Amber Archive Jul 2007 by thread
481 messages
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Starting
Sun Jul 01 2007 - 06:07:56 PDT,
Ending
Wed Aug 01 2007 - 06:07:44 PDT
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Re: AMBER: amber7 and xleap
Saiful Islam
(Sat Jun 30 2007 - 20:37:00 PDT)
Re: AMBER: amber7 and xleap
Saiful Islam
(Sun Jul 01 2007 - 06:43:45 PDT)
RE: AMBER: amber7 and xleap
Ross Walker
(Sun Jul 01 2007 - 10:32:45 PDT)
AMBER: xleap and amber7
Saiful Islam
(Sat Jun 30 2007 - 21:22:43 PDT)
RE: AMBER: xleap and amber7
Ross Walker
(Sun Jul 01 2007 - 10:33:15 PDT)
Re: AMBER: xleap and amber7
Saiful Islam
(Mon Jul 02 2007 - 07:05:34 PDT)
Re: AMBER: xleap and amber7
Adrian Roitberg
(Mon Jul 02 2007 - 07:20:28 PDT)
Re: AMBER: xleap and amber7
Saiful Islam
(Wed Jul 04 2007 - 20:53:42 PDT)
Re: AMBER: xleap and amber7
Ilyas Yildirim
(Wed Jul 04 2007 - 21:53:37 PDT)
Re: AMBER: xleap and amber7
Carlos Simmerling
(Thu Jul 05 2007 - 05:23:44 PDT)
Re: AMBER: xleap and amber7
Saiful Islam
(Fri Jul 06 2007 - 19:23:35 PDT)
Re: AMBER: xleap and amber7
Benjamin Juhl
(Mon Jul 09 2007 - 00:08:57 PDT)
Re: AMBER: xleap and amber7
Saiful Islam
(Tue Jul 10 2007 - 05:47:00 PDT)
Re: AMBER: Problem with leaprc
yen li
(Sun Jul 01 2007 - 06:10:09 PDT)
Re: AMBER: Problem with leaprc
yen li
(Sun Jul 01 2007 - 10:36:14 PDT)
Re: AMBER: Problem with leaprc
David A. Case
(Mon Jul 02 2007 - 07:44:59 PDT)
Re: AMBER: Problem with leaprc
yen li
(Wed Jul 04 2007 - 05:23:49 PDT)
Re: AMBER: Problem with leaprc
David A. Case
(Wed Jul 04 2007 - 09:15:39 PDT)
Re: AMBER: Problem with leaprc
yen li
(Wed Jul 04 2007 - 11:21:22 PDT)
Re: AMBER: Problem with leaprc
David A. Case
(Wed Jul 04 2007 - 13:31:29 PDT)
Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH
Francesco Pietra
(Sun Jul 01 2007 - 07:38:03 PDT)
Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH
M. L. Dodson
(Sun Jul 01 2007 - 08:57:05 PDT)
AMBER: large RMS fluctuations in turning off VDW interactions by TI
Holly Freedman
(Sun Jul 01 2007 - 12:13:17 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
Holly Freedman
(Sun Jul 01 2007 - 12:54:11 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
Julien Michel
(Sun Jul 01 2007 - 15:42:53 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
David Mobley
(Mon Jul 02 2007 - 13:03:17 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
David A. Case
(Mon Jul 02 2007 - 13:20:27 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
David Mobley
(Tue Jul 03 2007 - 12:55:54 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
steinbrt.scripps.edu
(Wed Jul 04 2007 - 05:51:08 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
Holly Freedman
(Mon Jul 02 2007 - 13:51:12 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
David A. Case
(Mon Jul 02 2007 - 23:34:13 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
Holly Freedman
(Tue Jul 03 2007 - 10:14:29 PDT)
Fwd: Re: Fwd: RE: Re: AMBER: $AMBERHOME on PATH
Francesco Pietra
(Sun Jul 01 2007 - 13:50:39 PDT)
AMBER: bug in nonbond_list.f (nee ew_setup.f)
Dan Kidger
(Mon Jul 02 2007 - 02:42:58 PDT)
AMBER: Saving (.)prepin file
Johnson Agbo
(Mon Jul 02 2007 - 13:35:00 PDT)
Re: AMBER: Saving (.)prepin file
David A. Case
(Mon Jul 02 2007 - 13:56:57 PDT)
Re: AMBER: Saving (.)prepin file
Bill Ross
(Mon Jul 02 2007 - 14:05:53 PDT)
AMBER: convergence criterion not reached
Jena M
(Mon Jul 02 2007 - 16:53:22 PDT)
Re: AMBER: convergence criterion not reached
David A. Case
(Mon Jul 02 2007 - 18:14:53 PDT)
AMBER: Slow Processor Loads when Using PMEMD
Jonathan Suever
(Mon Jul 02 2007 - 17:28:48 PDT)
RE: AMBER: Slow Processor Loads when Using PMEMD
Ross Walker
(Mon Jul 02 2007 - 18:42:01 PDT)
Re: AMBER: Slow Processor Loads when Using PMEMD
David A. Case
(Mon Jul 02 2007 - 18:24:09 PDT)
AMBER: How to use antechamber properly?
한재범
(Mon Jul 02 2007 - 22:57:33 PDT)
AMBER: O-acetylated sugar
Toshifumi Yui
(Tue Jul 03 2007 - 05:26:12 PDT)
AMBER: About amber7
Saiful Islam
(Tue Jul 03 2007 - 06:49:28 PDT)
Re: AMBER: About amber7
Carlos Simmerling
(Tue Jul 03 2007 - 06:57:14 PDT)
AMBER: ptraj: RMS per residues and per time
Sascha Rehm
(Tue Jul 03 2007 - 07:03:04 PDT)
Re: AMBER: ptraj: RMS per residues and per time
Jianyin Shao
(Fri Jul 06 2007 - 00:54:06 PDT)
AMBER: Nucleic acid : nonplanarity
Sophie Barbe
(Tue Jul 03 2007 - 08:48:07 PDT)
AMBER: antechamber save prmtop inpcrd
Francesco Pietra
(Tue Jul 03 2007 - 10:55:11 PDT)
AMBER: Who has the structure file of beta-chitin?
