Amber Archive Jan 2012 by author
517 messages
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Starting
Sat Dec 31 2011 - 17:30:03 PST,
Ending
Tue Jan 31 2012 - 19:30:02 PST
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abinayar.imsc.res.in
[AMBER] adding hydrogens to protein crystal structure
(Mon Jan 23 2012 - 04:43:45 PST)
Adrian Roitberg
Re: [AMBER] simulation with implicit solvent runs longer than explicit?
(Wed Jan 18 2012 - 14:22:35 PST)
Re: [AMBER] simulation with implicit solvent runs longer than explicit?
(Wed Jan 18 2012 - 14:22:16 PST)
Re: [AMBER] Question related to the B factor
(Mon Jan 16 2012 - 09:54:20 PST)
Re: [AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 09:41:33 PST)
Re: [AMBER] gpu information
(Mon Jan 09 2012 - 07:03:18 PST)
Re: [AMBER] how to set the dist.RST file in SMD using Amber11?
(Tue Jan 03 2012 - 17:50:50 PST)
Re: [AMBER] rounding issue
(Tue Jan 03 2012 - 07:54:37 PST)
Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ?
(Tue Jan 03 2012 - 07:22:59 PST)
Albert
[AMBER] which fitting methods should I use for OPLS FF?
(Fri Jan 20 2012 - 22:23:03 PST)
Aleksandra Skoric
[AMBER] Running NAB
(Thu Jan 12 2012 - 14:25:40 PST)
Amir Marcovitz
[AMBER] creating input files for a protein connected to a fatty acid chain - angle parameters missing error
(Tue Jan 24 2012 - 13:06:37 PST)
Andrew Voronkov
[AMBER] clustering in ptraj doesn't create mdrcd and pdb files
(Mon Jan 30 2012 - 02:29:29 PST)
[AMBER] improper torsions in old prep form
(Tue Jan 10 2012 - 05:09:15 PST)
Anglea A.
[AMBER] energy decomposition equation
(Tue Jan 24 2012 - 08:53:13 PST)
Aron Broom
Re: [AMBER] simulation with implicit solvent runs longer than explicit?
(Wed Jan 18 2012 - 14:01:35 PST)
Re: [AMBER] Gas Phase Simulations in PMEMD
(Fri Jan 13 2012 - 21:21:43 PST)
Re: [AMBER] i7 extreme for Amber GPU computing?
(Tue Jan 10 2012 - 21:14:33 PST)
Re: [AMBER] i7 extreme for Amber GPU computing?
(Tue Jan 10 2012 - 14:39:24 PST)
Re: [AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 10:02:25 PST)
Re: [AMBER] Gas Phase Simulations in PMEMD
(Thu Jan 05 2012 - 13:55:10 PST)
[AMBER] Gas Phase Simulations in PMEMD
(Thu Jan 05 2012 - 13:20:34 PST)
Astrid Maaß
Re: [AMBER] ptaj: RMSD
(Fri Jan 06 2012 - 05:49:13 PST)
Atila Petrosian
Re: [AMBER] analysis in all simulation time
(Wed Jan 25 2012 - 03:09:46 PST)
[AMBER] analysis in all simulation time
(Wed Jan 25 2012 - 02:44:40 PST)
Baptiste Legrand
Re: [AMBER] Minimization problem for a homotrimer of small molecules
(Wed Jan 18 2012 - 06:41:53 PST)
[AMBER] Minimization problem for a homotrimer of small molecules
(Wed Jan 18 2012 - 03:22:36 PST)
Beale, John
[AMBER] Adjusting density
(Wed Jan 18 2012 - 05:28:31 PST)
Ben Ahmady
Re: [AMBER] R.E.D. Server / Antechamber problem
(Fri Jan 06 2012 - 12:28:31 PST)
Re: [AMBER] R.E.D. Server / Antechamber problem
(Thu Jan 05 2012 - 09:53:50 PST)
Ben Roberts
Re: [AMBER] MCPB: error Pls help
(Mon Jan 23 2012 - 12:06:32 PST)
Re: [AMBER] MCPB : addFragment in case of CYM
(Sat Jan 21 2012 - 09:38:50 PST)
Re: [AMBER] Calculate the cosine content of PC
(Sat Jan 21 2012 - 09:31:45 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Sat Jan 21 2012 - 09:23:25 PST)
Re: [AMBER] AMBERTOOL1.5 installation
(Fri Jan 13 2012 - 05:49:35 PST)
Re: [AMBER] tleap/xleap segmenatation fault
(Fri Jan 13 2012 - 05:48:34 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Thu Jan 12 2012 - 07:53:30 PST)
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
(Thu Jan 12 2012 - 05:55:49 PST)
Re: [AMBER] antechamber parameter file issues?
(Mon Jan 09 2012 - 10:24:57 PST)
Re: [AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 09:44:39 PST)
Re: [AMBER] system breaks during simulation
(Sat Jan 07 2012 - 11:28:45 PST)
Re: [AMBER] No leap in ambertool11
(Fri Jan 06 2012 - 08:02:57 PST)
Re: [AMBER] Problem with oxygens bonded to three atoms in metal clusters
(Thu Jan 05 2012 - 13:25:27 PST)
Re: [AMBER] Problem with oxygens bonded to three atoms in metal clusters
(Wed Jan 04 2012 - 14:53:54 PST)
[AMBER] Problem with oxygens bonded to three atoms in metal clusters
(Wed Jan 04 2012 - 14:03:50 PST)
Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error
(Tue Jan 03 2012 - 16:24:18 PST)
Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error
(Tue Jan 03 2012 - 13:10:29 PST)
Bill Miller III
Re: [AMBER] bad atom type: f
(Wed Jan 11 2012 - 09:08:14 PST)
Bill Ross
Re: [AMBER] fortran error during installation
(Mon Jan 30 2012 - 17:27:26 PST)
Re: [AMBER] syntax error in ambpdb
(Sun Jan 29 2012 - 11:40:13 PST)
Re: [AMBER] Editing structure via Xleap
(Sun Jan 29 2012 - 11:07:57 PST)
Re: [AMBER] velocities in restart files taken from ptraj
(Tue Jan 24 2012 - 21:10:40 PST)
Re: [AMBER] velocities in restart files taken from ptraj
(Tue Jan 24 2012 - 16:29:05 PST)
Re: [AMBER] Question related to the B factor
(Mon Jan 16 2012 - 11:46:27 PST)
Re: [AMBER] Question related to the B factor
(Sat Jan 14 2012 - 11:25:36 PST)
Re: [AMBER] improper torsions in old prep form
(Tue Jan 10 2012 - 12:00:52 PST)
bin wang
[AMBER] Cannot find $AMBERHOME/test/antechamber
(Wed Jan 25 2012 - 13:28:03 PST)
Bing Xiong
Re: [AMBER] free energy calculation: turn off the VDW interactionbetween ligand and protein
(Tue Jan 03 2012 - 16:21:49 PST)
Brian Radak
Re: [AMBER] Can I set the direction of the pulling force?
(Sat Jan 28 2012 - 14:52:20 PST)
Re: [AMBER] Can I set the direction of the pulling force?
