Amber Archive Jan 2011 by author
613 messages
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Fri Dec 31 2010 - 21:30:02 PST,
Ending
Mon Jan 31 2011 - 15:00:07 PST
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475649770
[AMBER] 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Mon Jan 31 2011 - 06:04:18 PST)
[AMBER] 回复： 回复： MM-PBSA error about protein + Mg2+
(Mon Jan 31 2011 - 03:34:43 PST)
[AMBER] 回复： MM-PBSA error about protein + Mg2+
(Sun Jan 30 2011 - 01:18:00 PST)
ABEL Stephane 175950
[AMBER] RE : Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 09:21:52 PST)
Adrian Roitberg
Re: [AMBER] Fwd: Query regarding unusual water box in vmd
(Tue Jan 25 2011 - 02:29:21 PST)
Re: [AMBER] Monte Carlo Steps in Constant pH simulation
(Wed Jan 12 2011 - 02:52:23 PST)
Re: [AMBER] Running 606580 atoms system on Kraken
(Tue Jan 11 2011 - 11:56:34 PST)
Alan Wilter Sousa da Silva
[AMBER] antechamber is failing for a molecule
(Wed Jan 19 2011 - 03:30:04 PST)
amit dong
Re: [AMBER] MMPBSA.py.MPI query
(Tue Jan 11 2011 - 09:25:17 PST)
[AMBER] MMPBSA.py.MPI query
(Mon Jan 10 2011 - 14:30:55 PST)
Andre Serobian
Re: [AMBER] antechamber error
(Wed Jan 05 2011 - 16:22:42 PST)
Re: [AMBER] antechamber error
(Wed Jan 05 2011 - 13:59:08 PST)
[AMBER] antechamber error
(Tue Jan 04 2011 - 22:55:07 PST)
Andreas Goetz
Re: [AMBER] EGB AM1
(Wed Jan 05 2011 - 21:59:28 PST)
aneesh cna
Re: [AMBER] H-bond analysis interpratation
(Wed Jan 05 2011 - 02:16:52 PST)
Re: [AMBER] H-bond analysis interpratation
(Tue Jan 04 2011 - 04:20:41 PST)
Anindya Sarkar
Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER
(Thu Jan 13 2011 - 08:57:14 PST)
Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER
(Thu Jan 13 2011 - 07:29:43 PST)
[AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER
(Wed Jan 12 2011 - 21:27:14 PST)
Ashutosh Shandilya
[AMBER] free radicals in amber
(Thu Jan 27 2011 - 00:15:08 PST)
[AMBER] md
(Fri Jan 14 2011 - 04:11:49 PST)
atila petrosian
[AMBER] distance and angle cutoff values for hydrogen bond analysis
(Wed Jan 05 2011 - 23:30:14 PST)
Baldoni Hector Armando
[AMBER] local REMD
(Fri Jan 07 2011 - 11:06:35 PST)
Baptiste Legrand
Re: [AMBER] residue topology files
(Wed Jan 26 2011 - 07:31:31 PST)
[AMBER] residue topology files
(Wed Jan 26 2011 - 06:32:19 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 09:07:37 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 06:19:57 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 05:53:25 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 01:15:25 PST)
[AMBER] Can we load rst files in leap?
(Wed Jan 12 2011 - 10:36:04 PST)
Re: [AMBER] How to clean dihedral angles plot?
(Mon Jan 10 2011 - 05:51:12 PST)
Re: [AMBER] How to clean dihedral angles plot?
(Mon Jan 10 2011 - 01:25:22 PST)
[AMBER] How to clean dihedral angles plot?
(Mon Jan 10 2011 - 00:41:49 PST)
[AMBER] NMR refinement in water: which water box?
(Fri Jan 07 2011 - 08:40:21 PST)
[AMBER] How to clean dihedral angles plot?
(Fri Jan 07 2011 - 06:23:37 PST)
Beale, John
[AMBER] contacts
(Fri Jan 21 2011 - 07:01:01 PST)
[AMBER] Protein-Water Interaction Energy
(Fri Jan 14 2011 - 05:00:18 PST)
[AMBER] heavy atom rms
(Wed Jan 05 2011 - 05:06:26 PST)
Ben Roberts
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 11:21:55 PST)
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 10:57:02 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:18:07 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:00:50 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Tue Jan 11 2011 - 08:38:32 PST)
Bill Miller III
Re: [AMBER] MM-PBSA and handling of ions
(Mon Jan 31 2011 - 14:51:57 PST)
Re: [AMBER] 回复： 回复： MM-PBSA error about protein + Mg2+
(Mon Jan 31 2011 - 03:46:27 PST)
Re: [AMBER] 回复： MM-PBSA error about protein + Mg2+
(Sun Jan 30 2011 - 05:52:20 PST)
Bill Ross
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 12:53:20 PST)
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 11:02:30 PST)
Re: [AMBER] Using packmol to produce multiple instances of the same molecule
(Fri Jan 28 2011 - 10:17:34 PST)
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 15:52:00 PST)
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 12:04:19 PST)
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 11:44:42 PST)
Re: [AMBER] Problems with TIP5P water
(Tue Jan 25 2011 - 11:29:06 PST)
Re: [AMBER] Problems with TIP5P water
(Tue Jan 25 2011 - 10:11:11 PST)
Re: [AMBER] Problem regarding Same coordinate for two atoms
(Sun Jan 23 2011 - 19:29:27 PST)
Re: [AMBER] concentration
(Thu Jan 20 2011 - 11:09:39 PST)
Re: [AMBER] concentration
(Thu Jan 20 2011 - 11:01:19 PST)
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 14:32:01 PST)
Re: [AMBER] Use leaprc.ff99SB force field
(Fri Jan 14 2011 - 09:47:08 PST)
Re: [AMBER] Can we load rst files in leap?
(Wed Jan 12 2011 - 11:22:43 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Wed Jan 12 2011 - 09:44:50 PST)
Re: [AMBER] waters in interface between protein and dna / water mediated hydrogen bonds
(Sun Jan 09 2011 - 09:53:33 PST)
Re: [AMBER] Heating the system from 100K to 300K
(Sun Jan 09 2011 - 09:47:56 PST)
Re: [AMBER] Heating the system from 100K to 300K
(Fri Jan 07 2011 - 11:00:39 PST)
Re: [AMBER] heavy atom rms
(Wed Jan 05 2011 - 12:16:29 PST)
Re: [AMBER] Determining rings in a molecule
(Tue Jan 04 2011 - 12:57:59 PST)
Bill Snapko
[AMBER] Amber 11 - Bugfix 9
(Thu Jan 06 2011 - 13:12:24 PST)
Bongkeun Kim
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 19:08:29 PST)
[AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 13:14:14 PST)
Brent Krueger
[AMBER] Current opinions on compilers
(Fri Jan 21 2011 - 06:26:37 PST)
Carlos Simmerling
Re: [AMBER] REMD equilibration restart
(Mon Jan 31 2011 - 09:28:32 PST)
Re: [AMBER] REMD equilibration restart
(Mon Jan 31 2011 - 05:51:47 PST)
Re: [AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 06:23:25 PST)
Re: [AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 06:15:16 PST)
Re: [AMBER] conformation search
(Thu Jan 27 2011 - 08:13:02 PST)
Re: [AMBER] conformation search
(Thu Jan 27 2011 - 07:25:55 PST)
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 11:46:06 PST)
Re: [AMBER] REMD maximum temperature
(Mon Jan 17 2011 - 10:17:05 PST)
Re: [AMBER] REMD maximum temperature
(Mon Jan 17 2011 - 09:39:07 PST)
Re: [AMBER] REMD maximum temperature
(Thu Jan 13 2011 - 10:34:09 PST)
Re: [AMBER] Is it an artifact for potential-of-mean force calculation?