WANG,YING
(Tue Jul 03 2007 - 11:19:11 PDT)
AMBER: Fwd: antechamber save prmtop inpcrd
Francesco Pietra
(Tue Jul 03 2007 - 23:14:23 PDT)
Re: AMBER: Fwd: antechamber save prmtop inpcrd
David A. Case
(Wed Jul 04 2007 - 08:53:04 PDT)
Re: AMBER: Fwd: antechamber save prmtop inpcrd
Francesco Pietra
(Wed Jul 04 2007 - 09:54:08 PDT)
Re: AMBER: Fwd: antechamber save prmtop inpcrd
David A. Case
(Wed Jul 04 2007 - 13:15:21 PDT)
Re: AMBER: Fwd: antechamber save prmtop inpcrd
Francesco Pietra
(Wed Jul 04 2007 - 14:08:02 PDT)
AMBER: Simulated annealing - Nudget Elastic Band
Francesco Pietra
(Wed Jul 04 2007 - 00:01:58 PDT)
Re: AMBER: Simulated annealing - Nudget Elastic Band
Carlos Simmerling
(Wed Jul 04 2007 - 03:39:10 PDT)
Re: AMBER: Simulated annealing - Nudget Elastic Band
Francesco Pietra
(Wed Jul 04 2007 - 06:13:41 PDT)
AMBER: Slight_error_on_Compiling_Replica_Exchange
j j
(Wed Jul 04 2007 - 01:57:28 PDT)
Re: AMBER: Slight_error_on_Compiling_Replica_Exchange
Ye Mei
(Wed Jul 04 2007 - 02:30:09 PDT)
Re: AMBER: Slight_error_on_Compiling_Replica_Exchange
j j
(Wed Jul 04 2007 - 03:13:22 PDT)
AMBER: Generation of ESP(ind) within atomic charges derivation for polarizable force field
Anela Ivanova
(Wed Jul 04 2007 - 05:26:02 PDT)
AMBER: Nucleic acid : nonplanarity
Sophie Barbe
(Wed Jul 04 2007 - 05:37:26 PDT)
Re: AMBER: Nucleic acid : nonplanarity
Mathy Froeyen
(Wed Jul 04 2007 - 06:57:08 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
Holly Freedman
(Wed Jul 04 2007 - 12:53:01 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
David Mobley
(Thu Jul 05 2007 - 08:56:43 PDT)
Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI
Thomas Steinbrecher
(Fri Jul 06 2007 - 10:55:32 PDT)
AMBER: antechamber: mopac charges
Neelanjana Sengupta
(Wed Jul 04 2007 - 16:21:02 PDT)
Re: AMBER: antechamber: mopac charges
David A. Case
(Wed Jul 04 2007 - 16:27:02 PDT)
Re: AMBER: antechamber: mopac charges
Neelanjana Sengupta
(Thu Jul 05 2007 - 12:26:30 PDT)
Re: AMBER: antechamber: mopac charges
David A. Case
(Thu Jul 05 2007 - 13:24:09 PDT)
AMBER: testing amber9 for parallel use
Sally Pias
(Wed Jul 04 2007 - 23:47:22 PDT)
Re: AMBER: testing amber9 for parallel use
Carlos Simmerling
(Thu Jul 05 2007 - 05:22:20 PDT)
AMBER: Convergence criteria in replica exchange simulations
Seongeun Yang
(Thu Jul 05 2007 - 04:18:17 PDT)
Re: AMBER: Convergence criteria in replica exchange simulations
Carlos Simmerling
(Thu Jul 05 2007 - 05:26:26 PDT)
AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Thu Jul 05 2007 - 07:31:03 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
Carlos Simmerling
(Thu Jul 05 2007 - 07:36:05 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Thu Jul 05 2007 - 08:10:23 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
Carlos Simmerling
(Thu Jul 05 2007 - 08:25:42 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Thu Jul 05 2007 - 08:57:59 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
Carlos Simmerling
(Thu Jul 05 2007 - 09:04:12 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Thu Jul 05 2007 - 09:40:41 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
Carlos Simmerling
(Thu Jul 05 2007 - 09:45:14 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Thu Jul 05 2007 - 23:58:28 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Fri Jul 06 2007 - 03:39:58 PDT)
Re: AMBER: How to extract energy of molecule from the system with explicit water molecules
priya priya
(Fri Jul 06 2007 - 05:25:02 PDT)
Re: AMBER: Sander Error
Colby C
(Tue Jul 03 2007 - 11:21:18 PDT)
Re: AMBER: Sander Error
Colby C
(Mon Jul 09 2007 - 08:39:50 PDT)
AMBER: Nudget Elastic Band query
Francesco Pietra
(Thu Jul 05 2007 - 10:43:43 PDT)
Re: AMBER: Nudget Elastic Band query
Carlos Simmerling
(Thu Jul 05 2007 - 10:53:53 PDT)
Re: AMBER: Nudget Elastic Band query
Francesco Pietra
(Thu Jul 05 2007 - 12:02:19 PDT)
Re: AMBER: Nudget Elastic Band query
Carlos Simmerling
(Thu Jul 05 2007 - 12:08:31 PDT)
Re: AMBER: Nudget Elastic Band query
Francesco Pietra
(Thu Jul 05 2007 - 13:28:31 PDT)
AMBER: QM/MM LJ parameters
Evan Kelly
(Thu Jul 05 2007 - 16:31:35 PDT)
RE: AMBER: QM/MM LJ parameters
Ross Walker
(Thu Jul 05 2007 - 17:58:49 PDT)
AMBER: Stirp command in ptraj
priya priya
(Fri Jul 06 2007 - 05:33:11 PDT)
Re: AMBER: Stirp command in ptraj
Carlos Simmerling
(Fri Jul 06 2007 - 05:35:33 PDT)
Re: AMBER: Stirp command in ptraj
Steven Winfield
(Fri Jul 06 2007 - 05:36:06 PDT)
Re: AMBER: Stirp command in ptraj
priya priya
(Fri Jul 06 2007 - 05:41:22 PDT)
Re: AMBER: Stirp command in ptraj
Carlos Simmerling
(Fri Jul 06 2007 - 06:14:20 PDT)
Re: AMBER: Stirp command in ptraj
priya priya
(Fri Jul 06 2007 - 06:27:27 PDT)
Re: AMBER: Stirp command in ptraj
Steven Winfield
(Fri Jul 06 2007 - 06:32:07 PDT)
Re: AMBER: Stirp command in ptraj
priya priya
(Fri Jul 06 2007 - 06:43:13 PDT)
Re: AMBER: Stirp command in ptraj
priya priya
(Fri Jul 06 2007 - 09:41:05 PDT)
Re: AMBER: Stirp command in ptraj
Carlos Simmerling
(Fri Jul 06 2007 - 09:45:43 PDT)
AMBER: Substitute for GAFF
Evan Kelly
(Fri Jul 06 2007 - 10:32:50 PDT)
AMBER: Simulated Annealing - Best way to create randomness
Francesco Pietra
(Sat Jul 07 2007 - 07:56:41 PDT)
Re: AMBER: Simulated Annealing - Best way to create randomness
Seth Lilavivat
(Mon Jul 09 2007 - 08:03:29 PDT)
AMBER: Problem with running Sander
Lili Peng
(Sat Jul 07 2007 - 16:10:06 PDT)
Re: AMBER: Problem with running Sander
David A. Case
(Sat Jul 07 2007 - 21:59:05 PDT)
Re: AMBER: Problem with running Sander
Carlos Simmerling
(Sun Jul 08 2007 - 04:28:58 PDT)
Re: AMBER: Problem with running Sander
Lili Peng
(Tue Jul 10 2007 - 14:50:45 PDT)
Re: AMBER: Problem with running Sander
David A. Case
(Tue Jul 10 2007 - 15:39:31 PDT)
Re: AMBER: Problem with running Sander
Lili Peng
(Tue Jul 10 2007 - 15:58:22 PDT)
Re: AMBER: Problem with running Sander
Lili Peng
(Tue Jul 10 2007 - 16:01:11 PDT)
Re: AMBER: Problem with running Sander
David A. Case
(Tue Jul 10 2007 - 16:17:56 PDT)
RE: AMBER: Problem with running Sander
Ross Walker
(Tue Jul 10 2007 - 16:09:29 PDT)
AMBER: RESP charge generation
Neelanjana Sengupta
(Sat Jul 07 2007 - 16:08:07 PDT)
Re: AMBER: RESP charge generation
FyD
(Sun Jul 08 2007 - 03:19:16 PDT)
AMBER: corrected reaction field energy and PBCAL
AYTUG TUNCEL
(Sun Jul 08 2007 - 17:40:53 PDT)
AMBER: program bug?
M. Maeda
(Sun Jul 08 2007 - 19:24:58 PDT)
Re: AMBER: program bug?
David A. Case
(Mon Jul 09 2007 - 07:48:35 PDT)
Re: AMBER: program bug?