(Sat Jan 28 2012 - 14:24:04 PST)
Re: [AMBER] Splitting cyclic molecule into QM and MM parts
(Sat Jan 28 2012 - 13:50:34 PST)
Re: [AMBER] Splitting cyclic molecule into QM and MM parts
(Fri Jan 27 2012 - 07:51:09 PST)
Re: [AMBER] Adjusting density
(Wed Jan 18 2012 - 05:45:42 PST)
Re: [AMBER] What is the parameters for Mg2+?
(Mon Jan 16 2012 - 20:08:30 PST)
Re: [AMBER] Problem with oxygens bonded to three atoms in metal clusters
(Thu Jan 05 2012 - 13:00:32 PST)
Re: [AMBER] Origin of calculated system temperature (in mdout file)
(Thu Jan 05 2012 - 12:50:10 PST)
bxiong
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Wed Jan 04 2012 - 16:31:32 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Sun Jan 01 2012 - 22:32:53 PST)
Carlos Simmerling
Re: [AMBER] PES for dialanine
(Fri Jan 13 2012 - 06:32:46 PST)
Carlos Sosa
[AMBER] [qm2_pm6_hof_module.o] Error 1
(Tue Jan 24 2012 - 14:11:51 PST)
case
Re: [AMBER] ptraj.MPI
(Tue Jan 31 2012 - 18:35:32 PST)
Re: [AMBER] makeDIST_RST command problem
(Tue Jan 31 2012 - 18:33:47 PST)
Re: [AMBER] fortran error during installation
(Tue Jan 31 2012 - 18:28:59 PST)
Re: [AMBER] syntax error in ambpdb
(Sun Jan 29 2012 - 09:05:23 PST)
Re: [AMBER] problem with SASA calculation
(Sat Jan 28 2012 - 09:43:58 PST)
Re: [AMBER] problem with SASA calculation
(Sat Jan 28 2012 - 06:47:57 PST)
Re: [AMBER] Editing structure via Xleap
(Sat Jan 28 2012 - 06:39:31 PST)
Re: [AMBER] [qm2_pm6_hof_module.o] Error 1
(Wed Jan 25 2012 - 04:52:10 PST)
Re: [AMBER] installation
(Sun Jan 22 2012 - 12:36:00 PST)
Re: [AMBER] :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1]
(Tue Jan 17 2012 - 18:14:10 PST)
Re: [AMBER] antechamber parameter file issues?
(Sun Jan 15 2012 - 08:33:34 PST)
Re: [AMBER] antechamber parameter file issues?
(Sat Jan 14 2012 - 14:01:36 PST)
Re: [AMBER] Question related to the Force Field and water
(Sat Jan 14 2012 - 06:07:03 PST)
Re: [AMBER] antechamber parameter file issues?
(Fri Jan 13 2012 - 18:46:00 PST)
Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ?
(Mon Jan 02 2012 - 19:38:18 PST)
Re: [AMBER] Chloroform in Amber, a rigid model?
(Mon Jan 02 2012 - 19:36:39 PST)
Re: [AMBER-Developers] [AMBER] Using antechamber -Heme molecule
(Mon Jan 02 2012 - 06:20:19 PST)
Cenk \(Jenk\) Andac
Re: [AMBER] nmode error
(Wed Jan 18 2012 - 05:19:42 PST)
Charles Johnson
[AMBER] SANDER NMR violations
(Thu Jan 05 2012 - 13:40:21 PST)
Chinh Su Tran To
Re: [AMBER] AMBER11, pmemd.cuda: the system crashed.
(Thu Jan 12 2012 - 21:23:57 PST)
Re: [AMBER] AMBER11, pmemd.cuda: the system crashed.
(Wed Jan 11 2012 - 00:04:48 PST)
Chris Bryant
Re: [AMBER] ACE and NME caps
(Thu Jan 19 2012 - 06:35:30 PST)
Re: [AMBER] ACE and NME caps
(Wed Jan 18 2012 - 11:18:42 PST)
[AMBER] ACE and NME caps
(Fri Jan 13 2012 - 11:53:57 PST)
[AMBER] Deleting Cymal-6 from PDB
(Wed Jan 04 2012 - 10:20:52 PST)
colvin
Re: [AMBER] chamber-fortran runtime error
(Wed Jan 04 2012 - 01:23:45 PST)
Cristina Airoldi
Re: [AMBER] Problem with xleap installation
(Fri Jan 13 2012 - 06:51:20 PST)
Re: [AMBER] Problem with xleap installation
(Fri Jan 13 2012 - 05:31:23 PST)
Re: [AMBER] Problem with xleap installation
(Fri Jan 13 2012 - 02:55:09 PST)
[AMBER] Problem with xleap installation
(Fri Jan 13 2012 - 02:20:12 PST)
Daniel Roe
Re: [AMBER] problem with SASA calculation
(Sat Jan 28 2012 - 07:29:22 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 13:22:11 PST)
Re: [AMBER] superimpose on first snapshot
(Mon Jan 23 2012 - 08:02:31 PST)
Re: [AMBER] adding hydrogens to protein crystal structure
(Mon Jan 23 2012 - 06:22:58 PST)
Re: [AMBER] MD trajectory extraction using ptraj
(Fri Jan 20 2012 - 07:50:39 PST)
Re: [AMBER] nab string functions
(Sun Jan 15 2012 - 17:51:03 PST)
Re: [AMBER] nab string functions
(Sun Jan 15 2012 - 16:55:33 PST)
Re: [AMBER] PES for dialanine
(Fri Jan 13 2012 - 05:15:30 PST)
Re: [AMBER] closest water
(Thu Jan 12 2012 - 10:21:16 PST)
Daniel Sindhikara
Re: [AMBER] md.crd file is very large!
(Mon Jan 23 2012 - 01:18:24 PST)
Re: [AMBER] md.crd file is very large!
(Mon Jan 23 2012 - 00:32:54 PST)
Re: [AMBER] Problem with clashing solvent molecules with solvateoct
(Thu Jan 05 2012 - 21:48:16 PST)
Re: [AMBER] Solvation of a system in AMBER11.
(Thu Jan 05 2012 - 16:32:15 PST)
Re: [AMBER] Solvation of a system in AMBER11.
(Wed Jan 04 2012 - 20:39:55 PST)
Re: [AMBER] Regarding solvating a protein using amber
(Sun Jan 01 2012 - 22:30:50 PST)
Re: [AMBER] Solvate a system in AMBER 11.