(Tue Jan 11 2011 - 08:02:48 PST)
Re: [AMBER] Multiple-step Structural Overlay
(Tue Jan 11 2011 - 07:57:04 PST)
Re: [AMBER] How to clean dihedral angles plot?
(Mon Jan 10 2011 - 03:21:26 PST)
Re: [AMBER] Heating the system from 100K to 300K
(Fri Jan 07 2011 - 05:50:10 PST)
Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ?
(Sat Jan 01 2011 - 07:02:05 PST)
case
Re: [AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ?
(Sun Jan 30 2011 - 18:11:57 PST)
Re: [AMBER] Using packmol to produce multiple instances of the same molecule
(Sat Jan 29 2011 - 06:55:34 PST)
Re: [AMBER] Query regarding NVT ensemble with less restraint on solute
(Sat Jan 29 2011 - 06:21:27 PST)
Re: [AMBER] QM/MM-GBSA calculation : No convergence in SCF after 1000 steps.
(Fri Jan 28 2011 - 05:14:17 PST)
Re: [AMBER] installing ambertools1.4
(Fri Jan 28 2011 - 05:09:53 PST)
Re: [AMBER] free radicals in amber
(Thu Jan 27 2011 - 05:54:29 PST)
Re: [AMBER] urea force field
(Thu Jan 27 2011 - 05:32:06 PST)
Re: [AMBER] Query regarding parmchk
(Wed Jan 26 2011 - 08:53:24 PST)
Re: [AMBER] residue topology files
(Wed Jan 26 2011 - 08:41:34 PST)
Re: [AMBER] residue topology files
(Wed Jan 26 2011 - 06:46:09 PST)
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 06:43:49 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 06:04:16 PST)
Re: [AMBER] Problems with TIP5P water
(Wed Jan 26 2011 - 06:01:54 PST)
Re: [AMBER] AMBER: SPCFW problems
(Tue Jan 25 2011 - 06:51:16 PST)
Re: [AMBER] calculate entropy ptraj
(Tue Jan 25 2011 - 05:33:29 PST)
Re: [AMBER] maximum number of atoms
(Mon Jan 24 2011 - 05:24:08 PST)
Re: [AMBER] Ptraj for diffusion coefficient of water
(Sat Jan 22 2011 - 14:39:25 PST)
Re: [AMBER] Ptraj for diffusion coefficient of water
(Sat Jan 22 2011 - 07:03:22 PST)
Re: [AMBER] error in prmtop,inpcrd
(Sat Jan 22 2011 - 06:54:11 PST)
Re: [AMBER] Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 09:15:05 PST)
Re: [AMBER] Current opinions on compilers
(Fri Jan 21 2011 - 06:50:37 PST)
Re: [AMBER] missing parameter not present in antechamber generated frcmod
(Thu Jan 20 2011 - 11:29:41 PST)
Re: [AMBER] antechamber is failing for a molecule
(Thu Jan 20 2011 - 08:59:52 PST)
Re: [AMBER] docking in AMBER for protein complex
(Thu Jan 20 2011 - 08:38:05 PST)
Re: [AMBER] Story of bugfix 18-Amber10
(Thu Jan 20 2011 - 05:21:43 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Thu Jan 20 2011 - 05:19:37 PST)
Re: [AMBER] Story of bugfix 18-Amber10
(Wed Jan 19 2011 - 19:43:52 PST)
Re: [AMBER] Use leaprc.ff99SB force field
(Sat Jan 15 2011 - 06:48:24 PST)
Re: [AMBER] water simulation
(Mon Jan 10 2011 - 06:56:13 PST)
Re: [AMBER] How to build Amber topology and other files for inorganic crystalline material?
(Mon Jan 10 2011 - 06:22:28 PST)
Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
(Mon Jan 10 2011 - 06:05:50 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 07:54:31 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 05:16:37 PST)
Re: [AMBER] Amber
(Sat Jan 08 2011 - 05:12:19 PST)
Re: [AMBER] NMR refinement in water: which water box?
(Sat Jan 08 2011 - 05:00:35 PST)
[AMBER] SQM error
(Thu Jan 06 2011 - 04:53:48 PST)
Re: [AMBER] antechamber error
(Wed Jan 05 2011 - 05:20:35 PST)
Catein Catherine
[AMBER] Any review or article commands on the use of amber to study protein-DNA complexes?
(Tue Jan 18 2011 - 02:24:09 PST)
[AMBER] Is it an artifact for potential-of-mean force calculation?
(Tue Jan 11 2011 - 07:59:40 PST)
[AMBER] Can I use bfactor (rmsf) to conclude if the protein is stabilized upon drug binding?
(Tue Jan 04 2011 - 08:26:21 PST)
[AMBER] Any way to restraint the helicity of an alpha-helix chains
(Tue Jan 04 2011 - 06:10:49 PST)
[AMBER] Any beta-alanine parameter in amber?
(Tue Jan 04 2011 - 06:04:13 PST)
[AMBER] Can we doing potential of mean force for two protein complex?
(Mon Jan 03 2011 - 03:32:04 PST)
Chinh Su Tran To
[AMBER] docking in AMBER for protein complex
(Tue Jan 18 2011 - 19:22:15 PST)
Dairsie Latimer
Re: [AMBER] Amber11 using CUDA-enabled GPUs
(Tue Jan 18 2011 - 11:35:22 PST)
Daniel Roe
Re: [AMBER] problem with GB REMD trajectories and ptraj
(Thu Jan 20 2011 - 18:47:18 PST)
Re: [AMBER] RMSD and reference structure
(Mon Jan 17 2011 - 21:18:10 PST)
Re: [AMBER] strip :WAT command in ptraj
(Tue Jan 11 2011 - 13:48:21 PST)
Re: [AMBER] Amber
(Tue Jan 11 2011 - 07:18:18 PST)
Re: [AMBER] Troubleshooting script <measure_equil_rmsd.ptraj>
(Thu Jan 06 2011 - 06:47:28 PST)
Daniel Scott
[AMBER] VMD Movie
(Fri Jan 14 2011 - 09:04:31 PST)
[AMBER] strip :WAT command in ptraj
(Tue Jan 11 2011 - 12:39:52 PST)
[AMBER] stripWAT command and saving a new trajectory
(Mon Jan 10 2011 - 14:52:56 PST)
Daniel Sindhikara
Re: [AMBER] Local REMD
(Thu Jan 13 2011 - 19:53:14 PST)
David A. Case
Re: [AMBER] Use leaprc.ff99SB force field
(Fri Jan 14 2011 - 07:12:45 PST)
Re: [AMBER] parmchk
(Wed Jan 12 2011 - 10:25:46 PST)
Re: [AMBER] SGLD
(Wed Jan 12 2011 - 10:03:04 PST)
Re: [AMBER] Amber
(Tue Jan 11 2011 - 12:00:45 PST)
Re: [AMBER] problem with antechamber
(Tue Jan 11 2011 - 12:00:30 PST)
David Case
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 19:02:47 PST)
Re: [AMBER] maximum number of atoms
(Thu Jan 20 2011 - 18:54:20 PST)
david condon
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 05:49:11 PST)
Re: [AMBER] Different Versions of Amber: Comparable results?