M. Maeda
(Wed Jul 11 2007 - 21:47:19 PDT)
Re: AMBER: program bug?
M. Maeda
(Wed Jul 11 2007 - 21:41:34 PDT)
Re: AMBER: program bug?
Benjamin Juhl
(Thu Jul 12 2007 - 00:17:31 PDT)
Re: AMBER: program bug?
M. Maeda
(Thu Jul 12 2007 - 04:29:03 PDT)
Re: AMBER: program bug?
David A. Case
(Thu Jul 12 2007 - 08:22:35 PDT)
Re: AMBER: program bug?
Carlos Simmerling
(Thu Jul 12 2007 - 08:32:54 PDT)
AMBER: adding water molecules in lipid bilayer model
Vijay Manickam Achari
(Sun Jul 08 2007 - 20:22:46 PDT)
Re: AMBER: adding water molecules in lipid bilayer model
M. L. Dodson
(Mon Jul 09 2007 - 05:59:01 PDT)
Re: AMBER: adding water molecules in lipid bilayer model
Vijay Manickam Achari
(Tue Jul 10 2007 - 19:00:30 PDT)
Re: AMBER: adding water molecules in lipid bilayer model
Fenghui Fan
(Mon Jul 09 2007 - 16:11:45 PDT)
AMBER: Question on TIP4P model
Du, Shiyu
(Mon Jul 09 2007 - 17:01:58 PDT)
AMBER: antechamber
Marie Brut
(Mon Jul 09 2007 - 04:56:19 PDT)
Re: AMBER: antechamber
David A. Case
(Mon Jul 09 2007 - 07:41:23 PDT)
Re: AMBER: antechamber
Francesco Pietra
(Mon Jul 09 2007 - 14:57:45 PDT)
Re: AMBER: antechamber
M. L. Dodson
(Mon Jul 09 2007 - 17:08:27 PDT)
Re: AMBER: antechamber
Francesco Pietra
(Tue Jul 10 2007 - 00:04:39 PDT)
Re: AMBER: antechamber
Barbault Florent
(Mon Jul 09 2007 - 07:59:03 PDT)
AMBER: Specific/Non-specific dihedral issue in Amber
Narayanan Veeraraghavan
(Mon Jul 09 2007 - 07:30:44 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
David A. Case
(Mon Jul 09 2007 - 07:58:51 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
Narayanan Veeraraghavan
(Mon Jul 09 2007 - 11:02:38 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
Bill Ross
(Mon Jul 09 2007 - 11:48:28 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
Narayanan Veeraraghavan
(Mon Jul 16 2007 - 14:35:53 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
David A. Case
(Mon Jul 16 2007 - 17:13:45 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
Narayanan Veeraraghavan
(Tue Jul 17 2007 - 15:01:10 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
David A. Case
(Tue Jul 17 2007 - 16:15:59 PDT)
Re: AMBER: Specific/Non-specific dihedral issue in Amber
Bill Ross
(Mon Jul 16 2007 - 16:38:26 PDT)
AMBER: Could not find cntrl namelist
Francesco Pietra
(Mon Jul 09 2007 - 09:56:58 PDT)
Re: AMBER: Could not find cntrl namelist
M. L. Dodson
(Mon Jul 09 2007 - 10:10:58 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Mon Jul 09 2007 - 13:53:43 PDT)
Re: AMBER: Could not find cntrl namelist
M. L. Dodson
(Mon Jul 09 2007 - 14:09:06 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Mon Jul 09 2007 - 14:22:30 PDT)
Re: AMBER: Could not find cntrl namelist
Thomas Cheatham III
(Mon Jul 09 2007 - 14:17:23 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Mon Jul 09 2007 - 14:31:18 PDT)
RE: AMBER: Could not find cntrl namelist
Ross Walker
(Mon Jul 09 2007 - 14:38:01 PDT)
RE: AMBER: Could not find cntrl namelist
Francesco Pietra
(Mon Jul 09 2007 - 23:26:54 PDT)
Re: AMBER: Could not find cntrl namelist
David A. Case
(Tue Jul 10 2007 - 10:52:10 PDT)
RE: AMBER: Could not find cntrl namelist
Ross Walker
(Tue Jul 10 2007 - 11:21:12 PDT)
RE: AMBER: Could not find cntrl namelist
Francesco Pietra
(Tue Jul 10 2007 - 14:11:48 PDT)
Re: AMBER: Could not find cntrl namelist
Robert Duke
(Tue Jul 10 2007 - 14:57:54 PDT)
RE: AMBER: Could not find cntrl namelist
Ross Walker
(Tue Jul 10 2007 - 16:00:38 PDT)
Re: AMBER: Could not find cntrl namelist
Robert Duke
(Tue Jul 10 2007 - 19:21:07 PDT)
Re: AMBER: Could not find cntrl namelist
M. L. Dodson
(Tue Jul 10 2007 - 15:25:17 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Wed Jul 11 2007 - 03:14:51 PDT)
Re: AMBER: Could not find cntrl namelist
Robert Duke
(Wed Jul 11 2007 - 06:07:36 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Wed Jul 11 2007 - 08:10:42 PDT)
Re: AMBER: Could not find cntrl namelist
Robert Duke
(Wed Jul 11 2007 - 10:47:57 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Wed Jul 11 2007 - 14:50:37 PDT)
Re: AMBER: Could not find cntrl namelist
David A. Case
(Tue Jul 10 2007 - 16:04:15 PDT)
Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Tue Jul 10 2007 - 23:48:41 PDT)
RE: AMBER: Could not find cntrl namelist
Ross Walker
(Tue Jul 10 2007 - 14:57:39 PDT)
RE: AMBER: Could not find cntrl namelist
Francesco Pietra
(Tue Jul 10 2007 - 23:48:59 PDT)
RE: AMBER: Could not find cntrl namelist
Ross Walker
(Mon Jul 09 2007 - 10:26:29 PDT)
AMBER: TIP4P MD simulations
Hashem Taha
(Mon Jul 09 2007 - 10:53:28 PDT)
Re: AMBER: TIP4P MD simulations
Melinda Layten
(Mon Jul 09 2007 - 11:05:39 PDT)
Re: AMBER: TIP4P MD simulations
David A. Case
(Mon Jul 09 2007 - 11:31:15 PDT)
Re: AMBER: TIP4P MD simulations
Robert Duke
(Mon Jul 09 2007 - 12:35:04 PDT)
AMBER: manganese ion
Davide Moiani
(Mon Jul 09 2007 - 14:02:31 PDT)
Re: AMBER: manganese ion
Guillermo Mulliert Carlín
(Tue Jul 10 2007 - 01:39:40 PDT)
Re: AMBER: manganese ion
Davide Moiani
(Tue Jul 10 2007 - 09:47:38 PDT)
Re: AMBER: manganese ion
neetu.imtech.res.in
(Tue Jul 10 2007 - 21:03:54 PDT)
Re: AMBER: manganese ion
Davide Moiani
(Wed Jul 11 2007 - 14:47:18 PDT)
AMBER: surface area over the trajectory
mkseo
(Mon Jul 09 2007 - 14:52:32 PDT)
Re: AMBER: surface area over the trajectory
Carlos Simmerling
(Mon Jul 09 2007 - 15:30:54 PDT)
Re: AMBER: surface area over the trajectory
mkseo
(Mon Jul 09 2007 - 15:55:18 PDT)
Re: AMBER: surface area over the trajectory
Carlos Simmerling
(Tue Jul 10 2007 - 03:33:44 PDT)
Re: AMBER: surface area over the trajectory
Mikyung
(Tue Jul 10 2007 - 09:20:12 PDT)
Re: AMBER: surface area over the trajectory
Carlos Simmerling
(Tue Jul 10 2007 - 12:09:51 PDT)
AMBER: tgtrmsmask and tgtfitmask
Holly Freedman
(Mon Jul 09 2007 - 19:03:39 PDT)
Re: AMBER: tgtrmsmask and tgtfitmask
Carlos Simmerling
(Tue Jul 10 2007 - 04:26:08 PDT)
Re: AMBER: tgtrmsmask and tgtfitmask
David A. Case
(Tue Jul 10 2007 - 09:01:27 PDT)
AMBER: 来自pig5678的邮件
pig5678
(Mon Jul 09 2007 - 23:59:22 PDT)
Re: AMBER: ????pig5678??????