(Sat Dec 31 2011 - 17:27:32 PST)
David A Case
Re: [AMBER] Ambiguous C0 atom type
(Tue Jan 31 2012 - 06:45:46 PST)
Re: [AMBER] makeDIST_RST command problem
(Tue Jan 31 2012 - 06:35:39 PST)
Re: [AMBER] ptraj.MPI
(Tue Jan 31 2012 - 05:03:27 PST)
Re: [AMBER] Problem during pnetcdf build on CentOS 5
(Tue Jan 31 2012 - 05:01:46 PST)
Re: [AMBER] AMBER9
(Tue Jan 31 2012 - 04:51:06 PST)
Re: [AMBER] makeDIST_RST command problem
(Tue Jan 31 2012 - 04:47:42 PST)
Re: [AMBER] makeDIST_RST command problem
(Mon Jan 30 2012 - 14:37:28 PST)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Mon Jan 30 2012 - 14:32:09 PST)
Re: [AMBER] Editing structure via Xleap
(Fri Jan 27 2012 - 12:21:18 PST)
Re: [AMBER] makeDIST_RST command problem
(Fri Jan 27 2012 - 11:58:58 PST)
Re: [AMBER] makeDIST_RST command problem
(Thu Jan 26 2012 - 13:34:51 PST)
Re: [AMBER] installation of sander.MPI
(Thu Jan 26 2012 - 07:20:24 PST)
Re: [AMBER] positive van der Waal energy and comparison
(Thu Jan 26 2012 - 05:13:39 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Thu Jan 26 2012 - 05:07:41 PST)
Re: [AMBER] solvation in a cubic box
(Wed Jan 25 2012 - 06:39:18 PST)
Re: [AMBER] anal in parallel
(Wed Jan 25 2012 - 04:50:47 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Thu Jan 19 2012 - 12:53:25 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 19 2012 - 11:06:04 PST)
Re: [AMBER] error message for installing amber 10
(Thu Jan 19 2012 - 06:15:10 PST)
Re: [AMBER] amber hangs on minimization
(Thu Jan 19 2012 - 06:12:12 PST)
Re: [AMBER] error message for installing amber 10
(Thu Jan 19 2012 - 05:16:03 PST)
Re: [AMBER] amber hangs on minimization
(Thu Jan 19 2012 - 04:49:11 PST)
Re: [AMBER] FW: FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1]
(Thu Jan 19 2012 - 04:43:26 PST)
Re: [AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 12:19:43 PST)
Re: [AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 08:49:28 PST)
Re: [AMBER] nab string functions
(Mon Jan 16 2012 - 05:51:20 PST)
Re: [AMBER] antechamber parameter file issues?
(Fri Jan 13 2012 - 05:12:08 PST)
Re: [AMBER] Amber 11 installation problem
(Wed Jan 11 2012 - 04:34:56 PST)
Re: [AMBER] installation amber10
(Tue Jan 10 2012 - 07:01:28 PST)
Re: [AMBER] improper torsions in old prep form
(Tue Jan 10 2012 - 06:59:28 PST)
Re: [AMBER] PMEMD installation error
(Mon Jan 09 2012 - 05:52:19 PST)
David A. Case
Re: [AMBER] installation
(Sat Jan 07 2012 - 09:51:01 PST)
Re: [AMBER] calculation of spectral density
(Sat Jan 07 2012 - 09:46:56 PST)
Re: [AMBER] SANDER NMR violations
(Sat Jan 07 2012 - 09:44:03 PST)
Re: [AMBER] Origin of calculated system temperature (in mdout file)
(Sat Jan 07 2012 - 09:39:14 PST)
Dean Cuebas
Re: [AMBER] Editing structure via Xleap
(Fri Jan 27 2012 - 12:55:31 PST)
Re: [AMBER] antechamber parameter file issues?
(Sat Jan 14 2012 - 11:37:22 PST)
Devlina Chakravarty
[AMBER] Problem with generating topology file using tleap
(Thu Jan 05 2012 - 00:19:14 PST)
Dian Jiao
[AMBER] antechamber doesn't create mol2 file
(Mon Jan 30 2012 - 22:01:27 PST)
Dmitry Mukha
Re: [AMBER] rounding issue
(Wed Jan 04 2012 - 00:04:21 PST)
Re: [AMBER] rounding issue
(Tue Jan 03 2012 - 08:07:36 PST)
[AMBER] rounding issue
(Tue Jan 03 2012 - 07:49:41 PST)
Dmitry Nilov
Re: [AMBER] Splitting cyclic molecule into QM and MM parts
(Sat Jan 28 2012 - 01:33:53 PST)
[AMBER] Splitting cyclic molecule into QM and MM parts
(Fri Jan 27 2012 - 05:12:33 PST)
Dwight McGee
Re: [AMBER] Steered Molecular Dynamics: some questions
(Tue Jan 31 2012 - 11:15:31 PST)
Re: [AMBER] Steered Molecular Dynamics: some questions
(Tue Jan 24 2012 - 18:06:57 PST)
Elisa Frezza
Re: [AMBER] gpu information
(Mon Jan 09 2012 - 07:39:43 PST)
[AMBER] gpu information
(Mon Jan 09 2012 - 07:01:14 PST)
Fernando Martín García
[AMBER] Glycine in QM region
(Thu Jan 19 2012 - 02:36:18 PST)
filip fratev
Re: [AMBER] i7 extreme for Amber GPU computing?
(Tue Jan 10 2012 - 15:29:38 PST)
Re: [AMBER] i7 extreme for Amber GPU computing?
(Tue Jan 10 2012 - 15:24:14 PST)
Francesco Oteri
Re: [AMBER] system breaks during simulation
(Sat Jan 07 2012 - 11:29:44 PST)
FyD
Re: [AMBER] antechamber doesn't create mol2 file
(Tue Jan 31 2012 - 00:06:59 PST)
Re: [AMBER] Preparation of the topology file by means of Antechamber
(Mon Jan 30 2012 - 23:58:32 PST)
Re: [AMBER] ACE and NME caps
(Mon Jan 30 2012 - 23:48:25 PST)
Re: [AMBER] loading of fullerene2160
(Sun Jan 29 2012 - 22:26:59 PST)
Re: [AMBER] loading of fullerene2160
(Sun Jan 29 2012 - 10:09:04 PST)
Re: [AMBER] Editing structure via Xleap
(Sat Jan 28 2012 - 09:03:28 PST)
Re: [AMBER] Editing structure via Xleap
(Fri Jan 27 2012 - 23:19:35 PST)
Re: [AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file
(Thu Jan 26 2012 - 00:06:21 PST)
Re: [AMBER] peptide+sugar
(Wed Jan 25 2012 - 07:22:05 PST)
Re: [AMBER] creating input files for a protein connected to a fatty acid chain - angle parameters missing error
(Tue Jan 24 2012 - 23:42:09 PST)
Re: [AMBER] ACE and NME caps
(Tue Jan 24 2012 - 03:08:03 PST)
Re: [AMBER] [q4md-fft] which fitting methods should I use for OPLS FF?
(Sat Jan 21 2012 - 09:03:37 PST)
Re: [AMBER] ACE and NME caps
(Thu Jan 19 2012 - 00:50:30 PST)
Re: [AMBER] ACE and NME caps
(Wed Jan 18 2012 - 23:13:23 PST)
Re: [AMBER] ACE and NME caps
(Wed Jan 18 2012 - 22:12:40 PST)
Re: [AMBER] antechamber parameter file issues?
(Sun Jan 15 2012 - 02:31:38 PST)
Re: [AMBER] antechamber parameter file issues?