(Wed Jan 12 2011 - 13:32:03 PST)
[AMBER] Different Versions of Amber: Comparable results?
(Tue Jan 11 2011 - 12:05:26 PST)
David Watson
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 11:07:15 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:01:47 PST)
dhacademic
Re: [AMBER] image for lipid/water system
(Thu Jan 20 2011 - 09:02:30 PST)
Re: [AMBER] image for lipid/water system
(Thu Jan 20 2011 - 08:47:02 PST)
[AMBER] image for lipid/water system
(Thu Jan 20 2011 - 07:21:46 PST)
Dmitry Mukha
Re: [AMBER] NPT and restraints
(Mon Jan 31 2011 - 07:35:22 PST)
[AMBER] NPT and restraints
(Sun Jan 30 2011 - 07:13:22 PST)
[AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied)
(Sun Jan 02 2011 - 06:12:13 PST)
Dmitry Nilov
Re: [AMBER] Only Hydrogen Minimization
(Fri Jan 28 2011 - 05:05:48 PST)
Re: [AMBER] Query regarding parmchk
(Wed Jan 26 2011 - 02:22:57 PST)
Re: [AMBER] Query regarding restrain during minimization
(Mon Jan 24 2011 - 03:54:57 PST)
Re: [AMBER] Is it an artifact for potential-of-mean force calculation?
(Tue Jan 11 2011 - 08:31:31 PST)
Dwight McGee
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Tue Jan 25 2011 - 12:06:38 PST)
Ed Pate
[AMBER] problem with antechamber
(Mon Jan 10 2011 - 19:54:36 PST)
Edward M.
[AMBER] Multiple-step Structural Overlay
(Tue Jan 11 2011 - 07:47:53 PST)
Eliac Brown
Re: [AMBER] Story of bugfix 18-Amber10
(Wed Jan 19 2011 - 23:26:12 PST)
[AMBER] Story of bugfix 18-Amber10
(Wed Jan 19 2011 - 15:46:36 PST)
[AMBER] QMMM-IGB=2
(Mon Jan 10 2011 - 22:14:11 PST)
Re: [AMBER] EEL energy term
(Thu Jan 06 2011 - 16:34:48 PST)
[AMBER] EEL energy term
(Thu Jan 06 2011 - 16:06:32 PST)
[AMBER] EGB AM1
(Wed Jan 05 2011 - 16:31:50 PST)
[AMBER] QM/MM energy
(Sat Jan 01 2011 - 20:03:41 PST)
Enrico Caldarulo
[AMBER] parametrize perchlorate
(Fri Jan 21 2011 - 07:46:35 PST)
Federica Chiappori
Re: [AMBER] Multiple-step Structural Overlay
(Tue Jan 11 2011 - 09:40:32 PST)
filip fratev
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 10:53:50 PST)
Re: [AMBER] NaN error in .rst files
(Thu Jan 27 2011 - 07:33:30 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 07:42:56 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 10:09:17 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 00:25:08 PST)
Re: [AMBER] docking in AMBER for protein complex
(Thu Jan 20 2011 - 10:37:06 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 19 2011 - 17:14:18 PST)
[AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 19 2011 - 14:26:53 PST)
Re: [AMBER] GPU Code Update
(Sun Jan 09 2011 - 16:26:56 PST)
Re: [AMBER] GPU Code Update
(Sat Jan 08 2011 - 13:27:11 PST)
Frank X. Vázquez
[AMBER] Using Chamber to convert psf to prmtop
(Fri Jan 21 2011 - 12:33:04 PST)
FyD
Re: [AMBER] Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 22:51:30 PST)
Re: [AMBER] phosphorylated cysteine
(Mon Jan 17 2011 - 03:02:11 PST)
g t
Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files)
(Fri Jan 07 2011 - 02:53:14 PST)
Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files)
(Thu Jan 06 2011 - 04:04:01 PST)
[AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files)
(Wed Jan 05 2011 - 23:02:15 PST)
Ganesh Kamath
Re: [AMBER] Ptraj for diffusion coefficient of water
(Sun Jan 23 2011 - 10:01:36 PST)
Re: [AMBER] Ptraj for diffusion coefficient of water
(Sat Jan 22 2011 - 12:32:33 PST)
[AMBER] Ptraj for diffusion coefficient of water
(Fri Jan 21 2011 - 12:52:54 PST)
[AMBER] question on diffusion coefficient calculation using ptraj
(Fri Jan 21 2011 - 07:19:16 PST)
George Tzotzos
[AMBER] Drifting RMSD
(Fri Jan 07 2011 - 10:32:58 PST)
Re: [AMBER] Troubleshooting script <measure_equil_rmsd.ptraj>
(Thu Jan 06 2011 - 07:06:21 PST)
[AMBER] Troubleshooting script <measure_equil_rmsd.ptraj>
(Wed Jan 05 2011 - 08:12:31 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Wed Jan 05 2011 - 04:28:12 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 11:35:01 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 10:03:56 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 03:02:03 PST)
[AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 02:41:00 PST)
gilbert
Re: [AMBER] Determining rings in a molecule
(Tue Jan 04 2011 - 19:07:30 PST)
Gould, Ian R
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 09:10:31 PST)
Guillermo Mulliert Carlín
Re: [AMBER] docking in AMBER for protein complex
(Fri Jan 21 2011 - 00:24:47 PST)
Gustaf Olsson
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 11:57:19 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 11:19:27 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:40:16 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:20:00 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:08:39 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 09:46:44 PST)
[AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 07:33:14 PST)
Hannes Loeffler
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 07:02:49 PST)
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 05:47:52 PST)
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 02:27:02 PST)
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 00:48:07 PST)
Hector A. Baldoni
[AMBER] Local REMD
(Thu Jan 13 2011 - 14:31:17 PST)
Hector Chang
[AMBER] Running 606580 atoms system on Kraken
(Tue Jan 11 2011 - 11:52:39 PST)
Hirdesh Kumar
Re: [AMBER] Query regarding NVT ensemble with less restraint on solute
(Sat Jan 29 2011 - 09:55:43 PST)
[AMBER] Query regarding NVT ensemble with less restraint on solute
(Sat Jan 29 2011 - 00:45:50 PST)
Re: [AMBER] problem in minimization with POL3
(Sat Jan 29 2011 - 00:40:02 PST)
Re: [AMBER] Display CPU time in mdout file
(Fri Jan 28 2011 - 23:23:48 PST)
Re: [AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 08:33:37 PST)
Re: [AMBER] Display CPU time in mdout file
(Fri Jan 28 2011 - 08:09:14 PST)
Re: [AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 06:18:51 PST)
[AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 05:58:20 PST)
Re: [AMBER] Only Hydrogen Minimization
(Fri Jan 28 2011 - 05:49:14 PST)
[AMBER] Display CPU time in mdout file
(Fri Jan 28 2011 - 04:37:12 PST)
[AMBER] Only Hydrogen Minimization
(Fri Jan 28 2011 - 04:20:02 PST)
Re: [AMBER] Fwd: Query regarding unusual water box in vmd
(Tue Jan 25 2011 - 04:14:52 PST)
Re: [AMBER] Fwd: Query regarding unusual water box in vmd
(Tue Jan 25 2011 - 03:12:29 PST)
Re: [AMBER] Fwd: Query regarding unusual water box in vmd
(Tue Jan 25 2011 - 02:22:32 PST)
[AMBER] Fwd: Query regarding unusual water box in vmd
(Mon Jan 24 2011 - 22:12:39 PST)
[AMBER] Query regarding unusual water box in vmd
(Mon Jan 24 2011 - 22:05:38 PST)
Re: [AMBER] Query regarding restrain during minimization