David A. Case
(Tue Jul 10 2007 - 08:14:45 PDT)
Re:Re: AMBER: ????pig5678??????
pig5678
(Tue Jul 10 2007 - 20:27:55 PDT)
Re:Re: AMBER: ????pig5678??????
pig5678
(Thu Jul 12 2007 - 18:36:10 PDT)
AMBER: Saving (.)prepin file
Johnson Agbo
(Mon Jul 09 2007 - 11:22:40 PDT)
Re: AMBER: Saving (.)prepin file
David A. Case
(Tue Jul 10 2007 - 10:45:58 PDT)
AMBER: Input required for RESP
Neelanjana Sengupta
(Tue Jul 10 2007 - 11:03:54 PDT)
Re: AMBER: Input required for RESP
FyD
(Tue Jul 10 2007 - 23:21:42 PDT)
AMBER: extract protein energy from MD trajectory
Mikyung
(Tue Jul 10 2007 - 14:47:53 PDT)
Re: AMBER: extract protein energy from MD trajectory
Carlos Simmerling
(Tue Jul 10 2007 - 15:08:32 PDT)
Re: AMBER: extract protein energy from MD trajectory
Mikyung
(Tue Jul 10 2007 - 23:58:31 PDT)
Re: AMBER: extract protein energy from MD trajectory
Carlos Simmerling
(Wed Jul 11 2007 - 01:34:31 PDT)
AMBER: MPI Quiescence problem in REMD
In Hee Park
(Tue Jul 10 2007 - 21:03:08 PDT)
Re: AMBER: MPI Quiescence problem in REMD
Carlos Simmerling
(Wed Jul 11 2007 - 02:28:56 PDT)
Re: AMBER: MPI Quiescence problem in REMD
In Hee Park
(Wed Jul 11 2007 - 09:41:47 PDT)
Re: AMBER: MPI Quiescence problem in REMD
Carlos Simmerling
(Wed Jul 11 2007 - 10:08:23 PDT)
AMBER: Question about NAB (Nucleic Acid Builder)
Cenk Andac
(Wed Jul 11 2007 - 01:30:18 PDT)
Re: AMBER: Question about NAB (Nucleic Acid Builder)
David A. Case
(Wed Jul 11 2007 - 16:23:05 PDT)
AMBER: question about iwrap
Kailee
(Wed Jul 11 2007 - 06:17:29 PDT)
Re: AMBER: question about iwrap
David A. Case
(Wed Jul 11 2007 - 16:24:11 PDT)
Re: AMBER: question about iwrap
Kailee
(Thu Jul 12 2007 - 03:55:28 PDT)
Re: AMBER: question about iwrap
Carlos Simmerling
(Thu Jul 12 2007 - 04:34:08 PDT)
Re: AMBER: question about iwrap
Kailee
(Thu Jul 12 2007 - 06:17:32 PDT)
Re: AMBER: question about iwrap
Carlos Simmerling
(Thu Jul 12 2007 - 06:28:29 PDT)
Re: AMBER: question about iwrap
Kailee
(Thu Jul 12 2007 - 06:55:06 PDT)
AMBER: Basic AMBER question
Lili Peng
(Wed Jul 11 2007 - 12:15:48 PDT)
Re: AMBER: Basic AMBER question
Melinda Layten
(Wed Jul 11 2007 - 13:05:11 PDT)
RE: AMBER: Basic AMBER question
Ross Walker
(Wed Jul 11 2007 - 13:07:42 PDT)
AMBER: Belly Restraints and Distance Restraints
Seth Lilavivat
(Wed Jul 11 2007 - 12:13:04 PDT)
Fwd: Re: AMBER: Could not find cntrl namelist
Francesco Pietra
(Wed Jul 11 2007 - 14:52:25 PDT)
AMBER: computational Ala scan
Sergio Wong
(Wed Jul 11 2007 - 16:36:58 PDT)
AMBER: Amber9 analyze timecorr manual ambigous
Nicolas Lux Fawzi
(Thu Jul 12 2007 - 12:26:19 PDT)
Re: AMBER: Amber9 analyze timecorr manual ambigous
David A. Case
(Thu Jul 12 2007 - 12:55:15 PDT)
Re: AMBER: Amber9 analyze timecorr manual ambigous
Nicolas Lux Fawzi
(Thu Jul 12 2007 - 15:11:30 PDT)
Re: AMBER: Amber9 analyze timecorr manual ambigous
David A. Case
(Thu Jul 12 2007 - 15:58:30 PDT)
AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
Hashem Taha
(Thu Jul 12 2007 - 13:31:59 PDT)
Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
Robert Duke
(Thu Jul 12 2007 - 13:55:15 PDT)
Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
Hashem Taha
(Thu Jul 12 2007 - 14:45:50 PDT)
RE: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
Ross Walker
(Thu Jul 12 2007 - 15:06:56 PDT)
Re: AMBER: Molecular Dynamic Simulations using TIP4P water - Please Help
David A. Case
(Thu Jul 12 2007 - 16:03:45 PDT)
AMBER: Ne van del waals potential
Lishan Yao
(Fri Jul 13 2007 - 09:09:37 PDT)
AMBER: related to new amber force field
snoze pa
(Fri Jul 13 2007 - 08:57:38 PDT)
Re: AMBER: related to new amber force field
Carlos Simmerling
(Fri Jul 13 2007 - 09:33:12 PDT)
AMBER: Multiple residues position
snoze pa
(Fri Jul 13 2007 - 09:04:59 PDT)
Re: AMBER: Multiple residues position
Carlos Simmerling
(Fri Jul 13 2007 - 09:20:19 PDT)
AMBER: Cutoff list exceeds largest sphere in unit cell
Andrew Borgert
(Fri Jul 13 2007 - 09:18:05 PDT)
Re: AMBER: Cutoff list exceeds largest sphere in unit cell
Andrew Borgert
(Fri Jul 13 2007 - 09:27:44 PDT)
Re: AMBER: Cutoff list exceeds largest sphere in unit cell
Robert Duke
(Fri Jul 13 2007 - 09:30:40 PDT)
Re: AMBER: Cutoff list exceeds largest sphere in unit cell
neville forlemu
(Sat Jul 14 2007 - 19:09:36 PDT)
Re: AMBER: Non bond list overflow
David A. Case
(Sun Jul 15 2007 - 16:50:11 PDT)
Re: AMBER: Cutoff list exceeds largest sphere in unit cell
Barbault Florent
(Fri Jul 13 2007 - 11:54:36 PDT)
AMBER: MPI script
Taryn Hartley
(Fri Jul 13 2007 - 15:06:45 PDT)
Re: AMBER: MPI script
Carlos Simmerling
(Fri Jul 13 2007 - 15:15:36 PDT)
Re: AMBER: MPI script
Thomas Cheatham III