(Sun Jan 15 2012 - 02:17:22 PST)
Re: [AMBER] ACE and NME caps
(Fri Jan 13 2012 - 23:27:59 PST)
Re: [AMBER] antechamber parameter file issues?
(Thu Jan 12 2012 - 12:49:38 PST)
[AMBER] Fwd: Re: [q4md-fft] When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar
(Thu Jan 12 2012 - 09:57:01 PST)
Re: [AMBER] R.E.D. Server / Antechamber problem
(Sat Jan 07 2012 - 00:32:14 PST)
Re: [AMBER] R.E.D. Server / Antechamber problem
(Fri Jan 06 2012 - 00:52:59 PST)
g t
Re: [AMBER] Fwd: Re: [q4md-fft] When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar
(Thu Jan 12 2012 - 10:14:30 PST)
[AMBER] q4md: When using red, it outputs incorrect primary amine geometry as tetrahedral instead of trigonal planar
(Thu Jan 12 2012 - 03:23:51 PST)
Ganesh Kamath
[AMBER] Conversion of binary velocity files to pdb style
(Tue Jan 17 2012 - 09:22:14 PST)
gargi borgohai
[AMBER] loading of fullerene2160
(Sun Jan 29 2012 - 20:49:41 PST)
[AMBER] loading of fullerene2160
(Sat Jan 28 2012 - 09:49:03 PST)
George M Giambasu
Re: [AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 10:26:26 PST)
Re: [AMBER] Gas Phase Simulations in PMEMD
(Thu Jan 05 2012 - 13:29:47 PST)
George Tzotzos
[AMBER] SMD: Segmentation fault
(Tue Jan 31 2012 - 10:32:28 PST)
Re: [AMBER] Steered Molecular Dynamics: some questions
(Tue Jan 31 2012 - 09:44:23 PST)
Re: [AMBER] Constant pH
(Tue Jan 31 2012 - 05:08:20 PST)
[AMBER] Constant pH
(Tue Jan 31 2012 - 04:26:04 PST)
Re: [AMBER] Steered Molecular Dynamics: some questions
(Tue Jan 24 2012 - 23:39:21 PST)
[AMBER] Steered Molecular Dynamics: some questions
(Tue Jan 24 2012 - 05:40:57 PST)
Re: [AMBER] closest water
(Thu Jan 12 2012 - 10:57:28 PST)
[AMBER] closest water
(Thu Jan 12 2012 - 09:29:18 PST)
Re: [AMBER] ptaj: RMSD
(Fri Jan 06 2012 - 10:15:16 PST)
[AMBER] ptaj: RMSD
(Wed Jan 04 2012 - 10:15:38 PST)
Gonzalo Jimenez Oses
[AMBER] Problem with clashing solvent molecules with solvateoct
(Thu Jan 05 2012 - 09:07:33 PST)
Hannes Loeffler
Re: [AMBER] chamber segfault
(Wed Jan 18 2012 - 06:38:32 PST)
[AMBER] chamber segfault
(Wed Jan 18 2012 - 02:44:12 PST)
Harald Lanig
[AMBER] Molecular Modelling Workshop 2012 in Erlangen, Germany
(Mon Jan 23 2012 - 08:15:17 PST)
hari krishna
Re: [AMBER] PMEMD installation error
(Mon Jan 09 2012 - 21:30:30 PST)
[AMBER] PMEMD installation error
(Tue Jan 03 2012 - 21:05:45 PST)
Hector A. Baldoni
Re: [AMBER] calculation of spectral density
(Sat Jan 07 2012 - 15:23:01 PST)
Hevener, Kirk
Re: [AMBER] AmberTools Installation Error
(Thu Jan 19 2012 - 06:00:40 PST)
[AMBER] AmberTools Installation Error
(Wed Jan 18 2012 - 08:59:15 PST)
Hirdesh Kumar
Re: [AMBER] strip water and save new trajectory
(Sun Jan 15 2012 - 20:36:53 PST)
[AMBER] strip water and save new trajectory
(Sat Jan 14 2012 - 06:27:49 PST)
Re: [AMBER] AMBERTOOL1.5 installation
(Fri Jan 13 2012 - 05:55:07 PST)
[AMBER] AMBERTOOL1.5 installation
(Fri Jan 13 2012 - 00:43:14 PST)
Hugh Heldenbrand
Re: [AMBER] Adjusting density
(Wed Jan 18 2012 - 05:51:04 PST)
Ian Slaymaker
[AMBER] Building Wrapped DNA in NAB
(Fri Jan 27 2012 - 09:56:55 PST)
Irene Newhouse
Re: [AMBER] AmberTools 1.5 & Centos6
(Wed Jan 25 2012 - 09:48:40 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 13:08:10 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 12:01:52 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 11:43:41 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 11:24:34 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 09:22:21 PST)
[AMBER] AmberTools 1.5 & Centos6
(Mon Jan 23 2012 - 11:49:36 PST)
Ismail, Mohd F.
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 12:08:13 PST)
James Starlight
Re: [AMBER] Preparation of the topology file by means of Antechamber
(Mon Jan 30 2012 - 22:11:44 PST)
[AMBER] Preparation of the topology file by means of Antechamber
(Sun Jan 29 2012 - 09:12:21 PST)
Re: [AMBER] Editing structure via Xleap
(Sat Jan 28 2012 - 00:44:11 PST)
[AMBER] Editing structure via Xleap
(Fri Jan 27 2012 - 10:28:06 PST)
Jan-Philip Gehrcke
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Tue Jan 31 2012 - 02:49:47 PST)
[AMBER] Problem during pnetcdf build on CentOS 5
(Tue Jan 31 2012 - 02:47:41 PST)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Mon Jan 30 2012 - 08:21:25 PST)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Fri Jan 27 2012 - 08:06:25 PST)
[AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Fri Jan 27 2012 - 05:51:27 PST)
Re: [AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html
(Fri Jan 13 2012 - 06:46:53 PST)
[AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html
(Fri Jan 13 2012 - 06:34:06 PST)
Re: [AMBER] i7 extreme for Amber GPU computing?
(Wed Jan 11 2012 - 07:51:29 PST)
Re: [AMBER] i7 extreme for Amber GPU computing?
(Wed Jan 11 2012 - 02:05:24 PST)
Re: [AMBER] Origin of calculated system temperature (in mdout file)
(Fri Jan 06 2012 - 07:05:21 PST)
[AMBER] Origin of calculated system temperature (in mdout file)
(Thu Jan 05 2012 - 09:01:56 PST)
Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein
(Tue Jan 03 2012 - 07:45:16 PST)
Jason Swails
Re: [AMBER] ptraj.MPI
(Tue Jan 31 2012 - 19:22:03 PST)
Re: [AMBER] Constant pH
(Tue Jan 31 2012 - 07:14:51 PST)
Re: [AMBER] Constant pH
(Tue Jan 31 2012 - 05:00:15 PST)
Re: [AMBER] fortran error during installation
(Mon Jan 30 2012 - 19:53:15 PST)
Re: [AMBER] Preparation of the topology file by means of Antechamber
(Mon Jan 30 2012 - 07:40:54 PST)
Re: [AMBER] NMODE list index out of range error
(Sat Jan 28 2012 - 07:42:42 PST)
Re: [AMBER] problem with SASA calculation
(Sat Jan 28 2012 - 07:32:56 PST)
Re: [AMBER] Building of Amber/APBS module
(Fri Jan 27 2012 - 13:28:16 PST)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Fri Jan 27 2012 - 10:15:12 PST)
Re: [AMBER] compiler-dependent error: "Invalid atom or grouping specified in restraint."