(Mon Jan 24 2011 - 03:39:27 PST)
[AMBER] Query regarding restrain during minimization
(Sun Jan 23 2011 - 23:15:18 PST)
Re: [AMBER] Problem regarding Same coordinate for two atoms
(Sat Jan 22 2011 - 01:24:12 PST)
Re: [AMBER] Problem regarding Same coordinate for two atoms
(Sat Jan 22 2011 - 00:05:46 PST)
[AMBER] Problem regarding Same coordinate for two atoms
(Fri Jan 21 2011 - 22:34:37 PST)
Re: [AMBER] Query regarding Linmin error
(Fri Jan 21 2011 - 01:05:13 PST)
Re: [AMBER] Query regarding Linmin error
(Thu Jan 20 2011 - 20:18:43 PST)
[AMBER] Query regarding Linmin error
(Wed Jan 19 2011 - 21:58:07 PST)
Ilyas Yildirim
Re: [AMBER] Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 07:28:43 PST)
Re: [AMBER] concentration
(Thu Jan 20 2011 - 11:26:24 PST)
Re: [AMBER] md
(Fri Jan 14 2011 - 07:16:25 PST)
Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch
(Wed Jan 12 2011 - 13:06:06 PST)
Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch
(Wed Jan 12 2011 - 10:49:55 PST)
[AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch
(Tue Jan 11 2011 - 12:58:54 PST)
Re: [AMBER] Any way to restraint the helicity of an alpha-helix chains
(Tue Jan 04 2011 - 07:50:31 PST)
Jagur Lambix
[AMBER] MM-PBSA and handling of ions
(Mon Jan 31 2011 - 14:12:06 PST)
[AMBER] Error with MM-PBSA
(Tue Jan 25 2011 - 13:05:31 PST)
Jan Wahl
Re: [AMBER] Use leaprc.ff99SB force field
(Fri Jan 14 2011 - 17:08:11 PST)
Re: [AMBER] Use leaprc.ff99SB force field
(Fri Jan 14 2011 - 07:40:57 PST)
[AMBER] Use leaprc.ff99SB force field
(Fri Jan 14 2011 - 06:21:34 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Wed Jan 12 2011 - 01:03:12 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Tue Jan 11 2011 - 11:05:13 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Tue Jan 11 2011 - 07:22:31 PST)
[AMBER] LINMIN FAILURE using amber 11
(Tue Jan 11 2011 - 05:11:02 PST)
Jason Swails
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 10:54:40 PST)
Re: [AMBER] AmberTool parallel compiling error
(Mon Jan 31 2011 - 10:47:40 PST)
Re: [AMBER] 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Mon Jan 31 2011 - 06:39:01 PST)
Re: [AMBER] Query regarding NVT ensemble with less restraint on solute
(Sat Jan 29 2011 - 12:05:27 PST)
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 10:54:57 PST)
Re: [AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 08:48:10 PST)
Re: [AMBER] AMBER11 parallel compiling problem
(Fri Jan 28 2011 - 08:41:10 PST)
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 08:14:59 PST)
Re: [AMBER] Problem During Gradual Heating
(Fri Jan 28 2011 - 06:42:28 PST)
Re: [AMBER] sander on amber12
(Fri Jan 28 2011 - 05:57:16 PST)
Re: [AMBER] MM-PBSA error about protein + Mg2+
(Fri Jan 28 2011 - 05:55:59 PST)
Re: [AMBER] Amber usage and enquiry - 280111
(Thu Jan 27 2011 - 21:29:03 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 08:58:06 PST)
Re: [AMBER] GPU vs CPU test
(Thu Jan 27 2011 - 08:13:50 PST)
Re: [AMBER] amber11 installation bugfix problem
(Thu Jan 27 2011 - 04:12:59 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 10:04:32 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 08:37:49 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 08:36:48 PST)
Re: [AMBER] residue topology files
(Wed Jan 26 2011 - 07:35:29 PST)
Re: [AMBER] MM-PBSA error about protein + Mg2+
(Wed Jan 26 2011 - 06:17:50 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 06:14:25 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 26 2011 - 06:10:02 PST)
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Tue Jan 25 2011 - 12:31:10 PST)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 23:29:43 PST)
Re: [AMBER] Fwd: Query regarding unusual water box in vmd
(Mon Jan 24 2011 - 22:20:49 PST)
Re: [AMBER] NaN error in .rst files
(Mon Jan 24 2011 - 21:57:01 PST)
Re: [AMBER] NaN error in .rst files
(Mon Jan 24 2011 - 21:45:50 PST)
Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.3
(Mon Jan 24 2011 - 20:45:17 PST)
Re: [AMBER] calculate entropy ptraj
(Mon Jan 24 2011 - 08:41:41 PST)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 07:17:43 PST)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 04:17:54 PST)
Re: [AMBER] error in prmtop,inpcrd
(Sun Jan 23 2011 - 20:46:02 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Sat Jan 22 2011 - 07:54:04 PST)
Re: [AMBER] Problem regarding Same coordinate for two atoms
(Sat Jan 22 2011 - 00:13:45 PST)
Re: [AMBER] Problem regarding Same coordinate for two atoms
(Fri Jan 21 2011 - 23:14:35 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Fri Jan 21 2011 - 23:11:57 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 11:50:14 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:56:15 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 10:45:14 PST)
Re: [AMBER] PATH/evironment problem on Mac OS X
(Fri Jan 21 2011 - 08:48:35 PST)
Re: [AMBER] Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 07:15:29 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 17:46:06 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 17:44:24 PST)
Re: [AMBER] maximum number of atoms
(Thu Jan 20 2011 - 15:44:41 PST)
Re: [AMBER] maximum number of atoms
(Thu Jan 20 2011 - 15:26:27 PST)
Re: [AMBER] concentration
(Thu Jan 20 2011 - 11:59:54 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Thu Jan 20 2011 - 09:13:24 PST)
Re: [AMBER] image for lipid/water system
(Thu Jan 20 2011 - 08:56:23 PST)
Re: [AMBER] image for lipid/water system
(Thu Jan 20 2011 - 08:05:01 PST)
Re: [AMBER] Query regarding Linmin error
(Thu Jan 20 2011 - 05:50:15 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 19 2011 - 19:21:11 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 19 2011 - 15:20:52 PST)
Re: [AMBER] missing parameter not present in antechamber generated frcmod
(Wed Jan 19 2011 - 10:07:24 PST)
Re: [AMBER] Torsional parameters for S-C-C-N bond
(Tue Jan 18 2011 - 10:26:52 PST)
Re: [AMBER] RMSD and reference structure
(Mon Jan 17 2011 - 21:13:52 PST)
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 21:00:58 PST)
Re: [AMBER] Torsional parameters for S-C-C-N bond
(Mon Jan 17 2011 - 21:00:06 PST)
Re: [AMBER] VMD Movie
(Fri Jan 14 2011 - 09:22:16 PST)
Re: [AMBER] md
(Fri Jan 14 2011 - 05:55:12 PST)
Re: [AMBER] Protein-Water Interaction Energy
(Fri Jan 14 2011 - 05:49:51 PST)
Re: [AMBER] MMPBSA
(Thu Jan 13 2011 - 20:14:35 PST)
Re: [AMBER] compilation failure of amber 10
(Thu Jan 13 2011 - 20:01:48 PST)
Re: [AMBER] compilation failure of amber 10
(Thu Jan 13 2011 - 15:11:11 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 06:39:48 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 06:09:33 PST)
Re: [AMBER] Can we load rst files in leap?