(Fri Jul 13 2007 - 15:19:37 PDT)
Re: AMBER: MPI script
Hashem Taha
(Tue Jul 17 2007 - 13:10:46 PDT)
AMBER: can open PDB file in xleap
Vijay Manickam Achari
(Sun Jul 15 2007 - 18:44:17 PDT)
AMBER: Can't open PDB file in xleap
Vijay Manickam Achari
(Mon Jul 16 2007 - 02:43:16 PDT)
Re: AMBER: Can t open PDB file in xleap
Benjamin Juhl
(Mon Jul 16 2007 - 03:53:16 PDT)
AMBER: convergence in classical MD
Seongeun Yang
(Mon Jul 16 2007 - 04:23:01 PDT)
Re: AMBER: convergence in classical MD
Carlos Simmerling
(Mon Jul 16 2007 - 04:37:09 PDT)
AMBER: Problems simulating a big system
Jordi Camps
(Mon Jul 16 2007 - 04:55:55 PDT)
Re: AMBER: Problems simulating a big system
David A. Case
(Mon Jul 16 2007 - 18:44:09 PDT)
Re: AMBER: Problems simulating a big system
Jordi Camps
(Tue Jul 17 2007 - 02:57:13 PDT)
AMBER: Atoms in conatct to a specific atoms during MD
Rafi Ahmad
(Mon Jul 16 2007 - 06:23:38 PDT)
AMBER: modelling substrate binding
Mattias Blomberg
(Mon Jul 16 2007 - 06:53:15 PDT)
Re: AMBER: Atoms in contact to a specific atoms during MD
Mark Williamson
(Mon Jul 16 2007 - 07:52:39 PDT)
SV: AMBER: Atoms in contact to a specific atoms during MD
Rafi Ahmad
(Mon Jul 16 2007 - 08:04:46 PDT)
Re: SV: AMBER: Atoms in contact to a specific atoms during MD
Mark Williamson
(Mon Jul 16 2007 - 08:18:00 PDT)
AMBER: Non-standard amino acid residue
Sergey Samsonov
(Mon Jul 16 2007 - 07:44:32 PDT)
Re: AMBER: Non-standard amino acid residue
FyD
(Mon Jul 16 2007 - 09:45:07 PDT)
AMBER: Setting nonbonded cutoff to 1
Hayden Eastwood
(Mon Jul 16 2007 - 10:27:45 PDT)
RE: AMBER: Setting nonbonded cutoff to 1
Ross Walker
(Mon Jul 16 2007 - 10:43:28 PDT)
Re: AMBER: Non-standard amino acid residue
Sergey Samsonov
(Tue Jul 17 2007 - 05:30:14 PDT)
Re: AMBER: Non-standard amino acid residue
FyD
(Tue Jul 17 2007 - 06:41:57 PDT)
Re: AMBER: Non-standard amino acid residue
Sergey Samsonov
(Wed Jul 18 2007 - 07:19:42 PDT)
Re: AMBER: Non-standard amino acid residue
FyD
(Wed Jul 18 2007 - 07:50:55 PDT)
Re: AMBER: Non-standard amino acid residue
Sergey Samsonov
(Thu Jul 19 2007 - 02:45:52 PDT)
Re: AMBER: Non-standard amino acid residue
FyD
(Thu Jul 19 2007 - 04:26:39 PDT)
AMBER: Re: RED problem
Sergey Samsonov
(Mon Jul 23 2007 - 04:35:32 PDT)
Re: AMBER: Re: RED problem
FyD
(Mon Jul 23 2007 - 05:08:14 PDT)
Re: AMBER: Non-standard amino acid residue
David A. Case
(Tue Jul 17 2007 - 07:53:46 PDT)
Re: AMBER: Non-standard amino acid residue
Sergey Samsonov
(Tue Jul 17 2007 - 08:37:03 PDT)
AMBER: help with phosphotyrosine
Samantha Kaye
(Mon Jul 16 2007 - 08:45:36 PDT)
Re: AMBER: help with phosphotyrosine
David A. Case
(Mon Jul 16 2007 - 11:11:51 PDT)
Re: AMBER: help with phosphotyrosine
Samantha Kaye
(Tue Jul 17 2007 - 06:00:23 PDT)
AMBER: Known residue, unknown error in teLeap
Neelanjana Sengupta
(Mon Jul 16 2007 - 12:19:07 PDT)
Re: AMBER: Known residue, unknown error in teLeap
David A. Case
(Mon Jul 16 2007 - 18:32:16 PDT)
Re: AMBER: Known residue, unknown error in teLeap
Neelanjana Sengupta
(Tue Jul 17 2007 - 09:33:39 PDT)
Re: AMBER: Known residue, unknown error in teLeap
David A. Case
(Tue Jul 17 2007 - 09:49:41 PDT)
Re: AMBER: Known residue, unknown error in teLeap
Neelanjana Sengupta
(Tue Jul 17 2007 - 11:53:16 PDT)
Re: AMBER: Known residue, unknown error in teLeap
Neelanjana Sengupta
(Tue Jul 17 2007 - 11:58:12 PDT)
AMBER: RESP_compilation
Karol Kaszuba
(Mon Jul 16 2007 - 12:14:32 PDT)
Re: AMBER: RESP_compilation
FyD
(Mon Jul 16 2007 - 15:55:20 PDT)
Re: AMBER: RESP_compilation
FyD
(Mon Jul 16 2007 - 15:59:06 PDT)
Re: AMBER: RESP_compilation_IT_WORKS
Karol Kaszuba
(Tue Jul 17 2007 - 01:32:59 PDT)
AMBER: running_RED-III
Karol Kaszuba
(Wed Jul 18 2007 - 12:02:10 PDT)
Re: AMBER: running_RED-III
FyD
(Wed Jul 18 2007 - 18:33:20 PDT)
Re: SV: AMBER: Atoms in contact to a specific atoms during MD
Bill Ross
(Mon Jul 16 2007 - 12:49:45 PDT)
AMBER: refc error
Lili Peng
(Mon Jul 16 2007 - 16:56:11 PDT)
Re: AMBER: refc error
Davide Moiani
(Mon Jul 16 2007 - 17:03:42 PDT)
Re: AMBER: refc error
Lili Peng
(Mon Jul 16 2007 - 17:08:18 PDT)
Re: AMBER: refc error
Davide Moiani
(Mon Jul 16 2007 - 17:17:18 PDT)
Re: AMBER: refc error
Lili Peng
(Tue Jul 17 2007 - 11:35:06 PDT)
Re: AMBER: refc error
David A. Case
(Mon Jul 16 2007 - 17:25:20 PDT)
Re: AMBER: refc error
Davide Moiani
(Tue Jul 17 2007 - 14:00:20 PDT)
Re: AMBER: refc error
Lili Peng
(Tue Jul 17 2007 - 15:40:26 PDT)
AMBER: potential energy calculation
Lili Peng
(Mon Jul 16 2007 - 17:03:55 PDT)
Re: AMBER: potential energy calculation
Carlos Simmerling
(Mon Jul 16 2007 - 18:34:01 PDT)
Re: AMBER: potential energy calculation
Lili Peng
