue Mar 22 2005 - 15:34:05 PST)
- Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 16:29:26 PST)
  - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Tue Mar 22 2005 - 16:46:26 PST)
    - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Tue Mar 22 2005 - 17:34:26 PST)
    - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Wed Mar 23 2005 - 14:18:45 PST)
    - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' luckyang.gmail.com (Wed Mar 23 2005 - 15:01:49 PST)
    - Re: AMBER: AMBER 8 installation problem -- undefined reference to `EXIT' Wei Zhang (Wed Mar 23 2005 - 16:49:14 PST)
AMBER: "ERROR TERMINATION DUE TO SHAKE OR TORCON" in Gibbs tanc.uci.edu (Tue Mar 22 2005 - 21:11:41 PST)
Re: AMBER: nonbonded interactions Svetlana Kirillova (Wed Mar 23 2005 - 01:23:47 PST)
AMBER: warning in PBSA Fabien Cailliez (Wed Mar 23 2005 - 05:39:00 PST)
- Re: AMBER: warning in PBSA Ray Luo (Wed Mar 23 2005 - 09:42:34 PST)
AMBER: Could not open file (trajin) with mode (r) Maciej (Wed Mar 23 2005 - 05:52:20 PST)
- RE: AMBER: Could not open file (trajin) with mode (r) Vineet Pande (Wed Mar 23 2005 - 08:26:06 PST)
- RE: AMBER: Could not open file (trajin) with mode (r) Ross Walker (Wed Mar 23 2005 - 10:13:56 PST)
AMBER: antechamber availability dmitri.mikhailov.novartis.com (Wed Mar 23 2005 - 12:40:47 PST)
- Re: AMBER: antechamber availability Guanglei Cui (Wed Mar 23 2005 - 15:21:23 PST)
- Re: AMBER: antechamber availability David A. Case (Thu Mar 24 2005 - 10:42:49 PST)
AMBER: A few question about RDF input preparation Maciej (Thu Mar 24 2005 - 03:13:10 PST)
- Re: AMBER: A few question about RDF input preparation Wei Zhang (Thu Mar 24 2005 - 03:58:47 PST)
AMBER: Make test error Amber (Thu Mar 24 2005 - 13:10:53 PST)
AMBER: question about placing a substrate in a protein pocket Kara Di Giorgio (Thu Mar 24 2005 - 20:33:26 PST)
- RE: AMBER: question about placing a substrate in a protein pocket Vineet Pande (Fri Mar 25 2005 - 01:41:18 PST)
AMBER: Re: ask for your help: parallel on mm_pbsa FyD (Sat Mar 26 2005 - 09:09:23 PST)
AMBER: PTRAJ:"hbond" doubts Vineet Pande (Sun Mar 27 2005 - 05:55:24 PST)
AMBER: missing residue xueping (Sun Mar 27 2005 - 23:34:17 PST)
- RE: AMBER: missing residue Ross Walker (Mon Mar 28 2005 - 08:23:47 PST)
AMBER: ptraj analysis Tatyana B Mamonova (Mon Mar 28 2005 - 09:24:55 PST)
AMBER: Parameter files for general lipids Nitin Bhardwaj (Mon Mar 28 2005 - 16:57:46 PST)
- RE: AMBER: Parameter files for general lipids Vineet Pande (Mon Mar 28 2005 - 23:28:48 PST)
AMBER: REM mdinfo file Sergio E. Wong (Mon Mar 28 2005 - 17:51:45 PST)
- Re: AMBER: REM mdinfo file Guanglei Cui (Tue Mar 29 2005 - 10:00:10 PST)
AMBER: vlimit exceeded in thermalization Holly Freedman (Mon Mar 28 2005 - 20:16:12 PST)
- Re: AMBER: vlimit exceeded in thermalization David A. Case (Tue Mar 29 2005 - 09:22:20 PST)
AMBER: Are the constant pH simulations with explicit water possible? Kateryna Miroshnychenko (Tue Mar 29 2005 - 05:54:14 PST)
- Re: AMBER: Are the constant pH simulations with explicit water possible? David A. Case (Tue Mar 29 2005 - 09:37:27 PST)
AMBER: protonated aspartic acid Adrian E. Roitberg (Tue Mar 29 2005 - 12:14:35 PST)
AMBER: tleap,xleap bond order for triple bonds Stern, Julie (Tue Mar 29 2005 - 14:49:38 PST)
- RE: AMBER: tleap,xleap bond order for triple bonds Ross Walker (Tue Mar 29 2005 - 15:58:51 PST)
  - Re: AMBER: tleap,xleap bond order for triple bonds David A. Case (Tue Mar 29 2005 - 20:43:39 PST)
AMBER: Minimization failure S.Sundar Raman (Tue Mar 29 2005 - 20:47:22 PST)
AMBER: how to cap regions S.Sundar Raman (Tue Mar 29 2005 - 21:00:12 PST)
- Re: AMBER: how to cap regions David A. Case (Thu Mar 31 2005 - 07:45:26 PST)
AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 07:32:10 PST)
- RE: AMBER: Amber Performance in Parallel on Itanium Ross Walker (Wed Mar 30 2005 - 08:20:14 PST)
  - Re: AMBER: Amber Performance in Parallel on Itanium Robert J. Woods (Wed Mar 30 2005 - 08:47:25 PST)
AMBER: PTRAJ:"hbond" analysis Vineet Pande (Wed Mar 30 2005 - 09:15:30 PST)
- Re: AMBER: PTRAJ:"hbond" analysis Thomas E. Cheatham, III (Wed Mar 30 2005 - 09:40:16 PST)
  - Re: AMBER: PTRAJ:"hbond" analysis Vineet Pande (Thu Mar 31 2005 - 01:17:57 PST)
AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 09:55:19 PST)
- Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 11:14:07 PST)
  - Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 14:03:53 PST)
    - Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 14:32:09 PST)
    - Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 14:50:03 PST)
    - Re: AMBER: OH- dynamics Carlos Simmerling (Wed Mar 30 2005 - 15:37:26 PST)
    - Re: AMBER: OH- dynamics Eric Hu (Wed Mar 30 2005 - 16:23:32 PST)
AMBER: igb10 vlimit exceeded Wells, David H (Thu Mar 31 2005 - 01:08:55 PST)
- Re: AMBER: igb10 vlimit exceeded Ray Luo (Thu Mar 31 2005 - 08:52:50 PST)
AMBER: All the tests passed except prmtop and prepin... mmv.whu.edu.cn (Thu Mar 31 2005 - 01:59:26 PST)
- Re: AMBER: All the tests passed except prmtop and prepin... David A. Case (Thu Mar 31 2005 - 07:40:18 PST)
AMBER: AMBER under MOSIX? Atro Tossavainen (Thu Mar 31 2005 - 03:47:47 PST)
AMBER: Compiling on dual-opteron with pathscale 2.1 on RHEL 4 AS Marc Petitmermet (Thu Mar 31 2005 - 07:32:31 PST)
AMBER: What does this mean .. ? Pavan Ghatty (Thu Mar 31 2005 - 11:14:53 PST)
- Re: AMBER: What does this mean .. ? Carlos Simmerling (Thu Mar 31 2005 - 11:33:25 PST)
AMBER: leap bond error Stern, Julie (Thu Mar 31 2005 - 17:11:29 PST)
AMBER: Target MD and nmode test hang Mingfeng Yang (Thu Mar 31 2005 - 18:08:13 PST)

Amber Archive Mar 2005 By Thread