(Thu Jan 13 2011 - 05:31:40 PST)
Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch
(Wed Jan 12 2011 - 11:45:14 PST)
Re: [AMBER] Can we load rst files in leap?
(Wed Jan 12 2011 - 10:38:32 PST)
Re: [AMBER] parmchk
(Wed Jan 12 2011 - 10:26:15 PST)
Re: [AMBER] MMPBSA.py.MPI fails to run on multiple nodes
(Wed Jan 12 2011 - 10:23:19 PST)
Re: [AMBER] MMPBSA.py.MPI query
(Wed Jan 12 2011 - 07:08:14 PST)
Re: [AMBER] Benchmarking sander.MPI and pmemd on a linux cluster with infiniband switch
(Tue Jan 11 2011 - 14:32:24 PST)
Re: [AMBER] Different Versions of Amber: Comparable results?
(Tue Jan 11 2011 - 12:20:38 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Tue Jan 11 2011 - 11:15:49 PST)
Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
(Tue Jan 11 2011 - 08:44:06 PST)
Re: [AMBER] Amber
(Tue Jan 11 2011 - 07:15:32 PST)
Re: [AMBER] LINMIN FAILURE using amber 11
(Tue Jan 11 2011 - 07:05:07 PST)
Re: [AMBER] stripWAT command and saving a new trajectory
(Mon Jan 10 2011 - 15:41:31 PST)
Re: [AMBER] MMPBSA.py.MPI query
(Mon Jan 10 2011 - 15:34:56 PST)
Re: [AMBER] Mutational energy on the protein
(Sun Jan 09 2011 - 04:29:25 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 12:25:22 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 09:42:21 PST)
Re: [AMBER] Drifting RMSD
(Fri Jan 07 2011 - 10:38:01 PST)
Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files)
(Thu Jan 06 2011 - 05:04:29 PST)
Re: [AMBER] antechamber error
(Wed Jan 05 2011 - 21:25:56 PST)
Re: [AMBER] compile Amber 11 on IBM Power 7
(Wed Jan 05 2011 - 08:13:52 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Wed Jan 05 2011 - 08:18:29 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 13:32:42 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 11:02:57 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 10:59:45 PST)
Re: [AMBER] Problem in using MMPBSA.py with Amber10
(Mon Jan 03 2011 - 15:29:38 PST)
Re: [AMBER] Progress of calculation in MMPBSA.py.MPI
(Mon Jan 03 2011 - 15:19:37 PST)
Re: [AMBER] Problem in using MMPBSA.py with Amber10
(Mon Jan 03 2011 - 11:27:18 PST)
Re: [AMBER] QM/MM energy
(Sat Jan 01 2011 - 21:52:03 PST)
Jesper Sørensen
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 26 2011 - 10:39:17 PST)
Re: [AMBER] MMPBSA.py.MPI Nmode problem
(Wed Jan 26 2011 - 05:14:42 PST)
Re: [AMBER] MMPBSA.py.MPI fails to run on multiple nodes
(Sun Jan 16 2011 - 10:44:41 PST)
[AMBER] MMPBSA.py.MPI fails to run on multiple nodes
(Wed Jan 12 2011 - 08:50:23 PST)
Jianhui Tian
Re: [AMBER] Parameter missing in Glycan
(Sun Jan 16 2011 - 09:55:53 PST)
Re: [AMBER] Parameter missing in Glycan
(Sun Jan 16 2011 - 09:22:58 PST)
[AMBER] Parameter missing in Glycan
(Sat Jan 15 2011 - 19:20:34 PST)
John S
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 12:40:29 PST)
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 12:35:42 PST)
Re: [AMBER] Solvate box
(Fri Jan 28 2011 - 10:50:11 PST)
[AMBER] Solvate box
(Fri Jan 28 2011 - 08:13:27 PST)
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 14:39:51 PST)
[AMBER] Solvate box
(Wed Jan 26 2011 - 11:31:27 PST)
[AMBER] MMPBSA increasing the number of receptor groups
(Fri Jan 14 2011 - 17:27:50 PST)
Re: [AMBER] MMPBSA
(Fri Jan 14 2011 - 11:06:53 PST)
[AMBER] MMPBSA
(Thu Jan 13 2011 - 19:22:24 PST)
Jorgen Simonsen
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 03:12:10 PST)
Re: [AMBER] PCA analysis for side chain atoms and backbone atoms
(Wed Jan 26 2011 - 01:52:42 PST)
[AMBER] PCA analysis for side chain atoms and backbone atoms
(Tue Jan 25 2011 - 11:31:03 PST)
Re: [AMBER] calculate entropy ptraj
(Tue Jan 25 2011 - 01:03:50 PST)
[AMBER] calculate entropy ptraj
(Mon Jan 24 2011 - 08:15:10 PST)
Jose Borreguero
Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ?
(Sat Jan 01 2011 - 08:30:44 PST)
Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ?
(Sat Jan 01 2011 - 06:56:02 PST)
Josh Berryman
Re: [AMBER] AMBER: SPCFW problems
(Mon Jan 31 2011 - 02:44:01 PST)
Re: [AMBER] AMBER: SPCFW problems
(Tue Jan 25 2011 - 06:36:42 PST)
Julia Romanowska
[AMBER] amber11 installation bugfix problem
(Thu Jan 27 2011 - 02:31:58 PST)
juzer stationwala
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 20:36:39 PST)
Kamali Sripathi
Re: [AMBER] Ptraj: Hbond and Bfactor analyses
(Wed Jan 26 2011 - 16:55:11 PST)
Re: [AMBER] Ptraj: Hbond and Bfactor analyses
(Wed Jan 26 2011 - 16:27:55 PST)
Re: [AMBER] Ptraj: Hbond and Bfactor analyses
(Wed Jan 26 2011 - 08:44:48 PST)
[AMBER] Ptraj: Hbond and Bfactor analyses
(Mon Jan 24 2011 - 14:26:18 PST)
[AMBER] Ptraj: Hbond and Bfactor analyses
(Sat Jan 22 2011 - 08:33:28 PST)
Ken Choy
[AMBER] Amber usage and enquiry - 280111
(Thu Jan 27 2011 - 21:12:17 PST)
Lachele Foley (Lists)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 06:19:34 PST)
Re: [AMBER] Parameter missing in Glycan
(Sun Jan 16 2011 - 10:10:02 PST)
Re: [AMBER] Parameter missing in Glycan
(Sun Jan 16 2011 - 09:38:31 PST)
Re: [AMBER] Parameter missing in Glycan
(Sat Jan 15 2011 - 20:44:15 PST)
Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER
(Thu Jan 13 2011 - 06:36:35 PST)
leila karami
[AMBER] waters in interface between protein and dna / water mediated hydrogen bonds
(Sat Jan 08 2011 - 03:50:17 PST)
[AMBER] waters in interface between protein and dna / water mediated hydrogen bonds
(Wed Jan 05 2011 - 23:46:55 PST)
[AMBER] water mediated hydrogen bonds - ptraj
(Sun Jan 02 2011 - 07:25:51 PST)
Liz Wheatley
[AMBER] using ptraj contacts command: double printing of last residue
(Tue Jan 11 2011 - 12:17:54 PST)
Lorenzo Gontrani
[AMBER] Imidazolium parameters
(Fri Jan 21 2011 - 09:49:32 PST)
M. L. Dodson
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 16:04:51 PST)
Re: [AMBER] Solvate box
(Wed Jan 26 2011 - 15:25:45 PST)
malay rana
[AMBER] How to build Amber topology and other files for inorganic crystalline material?