(Tue Jul 17 2007 - 15:46:55 PDT)
Re: AMBER: potential energy calculation
David A. Case
(Tue Jul 17 2007 - 16:08:54 PDT)
Re: AMBER: potential energy calculation
Rajendra P. OJHA
(Tue Jul 17 2007 - 23:03:55 PDT)
Re: AMBER: potential energy calculation
Lili Peng
(Wed Jul 18 2007 - 13:47:57 PDT)
AMBER: Gaff Charge
Colby C
(Mon Jul 16 2007 - 20:39:15 PDT)
Re: AMBER: Gaff Charge
David A. Case
(Mon Jul 16 2007 - 22:18:17 PDT)
AMBER: how to create an O linked N-acetylglucosamine in a protein
ming hui
(Mon Jul 16 2007 - 20:41:40 PDT)
AMBER: Re: how to create an O linked N-acetylglucosamine in a protein
ming hui
(Mon Jul 16 2007 - 20:44:08 PDT)
Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a
Austin B. Yongye
(Mon Jul 16 2007 - 23:22:12 PDT)
Re: AMBER: Re: how to create an O linked N-acetylglucosamine in a protein
Karl Kirschner
(Tue Jul 17 2007 - 06:39:43 PDT)
AMBER: General AMBER questions
Lili Peng
(Tue Jul 17 2007 - 15:51:32 PDT)
Re: AMBER: General AMBER questions
David A. Case
(Wed Jul 18 2007 - 16:12:34 PDT)
AMBER: incoherent intermediate scattering function
Jason Whitte
(Tue Jul 17 2007 - 15:59:21 PDT)
AMBER: Problems during compilation
Sébastien Kozlowskyj
(Wed Jul 18 2007 - 02:26:06 PDT)
AMBER: bound magnesium ions in proteins with GBSA
Wei Chen
(Wed Jul 18 2007 - 09:01:26 PDT)
AMBER: Error during compilation on a SGI Irix machine
Ruchi Sachdeva
(Wed Jul 18 2007 - 09:47:30 PDT)
Re: AMBER: Error during compilation on a SGI Irix machine
Carlos Simmerling
(Wed Jul 18 2007 - 09:57:27 PDT)
Re: AMBER: Error during compilation on a SGI Irix machine
Ruchi Sachdeva
(Wed Jul 18 2007 - 21:18:30 PDT)
Re: AMBER: Error during compilation on a SGI Irix machine
David A. Case
(Wed Jul 18 2007 - 21:34:18 PDT)
AMBER: Verifying Bond Angles
Seth Lilavivat
(Wed Jul 18 2007 - 14:32:30 PDT)
AMBER: (no subject)
n.buis.soton.ac.uk
(Thu Jul 19 2007 - 01:58:06 PDT)
AMBER: DNA RNA recognition problem
Steve Seibold
(Thu Jul 19 2007 - 06:51:43 PDT)
Re: AMBER: DNA RNA recognition problem
David A. Case
(Thu Jul 19 2007 - 08:01:17 PDT)
AMBER: Re: amber-developers: -y option in sander
Geoff Wood
(Thu Jul 19 2007 - 06:54:47 PDT)
AMBER: secstruct command
Anna Díaz Cirac
(Thu Jul 19 2007 - 10:35:42 PDT)
Re: AMBER: secstruct command
Carlos Simmerling
(Thu Jul 19 2007 - 10:46:30 PDT)
Re: AMBER: secstruct command
Holger Gohlke
(Thu Jul 19 2007 - 11:22:37 PDT)
AMBER: ptraj error
FyD
(Fri Jul 20 2007 - 14:21:17 PDT)
Re: AMBER: secstruct command
Tim Meyer
(Fri Jul 20 2007 - 06:55:47 PDT)
AMBER: temperature fluctuation in REMD
priya priya
(Fri Jul 20 2007 - 03:58:48 PDT)
Re: AMBER: temperature fluctuation in REMD
Carlos Simmerling
(Fri Jul 20 2007 - 04:44:36 PDT)
Re: AMBER: temperature fluctuation in REMD
priya priya
(Fri Jul 20 2007 - 05:11:17 PDT)
Re: AMBER: temperature fluctuation in REMD
Carlos Simmerling
(Fri Jul 20 2007 - 05:34:03 PDT)
Re: AMBER: temperature fluctuation in REMD
priya priya
(Fri Jul 20 2007 - 06:36:12 PDT)
Re: AMBER: temperature fluctuation in REMD
Carlos Simmerling
(Fri Jul 20 2007 - 06:57:13 PDT)
Re: AMBER: temperature fluctuation in REMD
priya priya
(Fri Jul 20 2007 - 07:23:08 PDT)
Re: AMBER: temperature fluctuation in REMD
Carlos Simmerling
(Fri Jul 20 2007 - 07:34:35 PDT)
Re: AMBER: temperature fluctuation in REMD
priya priya
(Fri Jul 20 2007 - 08:00:30 PDT)
Re: AMBER: temperature fluctuation in REMD
Adrian Roitberg
(Fri Jul 20 2007 - 05:44:01 PDT)
Re: AMBER: temperature fluctuation in REMD
priya priya
(Fri Jul 20 2007 - 06:13:32 PDT)
Re: AMBER: temperature fluctuation in REMD
David A. Case
(Fri Jul 20 2007 - 09:16:46 PDT)
RE: AMBER: problem in installing amber9
Syed Tarique Moin
(Fri Jul 20 2007 - 22:18:05 PDT)
AMBER: problem in compiling amber9 and running amber9
Prem Prakash Pathak
(Sat Jul 21 2007 - 05:27:18 PDT)
Re: AMBER: problem in compiling amber9 and running amber9
Mark Williamson
(Sat Jul 21 2007 - 07:21:18 PDT)
AMBER: RE Amber: Simulated Annealing
Francesco Pietra
(Sat Jul 21 2007 - 08:13:11 PDT)
AMBER: GDP UNKNOWN ATOM TYPE: O3 warning
j j
(Sat Jul 21 2007 - 10:21:32 PDT)
AMBER: offending restraint
Jena M
(Sat Jul 21 2007 - 17:15:42 PDT)
Re: AMBER: offending restraint
David A. Case
(Sat Jul 21 2007 - 18:35:51 PDT)
Re: AMBER: offending restraint
Carlos Simmerling
(Sun Jul 22 2007 - 04:32:51 PDT)
AMBER: question about formatted mdrcrd files...
Cenk Andac
(Sun Jul 22 2007 - 09:47:45 PDT)
Re: AMBER: question about formatted mdrcrd files...
David A. Case
(Sun Jul 22 2007 - 16:30:06 PDT)
Re: AMBER: question about formatted mdrcrd files...
Cenk Andac
(Sun Jul 22 2007 - 17:51:02 PDT)
Re: AMBER: question about formatted mdrcrd files...