(Fri Jan 27 2012 - 07:28:24 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 12:12:11 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 10:20:07 PST)
Re: [AMBER] problem python compiling when install AmberTools 1.5
(Thu Jan 26 2012 - 09:04:46 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 06:46:34 PST)
Re: [AMBER] problem python compiling when install AmberTools 1.5
(Thu Jan 26 2012 - 06:45:55 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 05:21:27 PST)
Re: [AMBER] Cannot find $AMBERHOME/test/antechamber
(Wed Jan 25 2012 - 16:56:37 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 12:04:31 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 12:16:22 PST)
Re: [AMBER] Amber11 tests fail
(Wed Jan 25 2012 - 12:07:46 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 11:23:34 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 09:56:13 PST)
Re: [AMBER] velocities in restart files taken from ptraj
(Tue Jan 24 2012 - 20:37:50 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 12:32:05 PST)
Re: [AMBER] energy decomposition equation
(Tue Jan 24 2012 - 10:25:31 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Tue Jan 24 2012 - 10:16:44 PST)
Re: [AMBER] AmberTools 1.5 & Centos6
(Mon Jan 23 2012 - 13:35:43 PST)
Re: [AMBER] md.crd file is very large!
(Mon Jan 23 2012 - 07:22:37 PST)
Re: [AMBER] Amber11 tests fail
(Sat Jan 21 2012 - 07:28:41 PST)
Re: [AMBER] Amber11 tests fail
(Fri Jan 20 2012 - 11:54:14 PST)
Re: [AMBER] Amber11 tests fail
(Fri Jan 20 2012 - 06:20:19 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 19 2012 - 11:33:47 PST)
Re: [AMBER] AmberTools Installation Error
(Thu Jan 19 2012 - 06:45:49 PST)
Re: [AMBER] FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1]
(Wed Jan 18 2012 - 11:43:26 PST)
Re: [AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 10:40:39 PST)
Re: [AMBER] AmberTools Installation Error
(Wed Jan 18 2012 - 10:38:07 PST)
Re: [AMBER] Minimization problem for a homotrimer of small molecules
(Wed Jan 18 2012 - 07:55:09 PST)
Re: [AMBER] Minimization problem for a homotrimer of small molecules
(Wed Jan 18 2012 - 06:08:03 PST)
Re: [AMBER] chamber segfault
(Wed Jan 18 2012 - 06:02:00 PST)
Re: [AMBER] Adjusting density
(Wed Jan 18 2012 - 05:53:06 PST)
Re: [AMBER] mpi4py installation for mmpbsa_py
(Sat Jan 14 2012 - 16:59:34 PST)
Re: [AMBER] water molecules within a distance cutoff; ptraj analysis
(Sat Jan 14 2012 - 06:49:51 PST)
Re: [AMBER] strip water and save new trajectory
(Sat Jan 14 2012 - 06:37:06 PST)
Re: [AMBER] Water considered in Amber11.
(Sat Jan 14 2012 - 06:31:21 PST)
Re: [AMBER] Running NAB
(Thu Jan 12 2012 - 19:32:57 PST)
Re: [AMBER] bad atom type: f
(Wed Jan 11 2012 - 13:38:43 PST)
Re: [AMBER] installation
(Sat Jan 07 2012 - 10:13:29 PST)
Re: [AMBER] Error while compiling AMBER11
(Wed Jan 04 2012 - 12:56:14 PST)
Re: [AMBER] Error while compiling AMBER11
(Wed Jan 04 2012 - 11:57:31 PST)
Re: [AMBER] rounding issue
(Wed Jan 04 2012 - 07:49:13 PST)
Jesper Sørensen
Re: [AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 12:42:58 PST)
Re: [AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 09:17:39 PST)
Re: [AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 08:33:50 PST)
[AMBER] Problem with magnesium ions using FF10 in leap
(Wed Jan 18 2012 - 08:05:56 PST)
Re: [AMBER] What is the parameters for Mg2+?
(Mon Jan 16 2012 - 21:29:35 PST)
Re: [AMBER] What is the parameters for Mg2+?
(Mon Jan 16 2012 - 18:30:58 PST)
Jio M
[AMBER] anal in parallel
(Wed Jan 25 2012 - 02:43:17 PST)
[AMBER] positive van der Waal energy and comparison
(Sat Jan 21 2012 - 02:34:13 PST)
JiYuan Liu
Re: [AMBER] Which method is the best way to solve metalloprotein?MCPB or Only consider Electrostatic and VDW
(Wed Jan 04 2012 - 00:07:08 PST)
john Kerk
Re: [AMBER] md.crd file is very large!
(Mon Jan 23 2012 - 01:10:53 PST)
[AMBER] md.crd file is very large!
(Mon Jan 23 2012 - 00:22:25 PST)
Re: [AMBER] Using glycam06 under Amber8
(Sun Jan 15 2012 - 23:42:00 PST)
[AMBER] Using glycam06 under Amber8
(Sun Jan 15 2012 - 10:45:19 PST)
Jorgen Simonsen
Re: [AMBER] installation of sander.MPI
(Thu Jan 26 2012 - 06:19:16 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 12:38:58 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 12:10:51 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 11:48:16 PST)
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 11:09:46 PST)
[AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 09:18:15 PST)
Re: [AMBER] amber hangs on minimization
(Thu Jan 19 2012 - 05:10:26 PST)
[AMBER] amber hangs on minimization
(Thu Jan 19 2012 - 01:04:08 PST)
Joshua Adelman
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Wed Jan 11 2012 - 10:51:40 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Wed Jan 11 2012 - 08:58:47 PST)
Josmar R. da Rocha
Re: [AMBER] Problem with xleap installation
(Fri Jan 13 2012 - 06:01:23 PST)
[AMBER] Chirality restraints in Simulated Annealing
(Thu Jan 12 2012 - 14:07:38 PST)
kanika singal
Re: [AMBER] MCPB: error Pls help
(Sat Jan 21 2012 - 23:26:48 PST)
[AMBER] MCPB: error Pls help
(Sat Jan 21 2012 - 02:18:56 PST)
[AMBER] MCPB: error Pls help
(Fri Jan 20 2012 - 06:46:27 PST)
[AMBER] MCPB : addFragment in case of CYM
(Tue Jan 17 2012 - 22:50:08 PST)
[AMBER] water molecules within a distance cutoff; ptraj analysis
(Fri Jan 13 2012 - 23:57:14 PST)
[AMBER] clarification regarding the charge on the cluster in MCPB
(Mon Jan 09 2012 - 01:15:49 PST)
Lachele Foley (Lists)
Re: [AMBER] Using glycam06 under Amber8
(Mon Jan 16 2012 - 10:52:14 PST)
Re: [AMBER] Using glycam06 under Amber8
(Sun Jan 15 2012 - 11:07:58 PST)
leila karami
[AMBER] how to obtain prmtop and inpcrd files truely from initial pdb file?