(Sun Jan 09 2011 - 02:06:52 PST)
manoj singh
Re: [AMBER] Determining rings in a molecule
(Sat Jan 01 2011 - 13:49:35 PST)
Marc-André Dubois
Re: [AMBER] maximum number of atoms
(Thu Jan 20 2011 - 18:58:32 PST)
Re: [AMBER] maximum number of atoms
(Thu Jan 20 2011 - 15:36:42 PST)
[AMBER] maximum number of atoms
(Thu Jan 20 2011 - 14:47:46 PST)
Marek Maly
[AMBER] MM_PBSA questions
(Mon Jan 31 2011 - 09:23:30 PST)
Re: [AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ?
(Mon Jan 31 2011 - 01:59:59 PST)
[AMBER] Any recommendations regarding IGB parameter in Normal Mode section of mm_pbsa analyses ?
(Sun Jan 30 2011 - 12:51:30 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Sat Jan 29 2011 - 18:43:51 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Fri Jan 28 2011 - 01:49:02 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 14:10:55 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 10:46:17 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 09:29:06 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 08:32:21 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 08:18:35 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 07:04:24 PST)
Re: [AMBER] NaN error in .rst files
(Thu Jan 27 2011 - 02:21:48 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 16:16:52 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 15:49:34 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Wed Jan 26 2011 - 14:58:43 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 09:49:53 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 09:34:52 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 08:37:52 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 08:23:01 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 06:21:26 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 06:28:09 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 04:19:45 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Sat Jan 22 2011 - 16:47:06 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Sat Jan 22 2011 - 16:44:06 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Sat Jan 22 2011 - 05:23:50 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Fri Jan 21 2011 - 19:05:40 PST)
Maria Pikoula
[AMBER] Using packmol to produce multiple instances of the same molecule
(Fri Jan 28 2011 - 09:34:27 PST)
Mark Abraham
Re: [AMBER] problem with GB REMD trajectories and ptraj
(Thu Jan 20 2011 - 19:08:57 PST)
[AMBER] problem with GB REMD trajectories and ptraj
(Thu Jan 20 2011 - 18:05:08 PST)
Maryam Hamzehee
[AMBER] MM-PBSA AND mm_pbsa_statistics.pl
(Sun Jan 02 2011 - 04:42:04 PST)
Massimiliano Porrini
Re: [AMBER] GPU vs CPU test
(Fri Jan 28 2011 - 03:44:46 PST)
[AMBER] GPU vs CPU test
(Thu Jan 27 2011 - 07:06:29 PST)
[AMBER] Amber11 using CUDA-enabled GPUs
(Tue Jan 18 2011 - 11:31:42 PST)
Millen, Andrea
Re: [AMBER] Torsional parameters for S-C-C-N bond
(Tue Jan 18 2011 - 10:20:12 PST)
[AMBER] Torsional parameters for S-C-C-N bond
(Mon Jan 17 2011 - 15:45:39 PST)
mish
Re: [AMBER] QM/MM-GBSA calculation : No convergence in SCF after 1000 steps.
(Fri Jan 28 2011 - 23:32:19 PST)
[AMBER] QM/MM-GBSA calculation : No convergence in SCF after 1000 steps.
(Fri Jan 28 2011 - 03:31:53 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 09:22:30 PST)
Re: [AMBER] MMPBSA.py.MPI - Output discrepancies
(Tue Jan 04 2011 - 02:52:47 PST)
[AMBER] How to setup QM/MM-GBSA calculation ?
(Mon Jan 03 2011 - 09:35:21 PST)
[AMBER] Progress of calculation in MMPBSA.py.MPI
(Mon Jan 03 2011 - 04:21:42 PST)
Nadine Utz
Re: [AMBER] REMD equilibration restart
(Mon Jan 31 2011 - 09:28:43 PST)
nicholus bhattacharjee
[AMBER] Monte Carlo Steps in Constant pH simulation
(Wed Jan 12 2011 - 02:27:42 PST)
Re: [AMBER] Heating the system from 100K to 300K
(Fri Jan 07 2011 - 21:02:31 PST)
[AMBER] Heating the system from 100K to 300K
(Fri Jan 07 2011 - 00:44:38 PST)
Oliver Grant
Re: [AMBER] Fwd: Query regarding unusual water box in vmd
(Tue Jan 25 2011 - 04:10:48 PST)
[AMBER] bad atom type: IP MMPBSA.py sodium Na+ ion [SOLVED]
(Fri Jan 14 2011 - 03:03:30 PST)
Re: [AMBER] Analyzing module for the glycosylations in glyco-protein using AMBER
(Thu Jan 13 2011 - 08:37:36 PST)
peker milas
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 12:29:28 PST)
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 10:56:55 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Mon Jan 31 2011 - 05:44:08 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Sat Jan 29 2011 - 15:08:41 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Sat Jan 29 2011 - 14:59:51 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Thu Jan 27 2011 - 20:38:57 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 10:28:55 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 08:09:42 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 07:07:31 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 22:07:34 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 21:41:36 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 16:06:08 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 15:32:38 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 14:30:53 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 07:28:26 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 05:28:06 PST)
Re: [AMBER] NaN error in .rst files
(Mon Jan 24 2011 - 21:30:03 PST)
[AMBER] NaN error in .rst files
(Mon Jan 24 2011 - 14:42:22 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 20:04:48 PST)
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 06:58:28 PST)
Re: [AMBER] AMBER
(Tue Jan 04 2011 - 22:15:08 PST)
Re: [AMBER] AMBER
(Tue Jan 04 2011 - 20:48:55 PST)
Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied)
(Mon Jan 03 2011 - 07:39:46 PST)
piotrek.vega.umcs.lublin.pl
Re: [AMBER] problem in minimization with POL3
(Mon Jan 31 2011 - 08:09:47 PST)
[AMBER] problem in minimization with POL3
(Fri Jan 28 2011 - 11:01:38 PST)
poll.chemie.uni-hamburg.de
Re: [AMBER] Query regarding parmchk
(Wed Jan 26 2011 - 08:11:05 PST)
[AMBER] Query regarding parmchk
(Wed Jan 26 2011 - 01:49:57 PST)
Pooja Khurana
[AMBER] Determining rings in a molecule
(Sat Jan 01 2011 - 01:51:14 PST)
Purisima, Enrico
Re: [AMBER] about the Sietraj
(Fri Jan 07 2011 - 13:23:21 PST)
Raman Parkesh
Re: [AMBER] AMBER
(Tue Jan 04 2011 - 20:29:36 PST)
Renata KWIECIEN
Re: [AMBER] Is there any Amber training programm in Europe?