Cenk Andac
(Sun Jul 22 2007 - 18:37:43 PDT)
AMBER: Truncated Octahedron box volume
Ilyas Yildirim
(Sun Jul 22 2007 - 19:52:16 PDT)
AMBER: using amber to minimize structure obatined from cyana
Prem Prakash Pathak
(Mon Jul 23 2007 - 00:27:26 PDT)
Re: AMBER: using amber to minimize structure obatined from cyana
David A. Case
(Mon Jul 23 2007 - 07:52:00 PDT)
AMBER: parallel compilation
Francesco Pietra
(Mon Jul 23 2007 - 03:16:35 PDT)
Re: AMBER: parallel compilation
David A. Case
(Mon Jul 23 2007 - 07:55:02 PDT)
Re: AMBER: parallel compilation
Francesco Pietra
(Mon Jul 23 2007 - 23:19:56 PDT)
Re: Re: AMBER: parallel compilation
Ye Mei
(Mon Jul 23 2007 - 23:44:43 PDT)
Re: Re: AMBER: parallel compilation
Francesco Pietra
(Tue Jul 24 2007 - 00:17:03 PDT)
AMBER: regarding distance restraints
gurpreet singh
(Mon Jul 23 2007 - 03:46:39 PDT)
Re: AMBER: regarding distance restraints
Carlos Simmerling
(Mon Jul 23 2007 - 04:26:27 PDT)
Re: AMBER: regarding distance restraints
David A. Case
(Mon Jul 23 2007 - 07:56:03 PDT)
AMBER: SHAKE failure in TI calculation of zero sum model system of "ethane-to-ethane" in water
Ye Mei
(Mon Jul 23 2007 - 06:00:34 PDT)
AMBER: RE: Query
Ross Walker
(Mon Jul 23 2007 - 08:13:13 PDT)
AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
Prem Prakash Pathak
(Mon Jul 23 2007 - 08:39:21 PDT)
Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
Steven Winfield
(Mon Jul 23 2007 - 08:43:17 PDT)
RE: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
Ross Walker
(Mon Jul 23 2007 - 08:52:00 PDT)
Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
Prem Prakash Pathak
(Tue Jul 24 2007 - 05:30:31 PDT)
Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
David A. Case
(Tue Jul 24 2007 - 08:20:30 PDT)
Re: AMBER: problem in compiling amber with suse 9.1 i686, finally in leap
Prem Prakash Pathak
(Tue Jul 24 2007 - 21:12:48 PDT)
AMBER: md potential energy
Francesco Pietra
(Mon Jul 23 2007 - 09:14:48 PDT)
Re: AMBER: netcdf support needed (Amber 9, sander imin = 5, -y flag)
Geoff Wood
(Mon Jul 23 2007 - 10:23:46 PDT)
AMBER: MPI error message
Taryn Hartley
(Mon Jul 23 2007 - 10:39:27 PDT)
RE: AMBER: MPI error message
Ross Walker
(Mon Jul 23 2007 - 10:56:35 PDT)
AMBER: DNA denatures during MD simulation
Prashanth Athri
(Mon Jul 23 2007 - 12:38:12 PDT)
Re: AMBER: DNA denatures during MD simulation
Carlos Simmerling
(Mon Jul 23 2007 - 12:44:35 PDT)
Re: AMBER: DNA denatures during MD simulation
Thomas Cheatham
(Mon Jul 23 2007 - 12:49:49 PDT)
Re: AMBER: DNA denatures during MD simulation
Prashanth Athri
(Mon Jul 23 2007 - 15:51:32 PDT)
AMBER: Bug report: a bug of xleap associated with NumLock
Ye Mei
(Mon Jul 23 2007 - 23:15:27 PDT)
Re: AMBER: Bug report: a bug of xleap associated with NumLock
David A. Case
(Tue Jul 24 2007 - 08:16:07 PDT)
Fwd: Re: Re: AMBER: parallel compilation
Francesco Pietra
(Tue Jul 24 2007 - 00:19:58 PDT)
Re: Fwd: Re: Re: AMBER: parallel compilation
Ye Mei
(Tue Jul 24 2007 - 03:07:31 PDT)
Re: Fwd: Re: Re: AMBER: parallel compilation
Ye Mei
(Tue Jul 24 2007 - 03:15:28 PDT)
Re: Fwd: Re: Re: AMBER: parallel compilation
Francesco Pietra
(Tue Jul 24 2007 - 07:07:10 PDT)
Re: Re: Fwd: Re: Re: AMBER: parallel compilation
Ye Mei
(Tue Jul 24 2007 - 07:26:26 PDT)
Re: Re: Fwd: Re: Re: AMBER: parallel compilation
Francesco Pietra
(Tue Jul 24 2007 - 08:02:01 PDT)
Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation
Ye Mei
(Tue Jul 24 2007 - 19:27:04 PDT)
Re: Re: Re: Fwd: Re: Re: AMBER: parallel compilation
Francesco Pietra
(Tue Jul 24 2007 - 23:10:17 PDT)
AMBER: not getting topology and restraint file
Prem Prakash Pathak
(Tue Jul 24 2007 - 07:09:40 PDT)
Re: AMBER: not getting topology and restraint file
Carlos Simmerling
(Tue Jul 24 2007 - 07:46:49 PDT)
Re: AMBER: not getting topology and restraint file
Prem Prakash Pathak
(Tue Jul 24 2007 - 21:11:00 PDT)
Re: AMBER: not getting topology and restraint file
Carlos Simmerling
(Wed Jul 25 2007 - 03:16:02 PDT)
Re: AMBER: not getting topology and restraint file
Prem Prakash Pathak
(Wed Jul 25 2007 - 06:45:57 PDT)
AMBER: FW: MPI error message
Taryn Hartley
(Tue Jul 24 2007 - 12:00:25 PDT)
RE: AMBER: FW: MPI error message
Gustavo Seabra
(Tue Jul 24 2007 - 12:32:52 PDT)
RE: AMBER: FW: MPI error message
Ross Walker
(Tue Jul 24 2007 - 14:31:12 PDT)
AMBER: MD simulation error
Lili Peng
(Tue Jul 24 2007 - 16:53:59 PDT)
Re: AMBER: MD simulation error
David A. Case
(Tue Jul 24 2007 - 17:55:09 PDT)
RE: AMBER: MD simulation error
Ross Walker
(Tue Jul 24 2007 - 18:01:13 PDT)
Re: AMBER: MD simulation error
Lili Peng
(Wed Jul 25 2007 - 10:38:10 PDT)
Re: AMBER: MD simulation error
Carlos Simmerling
(Wed Jul 25 2007 - 10:41:42 PDT)
RE: AMBER: MD simulation error
Ross Walker
(Wed Jul 25 2007 - 10:54:30 PDT)
Re: AMBER: MD simulation error
Lili Peng
(Wed Jul 25 2007 - 11:21:24 PDT)
AMBER: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Tue Jul 24 2007 - 23:24:22 PDT)
Re: AMBER: Amber9 parallel compilation openmpi issues
Mark Williamson
(Wed Jul 25 2007 - 06:33:35 PDT)
Re: AMBER: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Wed Jul 25 2007 - 07:00:58 PDT)
Re: AMBER: Amber9 parallel compilation openmpi issues
Benjamin Juhl
(Wed Jul 25 2007 - 07:18:28 PDT)
Re: AMBER: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Wed Jul 25 2007 - 07:44:46 PDT)
Re: AMBER: Amber9 parallel compilation openmpi issues
Mark Williamson
(Wed Jul 25 2007 - 08:28:06 PDT)
Re: AMBER: Amber9 parallel compilation openmpi issues
David A. Case
(Wed Jul 25 2007 - 09:09:18 PDT)
AMBER: Bad residue/molecule data in prmtop
neva.mmb.pcb.ub.es
(Wed Jul 25 2007 - 06:03:19 PDT)
RE: AMBER: Bad residue/molecule data in prmtop
Ross Walker
(Wed Jul 25 2007 - 07:17:00 PDT)
AMBER: Fwd: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Wed Jul 25 2007 - 06:24:10 PDT)
RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues
Ross Walker
(Wed Jul 25 2007 - 08:25:58 PDT)
RE: AMBER: Fwd: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Wed Jul 25 2007 - 10:07:15 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
David A. Case
(Wed Jul 25 2007 - 10:36:43 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
Mark Williamson
(Wed Jul 25 2007 - 12:19:29 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
David A. Case
(Wed Jul 25 2007 - 12:56:24 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Wed Jul 25 2007 - 13:43:08 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
David A. Case
(Wed Jul 25 2007 - 14:32:32 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
Mark Williamson
(Wed Jul 25 2007 - 15:20:37 PDT)
Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
David A. Case
(Wed Jul 25 2007 - 15:48:55 PDT)
AMBER: crg file
umbrita itl
(Wed Jul 25 2007 - 07:43:17 PDT)
RE: AMBER: crg file
Ross Walker
(Wed Jul 25 2007 - 08:26:28 PDT)
AMBER: RE: Contact TSRI: Ross Walker
Ross Walker
(Wed Jul 25 2007 - 08:31:53 PDT)
RE: AMBER:charge file
umbrita itl
(Wed Jul 25 2007 - 08:36:11 PDT)
Fwd: Re: AMBER: Fwd: Amber9 parallel compilation openmpi issues
Francesco Pietra
(Wed Jul 25 2007 - 15:01:40 PDT)
AMBER: rmsd residue wise
ravishk kumar
(Thu Jul 26 2007 - 06:02:20 PDT)
AMBER: methods to approach two atoms
Jena M
(Thu Jul 26 2007 - 06:53:09 PDT)
AMBER: RE: A little question
Ross Walker
(Thu Jul 26 2007 - 07:51:55 PDT)
AMBER: about wrap the trajectory
Rachel
(Thu Jul 26 2007 - 09:18:32 PDT)
Re: AMBER: about wrap the trajectory
Carlos Simmerling
(Thu Jul 26 2007 - 09:28:33 PDT)
Re: AMBER: about wrap the trajectory
Rachel
(Thu Jul 26 2007 - 09:43:48 PDT)
Re: AMBER: about wrap the trajectory
Carlos Simmerling
(Fri Jul 27 2007 - 04:29:48 PDT)
Re: AMBER: about wrap the trajectory
Rachel
(Fri Jul 27 2007 - 07:08:23 PDT)
Re: AMBER: about wrap the trajectory
Carlos Simmerling
(Fri Jul 27 2007 - 07:23:30 PDT)
Re: AMBER: about wrap the trajectory
Rachel
(Fri Jul 27 2007 - 07:38:12 PDT)
Re: AMBER: about wrap the trajectory
Carlos Simmerling
(Fri Jul 27 2007 - 07:44:53 PDT)
Re: AMBER: about wrap the trajectory
Rachel
(Fri Jul 27 2007 - 07:52:50 PDT)
Re: AMBER: about wrap the trajectory
Carlos Simmerling
(Fri Jul 27 2007 - 09:10:49 PDT)
AMBER: adding organic molecule to polypeptide residue
Lili Peng
(Thu Jul 26 2007 - 15:36:29 PDT)
Re: AMBER: adding organic molecule to polypeptide residue
FyD
(Sat Jul 28 2007 - 02:05:18 PDT)
AMBER: FLAG LENNARD_JONES_ACOEF NAN
Greg Gannon
(Fri Jul 27 2007 - 07:41:46 PDT)
Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN
David A. Case
(Fri Jul 27 2007 - 08:19:49 PDT)
Re: AMBER: FLAG LENNARD_JONES_ACOEF NAN
Greg Gannon
(Fri Jul 27 2007 - 08:55:52 PDT)
AMBER: RE: Query
Ross Walker
(Fri Jul 27 2007 - 08:24:56 PDT)
AMBER: errors in SHIFTS execution
Tom Pochapsky
(Sat Jul 28 2007 - 04:58:57 PDT)
Re: AMBER: errors in SHIFTS execution
David A. Case
(Sun Jul 29 2007 - 08:44:05 PDT)
Re: AMBER: errors in SHIFTS execution
Thomas Pochapsky
(Mon Jul 30 2007 - 06:49:47 PDT)
Re: AMBER: errors in SHIFTS execution
Thomas Pochapsky
(Mon Jul 30 2007 - 07:06:19 PDT)
Re: AMBER: errors in SHIFTS execution
David A. Case
(Mon Jul 30 2007 - 08:37:26 PDT)
Re: AMBER: errors in SHIFTS execution
Thomas Pochapsky
(Mon Jul 30 2007 - 10:06:04 PDT)
AMBER: PCA with ptraj
ravishk kumar
(Sat Jul 28 2007 - 05:02:13 PDT)
Re: AMBER: PCA with ptraj
Chris Moth
(Sun Jul 29 2007 - 05:27:32 PDT)
AMBER: thermodynamic data for conformers
Francesco Pietra
(Sun Jul 29 2007 - 10:11:11 PDT)
AMBER: what's the problem of "Missing BELE for MM in 1 (residue 246)" in MM-GBSA?
tonglei
(Sun Jul 29 2007 - 20:45:24 PDT)
AMBER: heme force field
hadi behzadi
(Mon Jul 30 2007 - 04:55:07 PDT)
Re: AMBER: heme force field
Marcelo Puiatti
(Mon Jul 30 2007 - 06:08:52 PDT)
AMBER: QM-MM output interpretation
Francesco Pietra
(Mon Jul 30 2007 - 07:08:36 PDT)
RE: AMBER: QM-MM output interpretation
Ross Walker
(Mon Jul 30 2007 - 08:51:36 PDT)
RE: AMBER: QM-MM output interpretation
Francesco Pietra
(Mon Jul 30 2007 - 10:59:13 PDT)
RE: AMBER: QM-MM output interpretation
Ross Walker
(Mon Jul 30 2007 - 21:11:50 PDT)
RE: AMBER: Average potential energies and conformer ratios
Francesco Pietra
(Mon Jul 30 2007 - 22:09:02 PDT)
AMBER: RE: Problem with sander.MPI
Ross Walker
(Mon Jul 30 2007 - 07:12:58 PDT)
AMBER: RE: help:- regarding "perl" in analyzing the simulation
Ross Walker
(Mon Jul 30 2007 - 09:38:33 PDT)
AMBER: QMMM to follow reaction involving water
M. L. Dodson
(Mon Jul 30 2007 - 11:23:14 PDT)
RE: AMBER: QMMM to follow reaction involving water
Gustavo Seabra
(Mon Jul 30 2007 - 12:41:17 PDT)
RE: AMBER: QMMM to follow reaction involving water
Ross Walker
(Mon Jul 30 2007 - 21:49:23 PDT)
Re: AMBER: QMMM to follow reaction involving water
M. L. Dodson
(Tue Jul 31 2007 - 08:14:57 PDT)
AMBER: Problem while saving .top and .crd files.
Anju Sharma
(Mon Jul 30 2007 - 20:47:39 PDT)
RE: AMBER: Problem while saving .top and .crd files.
Ross Walker
(Mon Jul 30 2007 - 21:28:42 PDT)
AMBER: Problem while creating input files in antechamber
Anju Sharma
(Mon Jul 30 2007 - 22:33:12 PDT)
Re: AMBER: Problem while creating input files in antechamber
Benjamin Juhl
(Tue Jul 31 2007 - 00:08:35 PDT)
AMBER: Linux install
Beale, John
(Tue Jul 31 2007 - 04:55:34 PDT)
Re: AMBER: Linux install
David A. Case
(Tue Jul 31 2007 - 08:35:37 PDT)
AMBER: Resp
hadi behzadi
(Tue Jul 31 2007 - 07:15:15 PDT)
AMBER: resp
hadi behzadi
(Tue Jul 31 2007 - 10:15:37 PDT)
AMBER: mm_pbsa and energy decomposition (missing BELE for MM in 1)
Alessandro Nascimento
(Tue Jul 31 2007 - 14:34:12 PDT)
Last message date
:
Wed Aug 01 2007 - 06:07:44 PDT
Archived on
: Wed Dec 25 2024 - 05:53:38 PST
481 messages
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