(Tue Jan 31 2012 - 06:09:07 PST)
[AMBER] syntax error in ambpdb
(Sun Jan 29 2012 - 03:01:38 PST)
Lianhu Wei
Re: [AMBER] MD trajectory extraction using ptraj
(Fri Jan 20 2012 - 11:54:56 PST)
Re: [AMBER] MD trajectory extraction using ptraj
(Fri Jan 20 2012 - 09:10:48 PST)
[AMBER] MD trajectory extraction using ptraj
(Fri Jan 20 2012 - 07:25:09 PST)
Lucas A. Defelipe
[AMBER] Error while compiling AMBER11
(Wed Jan 04 2012 - 08:17:30 PST)
M. L. Dodson
Re: [AMBER] nab string functions
(Sun Jan 15 2012 - 17:24:48 PST)
Re: [AMBER] nab string functions
(Sun Jan 15 2012 - 17:17:31 PST)
[AMBER] nab string functions
(Sun Jan 15 2012 - 16:34:33 PST)
Mahendra B Thapa
Re: [AMBER] FW: FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1]
(Wed Jan 18 2012 - 12:10:26 PST)
Re: [AMBER] FW: :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1]
(Wed Jan 18 2012 - 10:25:21 PST)
[AMBER] :How to get 1PLC_mod.pdb from 1PLC.pdb [TUTORIAL A1 - SECTION 1]
(Tue Jan 17 2012 - 14:24:19 PST)
[AMBER] calculation of spectral density
(Thu Jan 05 2012 - 14:51:35 PST)
manikanthan bhavaraju
[AMBER] Upcoming of Amber Workshop in USA
(Fri Jan 13 2012 - 09:45:25 PST)
Marc van der Kamp
Re: [AMBER] temperature and pressure coupling
(Wed Jan 25 2012 - 04:03:29 PST)
Re: [AMBER] analysis in all simulation time
(Wed Jan 25 2012 - 04:00:33 PST)
Re: [AMBER] analysis in all simulation time
(Wed Jan 25 2012 - 02:56:36 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Mon Jan 23 2012 - 06:00:23 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Thu Jan 12 2012 - 07:54:06 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Wed Jan 11 2012 - 08:53:08 PST)
Marek Maly
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Thu Jan 26 2012 - 09:30:53 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Thu Jan 26 2012 - 08:34:59 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Mon Jan 23 2012 - 16:17:13 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Fri Jan 06 2012 - 07:57:52 PST)
Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ?
(Tue Jan 03 2012 - 10:33:43 PST)
[AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ?
(Mon Jan 02 2012 - 17:07:23 PST)
Marina Grabar Branilović
Re: [AMBER] tleap/xleap segmenatation fault
(Mon Jan 16 2012 - 03:13:13 PST)
[AMBER] tleap/xleap segmenatation fault
(Fri Jan 13 2012 - 05:30:21 PST)
Mark Williamson
Re: [AMBER] Issue with HowToCompileAmberTools1.5AndAMBER11WithUbuntu10.04.3LTS.html
(Fri Jan 13 2012 - 06:53:46 PST)
Re: [AMBER] PMEMD parallelization on Ubuntu Lucid
(Mon Jan 09 2012 - 06:52:12 PST)
Martin Peters
Re: [AMBER] MCPB: error Pls help
(Fri Jan 20 2012 - 07:56:45 PST)
Maryam Hamzehee
Re: [AMBER] problem with SASA calculation
(Mon Jan 30 2012 - 03:23:38 PST)
Re: [AMBER] problem with SASA calculation
(Sun Jan 29 2012 - 05:31:15 PST)
[AMBER] problem with SASA calculation
(Sat Jan 28 2012 - 01:21:42 PST)
Massimiliano Porrini
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 11:04:30 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 09:06:34 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 05:27:41 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 26 2012 - 04:03:22 PST)
Re: [AMBER] Amber11 tests fail
(Wed Jan 25 2012 - 11:53:37 PST)
Re: [AMBER] Amber11 tests fail
(Tue Jan 24 2012 - 03:52:46 PST)
Re: [AMBER] Amber11 tests fail
(Sun Jan 22 2012 - 01:56:09 PST)
Re: [AMBER] Amber11 tests fail
(Sat Jan 21 2012 - 04:35:22 PST)
Re: [AMBER] Amber11 tests fail
(Sat Jan 21 2012 - 04:33:50 PST)
Re: [AMBER] Amber11 tests fail
(Fri Jan 20 2012 - 10:17:11 PST)
Re: [AMBER] Amber11 tests fail
(Fri Jan 20 2012 - 05:52:48 PST)
Re: [AMBER] Amber11 tests fail
(Thu Jan 19 2012 - 11:20:44 PST)
[AMBER] Amber11 tests fail
(Thu Jan 19 2012 - 10:05:10 PST)
Matthew Zwier
Re: [AMBER] Review MD sampling techniques
(Thu Jan 26 2012 - 05:20:56 PST)
mehdi bagherpoor
Re: [AMBER] syntax error in ambpdb
(Sun Jan 29 2012 - 08:52:36 PST)
Re: [AMBER] installation
(Sun Jan 22 2012 - 12:45:20 PST)
Meli Massimiliano
Re: [AMBER] rism1d solvent models
(Thu Jan 12 2012 - 09:32:30 PST)
[AMBER] rism1d solvent models
(Thu Jan 12 2012 - 07:27:39 PST)
Mettu, Ramgopal
Re: [AMBER] fortran error during installation
(Tue Jan 31 2012 - 07:36:26 PST)
Re: [AMBER] fortran error during installation
(Mon Jan 30 2012 - 18:35:16 PST)
[AMBER] fortran error during installation
(Mon Jan 30 2012 - 17:16:44 PST)
Michael Petukhov
[AMBER] Ser/Thr phosphorylation support in AMBER-11
(Mon Jan 02 2012 - 09:58:24 PST)
moitrayee.mbu.iisc.ernet.in
[AMBER] problem with ester bond between side chains
(Tue Jan 10 2012 - 02:33:17 PST)
[AMBER] system breaks during simulation
(Sat Jan 07 2012 - 11:20:16 PST)
Muhammad Khaled Tumbi
[AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb
(Tue Jan 17 2012 - 05:12:51 PST)
nicholus bhattacharjee
[AMBER] No leap in ambertool11
(Fri Jan 06 2012 - 05:36:11 PST)
Olena Dobrovolska
Re: [AMBER] makeDIST_RST command problem
(Tue Jan 31 2012 - 07:33:09 PST)
Re: [AMBER] makeDIST_RST command problem
(Tue Jan 31 2012 - 05:03:05 PST)
Re: [AMBER] makeDIST_RST command problem
(Tue Jan 31 2012 - 01:11:24 PST)
Re: [AMBER] makeDIST_RST command problem
(Mon Jan 30 2012 - 08:59:55 PST)
Re: [AMBER] makeDIST_RST command problem
(Fri Jan 27 2012 - 06:00:55 PST)
[AMBER] makeDIST_RST command problem
(Thu Jan 26 2012 - 08:39:05 PST)
Osman, Roman
Re: [AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 10:16:59 PST)
Re: [AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 09:46:55 PST)
[AMBER] Problems with amber topology in NAMD
(Mon Jan 09 2012 - 09:38:11 PST)
Patrick G Blachly
Re: [AMBER] mtkpp: parameters in metals.frcmod
(Tue Jan 10 2012 - 14:52:05 PST)
Per Jr. Greisen
Re: [AMBER] error message for installing amber 10
(Thu Jan 19 2012 - 05:57:04 PST)
[AMBER] error message for installing amber 10
(Thu Jan 19 2012 - 03:46:24 PST)
peter.stauffert.boehringer-ingelheim.com
[AMBER] Building of Amber/APBS module
(Fri Jan 27 2012 - 12:28:52 PST)
pxc.cqu.edu.cn
[AMBER] how to set the dist.RST file in SMD using Amber11?