(Wed Jan 05 2011 - 02:46:44 PST)
Rilei Yu
[AMBER] Mutational energy on the protein
(Sat Jan 08 2011 - 23:21:07 PST)
Roman Osman
Re: [AMBER] Mutational energy on the protein
(Sun Jan 09 2011 - 08:22:07 PST)
Ross Walker
Re: [AMBER] sander on amber12
(Sun Jan 30 2011 - 21:41:22 PST)
Re: [AMBER] Display CPU time in mdout file
(Fri Jan 28 2011 - 10:42:56 PST)
Re: [AMBER] sander on amber12
(Fri Jan 28 2011 - 07:30:59 PST)
Re: [AMBER] Display CPU time in mdout file
(Fri Jan 28 2011 - 07:27:30 PST)
Re: [AMBER] NaN error in .rst files - A request for some 'Clarity'
(Thu Jan 27 2011 - 18:26:48 PST)
Re: [AMBER] NaN error in .rst files - UPDATE
(Thu Jan 27 2011 - 18:20:42 PST)
Re: [AMBER] GPU vs CPU test
(Thu Jan 27 2011 - 08:46:17 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 22:59:31 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 22:51:11 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 22:46:15 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 19:05:00 PST)
Re: [AMBER] NaN error in .rst files
(Wed Jan 26 2011 - 08:45:07 PST)
Re: [AMBER] Problems with TIP5P water
(Tue Jan 25 2011 - 09:18:21 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 08:36:44 PST)
Re: [AMBER] Problems with TIP5P water
(Tue Jan 25 2011 - 08:31:53 PST)
Re: [AMBER] NaN error in .rst files
(Tue Jan 25 2011 - 07:10:44 PST)
Re: [AMBER] NaN error in .rst files
(Mon Jan 24 2011 - 21:45:04 PST)
Re: [AMBER] NaN error in .rst files
(Mon Jan 24 2011 - 19:54:03 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA - strange reproducable error
(Sat Jan 22 2011 - 12:24:33 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 18:02:14 PST)
Re: [AMBER] NaN error on traj and output with AMBER CUDA
(Thu Jan 20 2011 - 16:54:42 PST)
Re: [AMBER] Amber11 using CUDA-enabled GPUs
(Tue Jan 18 2011 - 15:35:54 PST)
Re: [AMBER] Different Versions of Amber: Comparable results?
(Tue Jan 11 2011 - 12:45:17 PST)
Re: [AMBER] QMMM-IGB=2
(Tue Jan 11 2011 - 09:58:17 PST)
[AMBER] GPU Code Update
(Sat Jan 08 2011 - 08:57:28 PST)
Re: [AMBER] Amber 11 - Bugfix 9
(Thu Jan 06 2011 - 13:26:35 PST)
Re: [AMBER] Is there any Amber training programm in Europe?
(Wed Jan 05 2011 - 08:09:58 PST)
Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied)
(Mon Jan 03 2011 - 10:17:21 PST)
Re: [AMBER] calculations failed on GPU with ntr=1 (with bugfix 11 applied)
(Sun Jan 02 2011 - 09:17:32 PST)
Sangita Kachhap
Re: [AMBER] REMD equilibration restart
(Mon Jan 31 2011 - 08:39:29 PST)
[AMBER] REMD equilibration restart
(Sat Jan 29 2011 - 23:45:45 PST)
Re: [AMBER] Query regarding NVT ensemble with less restraint on solute
(Sat Jan 29 2011 - 01:08:49 PST)
Re: [AMBER] conformation search
(Thu Jan 27 2011 - 08:29:52 PST)
Re: [AMBER] conformation search
(Thu Jan 27 2011 - 08:10:09 PST)
[AMBER] conformation search
(Thu Jan 27 2011 - 06:26:23 PST)
Re: [AMBER] Problem regarding Same coordinate for two atoms
(Sat Jan 22 2011 - 02:49:37 PST)
[AMBER] missing parameter not present in antechamber generated frcmod
(Wed Jan 19 2011 - 09:42:20 PST)
Re: [AMBER] REMD maximum temperature
(Mon Jan 17 2011 - 10:09:00 PST)
Re: [AMBER] REMD maximum temperature
(Thu Jan 13 2011 - 20:23:42 PST)
[AMBER] REMD maximum temperature
(Thu Jan 13 2011 - 10:30:32 PST)
Re: [AMBER] SGLD
(Wed Jan 12 2011 - 10:21:03 PST)
[AMBER] SGLD
(Wed Jan 12 2011 - 09:05:11 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 11:59:32 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 08:59:20 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 07:03:38 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 01:45:22 PST)
Re: [AMBER] how to add phosphate group in protein
(Sat Jan 08 2011 - 01:32:25 PST)
Re: [AMBER] H-bond analysis interpratation
(Wed Jan 05 2011 - 20:47:14 PST)
Re: [AMBER] H-bond analysis interpratation
(Wed Jan 05 2011 - 03:40:56 PST)
Re: [AMBER] H-bond analysis interpratation
(Tue Jan 04 2011 - 10:09:38 PST)
[AMBER] H-bond analysis interpratation
(Mon Jan 03 2011 - 19:57:44 PST)
[AMBER] H-bond analysis
(Sat Jan 01 2011 - 11:04:47 PST)
Scott Le Grand
Re: [AMBER] GPU vs CPU test
(Thu Jan 27 2011 - 13:12:48 PST)
Re: [AMBER] GPU vs CPU test
(Thu Jan 27 2011 - 13:19:38 PST)
Sergio R Aragon
Re: [AMBER] Ptraj for diffusion coefficient of water
(Fri Jan 21 2011 - 15:10:19 PST)
Re: [AMBER] Drifting RMSD
(Fri Jan 07 2011 - 10:57:56 PST)
setyanto md
Re: [AMBER] sander on amber12
(Sun Jan 30 2011 - 21:09:59 PST)
[AMBER] sander on amber12
(Fri Jan 28 2011 - 02:36:59 PST)
Shesh Nath
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 22:36:10 PST)
[AMBER] AMBER
(Mon Jan 17 2011 - 20:29:49 PST)
Re: [AMBER] AMBER
(Mon Jan 17 2011 - 19:55:50 PST)
[AMBER] AMBER
(Sun Jan 16 2011 - 20:38:45 PST)
[AMBER] amber
(Wed Jan 12 2011 - 22:27:14 PST)
Re: [AMBER] Amber
(Tue Jan 11 2011 - 20:06:57 PST)
[AMBER] Amber
(Mon Jan 10 2011 - 20:19:19 PST)
Re: [AMBER] Amber
(Sun Jan 09 2011 - 21:19:22 PST)
[AMBER] Amber
(Sat Jan 08 2011 - 01:08:25 PST)
Re: [AMBER] AMBER
(Tue Jan 04 2011 - 22:25:48 PST)
Re: [AMBER] AMBER
(Tue Jan 04 2011 - 22:04:57 PST)
[AMBER] AMBER
(Tue Jan 04 2011 - 20:21:53 PST)
Siavoush Dastmalchi
[AMBER] PowerEdge M710 with Intel Xeon
(Thu Jan 13 2011 - 03:11:17 PST)
Siti Mohamad
Re: [AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.3
(Tue Jan 25 2011 - 01:09:34 PST)
[AMBER] Compiling Ambertools 1.4 on MacBook SnowLeopard10.6.3
(Mon Jan 24 2011 - 19:52:44 PST)
[AMBER] RMSD and reference structure
(Mon Jan 17 2011 - 20:45:28 PST)
stefano_elli.libero.it
[AMBER] Disactivation torsional potential term in amber-NAMD
(Tue Jan 11 2011 - 15:49:58 PST)
steinbrt.rci.rutgers.edu
Re: [AMBER] TI calculation: viewing lambda trajectories that are not 0 or 1 - (writing parm files)
(Thu Jan 06 2011 - 02:36:49 PST)
Re: [AMBER] where are the parameters controlling the cis/trans configuration of Proline ?
(Fri Dec 31 2010 - 21:12:13 PST)
Stephane Abel
Re: [AMBER] Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 07:32:42 PST)
[AMBER] Dihedral parameters for TFE with GAFF
(Fri Jan 21 2011 - 06:51:04 PST)
subrata paul
Re: [AMBER] urea force field
(Fri Jan 28 2011 - 04:14:49 PST)
[AMBER] urea force field
(Thu Jan 27 2011 - 04:01:05 PST)
Re: [AMBER] trehalose concentation
(Tue Jan 25 2011 - 01:40:24 PST)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 23:18:57 PST)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 06:49:08 PST)
Re: [AMBER] trehalose concentation
(Mon Jan 24 2011 - 06:47:45 PST)
[AMBER] trehalose concentation
(Sun Jan 23 2011 - 21:58:36 PST)
Re: [AMBER] error in prmtop,inpcrd
(Sun Jan 23 2011 - 21:47:57 PST)
Re: [AMBER] error in prmtop,inpcrd
(Sun Jan 23 2011 - 20:35:56 PST)
[AMBER] error in prmtop,inpcrd
(Sat Jan 22 2011 - 06:14:21 PST)
[AMBER] concentration
(Thu Jan 20 2011 - 07:29:45 PST)
[AMBER] rdf
(Tue Jan 18 2011 - 02:44:59 PST)
Re: [AMBER] water simulation
(Mon Jan 10 2011 - 20:39:56 PST)
[AMBER] water simulation
(Mon Jan 10 2011 - 06:21:38 PST)
[AMBER] rdf
(Wed Jan 05 2011 - 05:18:31 PST)
sunita gupta
Re: [AMBER] Query regarding restrain during minimization
(Mon Jan 24 2011 - 01:26:53 PST)
Thomas Cheatham
Re: [AMBER] Ptraj: Hbond and Bfactor analyses
(Mon Jan 24 2011 - 15:04:14 PST)
Thomas Cheatham III
Re: [AMBER] Ptraj: Hbond and Bfactor analyses
(Wed Jan 26 2011 - 09:21:54 PST)
Re: [AMBER] rdf
(Tue Jan 18 2011 - 11:06:57 PST)
Re: [AMBER] Drifting RMSD
(Fri Jan 07 2011 - 11:00:48 PST)
Re: [AMBER] rdf
(Wed Jan 05 2011 - 13:57:45 PST)
Re: [AMBER] heavy atom rms
(Wed Jan 05 2011 - 12:19:52 PST)
Re: [AMBER] H-bond analysis interpratation
(Wed Jan 05 2011 - 12:10:57 PST)
tommaso.casalini.mail.polimi.it
Re: [AMBER] Problems with TIP5P water
(Wed Jan 26 2011 - 02:21:40 PST)
Re: [AMBER] Problems with TIP5P water
(Tue Jan 25 2011 - 08:55:32 PST)
[AMBER] Problems with TIP5P water
(Tue Jan 25 2011 - 08:09:09 PST)
Re: [AMBER] parametrize perchlorate
(Fri Jan 21 2011 - 08:26:05 PST)
[AMBER] Density of a solution water/propylene glycol
(Wed Jan 19 2011 - 03:34:23 PST)
tsurma.umich.edu
Re: [AMBER] parmchk
(Wed Jan 12 2011 - 10:41:03 PST)
Re: [AMBER] parmchk
(Wed Jan 12 2011 - 10:40:13 PST)
[AMBER] parmchk
(Wed Jan 12 2011 - 09:55:14 PST)
vani panguluri
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 11:15:29 PST)
Re: [AMBER] Doubts in the installation of Amber11
(Mon Jan 31 2011 - 10:48:03 PST)
Vijay Manickam Achari
[AMBER] installing ambertools1.4
(Fri Jan 28 2011 - 01:40:45 PST)
Vlad Cojocaru
[AMBER] sander.MPI compiled with mvapich2 fails to exit upon completion
(Wed Jan 05 2011 - 09:44:44 PST)
Wei Huang
Re: [AMBER] Problem in using MMPBSA.py with Amber10
(Mon Jan 03 2011 - 11:58:15 PST)
[AMBER] Problem in using MMPBSA.py with Amber10
(Mon Jan 03 2011 - 08:52:38 PST)
xuemeiwang1103
Re: [AMBER] about the Sietraj
(Wed Jan 05 2011 - 05:03:17 PST)
xueqin pang
[AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
(Tue Jan 11 2011 - 08:22:26 PST)
Re: [AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
(Mon Jan 10 2011 - 07:08:31 PST)
[AMBER] problem with amber11 dcd file when runing a 20ns MD at a time
(Mon Jan 10 2011 - 05:04:12 PST)
Ye MEI
[AMBER] rmsf byres for crystal structure
(Tue Jan 11 2011 - 06:22:36 PST)
Yubo Fan
Re: [AMBER] compilation failure of amber 10
(Thu Jan 13 2011 - 18:42:13 PST)
[AMBER] compilation failure of amber 10
(Thu Jan 13 2011 - 15:01:25 PST)
[AMBER] compile Amber 11 on IBM Power 7
(Wed Jan 05 2011 - 06:07:56 PST)
zhihong ke
[AMBER] the INP was not defined in MMPBSA.pl
(Tue Jan 11 2011 - 09:53:59 PST)
Zhongjie Liang
[AMBER] phosphorylated cysteine
(Sat Jan 15 2011 - 01:38:37 PST)
Zhu, James
[AMBER] AmberTool parallel compiling error
(Mon Jan 31 2011 - 10:32:35 PST)
Re: [AMBER] AMBER11 parallel compiling problem
(Fri Jan 28 2011 - 09:08:36 PST)
[AMBER] AMBER11 parallel compiling problem
(Fri Jan 28 2011 - 08:16:20 PST)
肖正涛
[AMBER] MM-PBSA error about protein + Mg2+
(Thu Jan 27 2011 - 23:47:44 PST)
[AMBER] MM-PBSA error about protein + Mg2+
(Wed Jan 26 2011 - 03:36:29 PST)
Last message date
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Mon Jan 31 2011 - 15:00:07 PST
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: Wed Apr 17 2024 - 05:54:06 PDT
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