(Tue Jan 03 2012 - 17:20:56 PST)
Qian Wang
Re: [AMBER] Can I set the direction of the pulling force?
(Sat Jan 28 2012 - 14:37:54 PST)
[AMBER] Can I set the direction of the pulling force?
(Sat Jan 28 2012 - 10:58:36 PST)
R. K. Kar
Re: [AMBER] Amber 11 installation problem
(Wed Jan 11 2012 - 03:50:41 PST)
[AMBER] Amber 11 installation problem
(Wed Jan 11 2012 - 00:19:59 PST)
Raik Grünberg
[AMBER] i7 extreme for Amber GPU computing?
(Tue Jan 10 2012 - 12:34:32 PST)
rainy908
Re: [AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file
(Wed Jan 25 2012 - 11:25:54 PST)
[AMBER] divcon: error while loading shared libraries: libvml.so: cannot open shared object file
(Wed Jan 25 2012 - 11:21:16 PST)
Rajesh Singh
Re: [AMBER] bad atom type: f
(Thu Jan 12 2012 - 08:19:07 PST)
[AMBER] bad atom type: f
(Wed Jan 11 2012 - 08:57:49 PST)
Rajeswari A.
[AMBER] ptraj contacts output query
(Sat Jan 21 2012 - 04:04:41 PST)
Ray Luo, Ph.D.
Re: [AMBER] Problem with PB calculation using ff99SBildn: PB Bomb in pb_aaradi(): No radius assigned for atom
(Thu Jan 05 2012 - 15:01:50 PST)
Ross Walker
Re: [AMBER] installation of sander.MPI
(Wed Jan 25 2012 - 15:10:22 PST)
[AMBER] Workshop and Tutorial Announcement: State-of-the-Art Algorithms for Molecular Dynamics, April 30th to May 4th 2012, Edinburgh UK
(Wed Jan 25 2012 - 11:38:24 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Wed Jan 11 2012 - 10:42:11 PST)
Re: [AMBER] i7 extreme for Amber GPU computing?
(Wed Jan 11 2012 - 07:03:53 PST)
Re: [AMBER] Gas Phase Simulations in PMEMD
(Thu Jan 05 2012 - 14:15:07 PST)
Re: [AMBER] CUDA PMEMD on Longhorn: MPI_Win_free fatal error
(Tue Jan 03 2012 - 13:18:59 PST)
Re: [AMBER] rounding issue
(Tue Jan 03 2012 - 10:50:48 PST)
Ryan Pavlovicz
[AMBER] Problem with PB calculation using ff99SBildn: PB Bomb in pb_aaradi(): No radius assigned for atom
(Thu Jan 05 2012 - 09:53:31 PST)
Sai Kumar Ramadugu
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Tue Jan 31 2012 - 09:16:00 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Mon Jan 30 2012 - 14:14:07 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 25 2012 - 10:14:01 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Tue Jan 24 2012 - 14:58:37 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Thu Jan 19 2012 - 11:22:39 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 18 2012 - 11:14:44 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 18 2012 - 10:43:25 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 18 2012 - 09:32:34 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Thu Jan 12 2012 - 11:06:15 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 04 2012 - 12:27:29 PST)
[AMBER] Free Energy Calculations of Potassium and Chloride
(Tue Jan 03 2012 - 11:58:51 PST)
SANCHEZ MURCIA, PEDRO ALEJANDRO
[AMBER] GBSA decomposition per reside
(Tue Jan 24 2012 - 13:53:09 PST)
[AMBER] GBSA decomposition per reside
(Tue Jan 24 2012 - 13:49:18 PST)
[AMBER] GBSA decomposition per reside
(Tue Jan 24 2012 - 13:48:58 PST)
Sangeetha B
Re: [AMBER] NMODE list index out of range error
(Mon Jan 30 2012 - 20:26:18 PST)
[AMBER] NMODE list index out of range error
(Fri Jan 27 2012 - 22:43:41 PST)
Sangita Kachhap
Re: [AMBER] Problem with generating topology file using tleap
(Thu Jan 05 2012 - 06:41:52 PST)
Scott Le Grand
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Thu Jan 12 2012 - 16:45:50 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Thu Jan 12 2012 - 07:47:47 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Wed Jan 11 2012 - 19:03:17 PST)
Re: [AMBER] combination of CHAMBER prmtop and pmemd.cuda is causing serious instability
(Wed Jan 11 2012 - 16:14:21 PST)
Re: [AMBER] AMBER11, pmemd.cuda: the system crashed.
(Wed Jan 11 2012 - 08:40:03 PST)
Sel Ercan
Re: [AMBER] ptraj.MPI
(Tue Jan 31 2012 - 08:41:13 PST)
[AMBER] ptraj.MPI
(Tue Jan 31 2012 - 03:55:12 PST)
setyanto md
Re: [AMBER] problem python compiling when install AmberTools 1.5
(Thu Jan 26 2012 - 07:13:30 PST)
[AMBER] problem python compiling when install AmberTools 1.5
(Thu Jan 26 2012 - 06:28:18 PST)
shahab shariati
[AMBER] solvation in a cubic box
(Wed Jan 25 2012 - 05:11:49 PST)
[AMBER] temperature and pressure coupling
(Wed Jan 25 2012 - 03:53:45 PST)
Sidney Elmer
Re: [AMBER] velocities in restart files taken from ptraj
(Tue Jan 24 2012 - 17:23:42 PST)
[AMBER] velocities in restart files taken from ptraj
(Tue Jan 24 2012 - 16:14:02 PST)
Simon Becker
Re: [AMBER] superimpose on first snapshot
(Mon Jan 23 2012 - 23:35:37 PST)
[AMBER] superimpose on first snapshot
(Mon Jan 23 2012 - 06:05:03 PST)
Sindrila Dutta banik
[AMBER] Problem related to the order parameter
(Wed Jan 25 2012 - 07:47:23 PST)
[AMBER] Amber for monolayer
(Sat Jan 21 2012 - 19:40:41 PST)
[AMBER] Question related to the B factor
(Mon Jan 16 2012 - 09:43:15 PST)
[AMBER] Question related to the B factor
(Sat Jan 14 2012 - 09:03:19 PST)
[AMBER] Question related to the Force Field and water
(Sat Jan 14 2012 - 00:56:05 PST)
steinbrt.rci.rutgers.edu
Re: [AMBER] how to obtain prmtop and inpcrd files truely from initial pdb file?
(Tue Jan 31 2012 - 07:25:57 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Tue Jan 31 2012 - 00:25:50 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Thu Jan 26 2012 - 09:18:03 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Thu Jan 26 2012 - 07:43:28 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Thu Jan 26 2012 - 07:39:31 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Thu Jan 19 2012 - 02:49:18 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 18 2012 - 10:54:59 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Wed Jan 18 2012 - 10:15:25 PST)
Re: [AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb
(Tue Jan 17 2012 - 06:31:01 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Fri Jan 13 2012 - 05:28:31 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Fri Jan 06 2012 - 08:06:51 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Thu Jan 05 2012 - 01:49:15 PST)
Re: [AMBER] free energy calculation: turn off the VDW interactionbetween ligand and protein
(Wed Jan 04 2012 - 01:45:30 PST)
Re: [AMBER] Free Energy Calculations of Potassium and Chloride
(Tue Jan 03 2012 - 12:37:44 PST)
Re: [AMBER] The per-partes ligand decoupling as the alternative to simultaneous decouplig of all ligand atoms with use of restraints ?
(Tue Jan 03 2012 - 01:26:37 PST)
Re: [AMBER] Ser/Thr phosphorylation support in AMBER-11
(Mon Jan 02 2012 - 10:06:14 PST)
Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein
(Mon Jan 02 2012 - 03:52:27 PST)
subrata paul
[AMBER] installation
(Sun Jan 22 2012 - 08:27:37 PST)
[AMBER] installation amber10
(Tue Jan 10 2012 - 05:46:11 PST)
[AMBER] installation
(Sat Jan 07 2012 - 02:55:05 PST)
Sudarshan Debnath
[AMBER] Water considered in Amber11.
(Sat Jan 14 2012 - 00:44:25 PST)
[AMBER] Solvation of a system in Amber11
(Tue Jan 10 2012 - 22:07:25 PST)
[AMBER] Ambertools installation.
(Thu Jan 05 2012 - 23:10:20 PST)
[AMBER] Solvation of a system in AMBER11.
(Thu Jan 05 2012 - 04:52:07 PST)
[AMBER] Solvation of a system in AMBER11.
(Wed Jan 04 2012 - 20:19:37 PST)
surasak chunsrivirot
Re: [AMBER] Calculate the cosine content of PC
(Thu Jan 26 2012 - 19:57:46 PST)
[AMBER] Calculate the cosine content of PC
(Mon Jan 16 2012 - 02:44:20 PST)
Tales Yuan
Re: [AMBER] Amber 11 installation problem
(Wed Jan 11 2012 - 17:23:51 PST)
Terry
Re: [AMBER] error message for installing amber 10
(Thu Jan 19 2012 - 05:30:17 PST)
Thomas Cheatham
Re: [AMBER] velocities in restart files taken from ptraj
(Tue Jan 24 2012 - 17:28:51 PST)
Thomas Cheatham III
Re: [AMBER] Problem regarding Molecular Dynamics simulation of DNA using Parmbsc0 and ff99sb
(Tue Jan 17 2012 - 14:49:21 PST)
Thomas Exner
[AMBER] Review MD sampling techniques
(Wed Jan 25 2012 - 09:57:55 PST)
Thomas Pochapsky
Re: [AMBER] antechamber parameter file issues?
(Thu Jan 12 2012 - 07:55:24 PST)
Re: [AMBER] antechamber parameter file issues?
(Mon Jan 09 2012 - 11:03:00 PST)
[AMBER] antechamber parameter file issues?
(Mon Jan 09 2012 - 10:15:40 PST)
thomas.fox.boehringer-ingelheim.com
[AMBER] antechamber and parm.frosst
(Fri Jan 27 2012 - 07:19:33 PST)
Tyler Luchko
Re: [AMBER] rism1d solvent models
(Thu Jan 12 2012 - 08:19:19 PST)
Re: [AMBER] Solvation of a system in Amber11
(Tue Jan 10 2012 - 22:38:57 PST)
Re: [AMBER] Ambertools installation.
(Sun Jan 08 2012 - 14:40:24 PST)
Re: [AMBER] Solvation of a system in AMBER11.
(Thu Jan 05 2012 - 16:46:41 PST)
Urszula Uciechowska
[AMBER] AMBER9
(Tue Jan 31 2012 - 00:25:45 PST)
[AMBER] peptide+sugar
(Wed Jan 25 2012 - 04:44:51 PST)
[AMBER] nmode error
(Wed Jan 18 2012 - 03:42:30 PST)
vaibhav dixit
[AMBER] negative DeltaGsolv in MMPBSA
(Thu Jan 19 2012 - 07:49:42 PST)
[AMBER] MMPBSA analysis
(Thu Jan 19 2012 - 04:44:58 PST)
Re: [AMBER] ptaj: RMSD
(Wed Jan 04 2012 - 22:00:31 PST)
Victor Ma
Re: [AMBER] simulation with implicit solvent runs longer than explicit?
(Wed Jan 18 2012 - 14:40:31 PST)
Re: [AMBER] simulation with implicit solvent runs longer than explicit?
(Wed Jan 18 2012 - 14:11:21 PST)
[AMBER] simulation with implicit solvent runs longer than explicit?
(Wed Jan 18 2012 - 13:48:01 PST)
Vlad Cojocaru
[AMBER] mpi4py installation for mmpbsa_py
(Sat Jan 14 2012 - 14:39:58 PST)
Vlastimil Zíma
[AMBER] Ambiguous C0 atom type
(Tue Jan 31 2012 - 05:23:47 PST)
Ye MEI
Re: [AMBER] PES for dialanine
(Fri Jan 13 2012 - 07:11:09 PST)
Re: [AMBER] PES for dialanine
(Fri Jan 13 2012 - 06:04:00 PST)
Re: [AMBER] Problem with xleap installation
(Fri Jan 13 2012 - 02:34:44 PST)
[AMBER] PES for dialanine
(Thu Jan 12 2012 - 19:25:51 PST)
Алексей Раевский
Re: [AMBER] ambertool question !!!
(Sun Jan 15 2012 - 13:57:27 PST)
יוכבד
[AMBER] Using antechamber -Heme molecule
(Mon Jan 02 2012 - 03:24:26 PST)
潘显超
[AMBER] How to set the dist.RST file in SMD using Amber11?
(Mon Jan 02 2012 - 23:12:00 PST)
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Tue Jan 31 2012 - 19:30:02 PST
Archived on
: Sun Dec 22 2024 - 05:54:30 PST
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