Amber Archive Feb 2011 by author
538 messages
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Starting
Mon Jan 31 2011 - 19:00:02 PST,
Ending
Mon Feb 28 2011 - 17:00:04 PST
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475649770
[AMBER] 回复： 回复： 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Wed Feb 16 2011 - 04:42:27 PST)
[AMBER] cluster using ptraj
(Wed Feb 16 2011 - 01:29:20 PST)
[AMBER] 回复： 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Wed Feb 16 2011 - 00:45:15 PST)
[AMBER] 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 15 2011 - 16:56:59 PST)
[AMBER] 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 15 2011 - 05:07:49 PST)
[AMBER] 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 15 2011 - 05:05:31 PST)
[AMBER] 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Mon Jan 31 2011 - 22:29:30 PST)
A. Gomez-Sicilia
[AMBER] High temperature at the beginning
(Thu Feb 24 2011 - 01:17:27 PST)
Aditya Padhi
[AMBER] MD simulation of protein with Calcium ion
(Fri Feb 18 2011 - 21:14:18 PST)
Re: [AMBER] MD simulation of protein with Calcium ion
(Fri Feb 18 2011 - 21:13:46 PST)
Re: [AMBER] MD simulation of protein with Calcium ion
(Thu Feb 17 2011 - 22:01:25 PST)
[AMBER] MD simulation of protein with Calcium ion
(Thu Feb 17 2011 - 21:31:28 PST)
Re: [AMBER] MD of protein with NADPH
(Wed Feb 16 2011 - 03:22:02 PST)
[AMBER] MD of protein with NADPH
(Wed Feb 16 2011 - 01:50:48 PST)
Adrian Roitberg
Re: [AMBER] REMD at constant pH
(Wed Feb 16 2011 - 06:27:11 PST)
Re: [AMBER] REMD at constant pH
(Tue Feb 15 2011 - 05:34:29 PST)
Re: [AMBER] Simulation of DNA using generalized Born model
(Tue Feb 15 2011 - 00:23:05 PST)
Re: [AMBER] Problem with QMMM umbrella sampling
(Mon Feb 14 2011 - 10:34:21 PST)
Re: [AMBER] frcmod.urea
(Tue Feb 01 2011 - 07:11:34 PST)
Ali M. Naserian-Nik
[AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal!
(Mon Feb 28 2011 - 09:56:40 PST)
Re: [AMBER] Simulation of DNA using generalized Born model
(Tue Feb 15 2011 - 02:45:39 PST)
Re: [AMBER] Simulation of DNA using generalized Born model
(Tue Feb 15 2011 - 03:19:30 PST)
[AMBER] Simulation of DNA using generalized Born model
(Tue Feb 15 2011 - 00:15:46 PST)
amit banerjee
[AMBER] Kindly help me out for the following errors during installation of AmberTools
(Sun Feb 06 2011 - 22:11:56 PST)
Andre Serobian
[AMBER] slowly relaxing individual residues
(Sun Feb 13 2011 - 12:07:21 PST)
Anselm Horn
[AMBER] AmberTools manual: AA residue names
(Wed Feb 16 2011 - 00:21:50 PST)
Re: [AMBER] nab problems: compile and use on different machines
(Mon Feb 14 2011 - 04:52:00 PST)
Re: [AMBER] nab problems: compile and use on different machines
(Sun Feb 13 2011 - 13:51:37 PST)
Re: [AMBER] nab problems: compile and use on different machines
(Sat Feb 12 2011 - 14:47:54 PST)
[AMBER] nab problems: compile and use on different machines
(Sat Feb 12 2011 - 09:55:40 PST)
Antje Wolf
Re: [AMBER] Principal COORDINATES analysis
(Thu Feb 24 2011 - 04:19:49 PST)
[AMBER] setBox command in sleap AMBER11
(Thu Feb 17 2011 - 04:02:52 PST)
Aparna P
Re: [AMBER] parametrization of sugar modified nucleic acids
(Sun Feb 13 2011 - 22:31:37 PST)
[AMBER] parametrization of sugar modified nucleic acids
(Fri Feb 11 2011 - 01:46:13 PST)
Ashok Das Mahapatra
[AMBER] New to Amber
(Tue Feb 08 2011 - 04:00:42 PST)
Ashutosh Shandilya
[AMBER] What is the unit for RMSF result?
(Thu Feb 24 2011 - 20:39:30 PST)
Re: [AMBER] free radicals in amber
(Fri Feb 04 2011 - 06:09:03 PST)
Baptiste Legrand
[AMBER] To fix dihedral angles during a simulation.
(Fri Feb 25 2011 - 09:54:53 PST)
Barbault Florent
Re: [AMBER] pdb error
(Sun Feb 06 2011 - 01:31:05 PST)
Beale, John
[AMBER] Question
(Thu Feb 24 2011 - 03:39:59 PST)
[AMBER] Distance restraints
(Mon Feb 07 2011 - 09:59:35 PST)
bharat lakhani
[AMBER] problem with analyzing trajectaries
(Sat Feb 12 2011 - 00:41:32 PST)
Bill Miller III
Re: [AMBER] binding energy calculation problem
(Thu Feb 24 2011 - 18:18:35 PST)
Re: [AMBER] MMPBSA.py keep_files
(Thu Feb 24 2011 - 03:59:45 PST)
Re: [AMBER] binding energy calculation problem
(Thu Feb 24 2011 - 03:56:40 PST)
Re: [AMBER] 回复： 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Wed Feb 16 2011 - 03:46:24 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Tue Feb 15 2011 - 13:34:01 PST)
Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G
(Tue Feb 15 2011 - 08:57:32 PST)
Re: [AMBER] 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 15 2011 - 05:47:22 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Tue Feb 15 2011 - 04:12:32 PST)
Bill Ross
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Sat Feb 26 2011 - 12:17:51 PST)
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Thu Feb 24 2011 - 13:14:33 PST)
Re: [AMBER] Angle setting
(Tue Feb 22 2011 - 11:02:40 PST)
Re: [AMBER] Query regarding atom type using xleap
(Thu Feb 17 2011 - 00:11:29 PST)
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 12:59:40 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 19:02:30 PST)
Re: [AMBER] increasing rmsd value
(Tue Feb 15 2011 - 17:42:35 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 17:36:30 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 17:30:08 PST)
Re: [AMBER] increasing rmsd value
(Tue Feb 15 2011 - 10:49:03 PST)
Re: [AMBER] break down of simulation after approximately 60 ns
(Wed Feb 09 2011 - 11:54:58 PST)
Re: [AMBER] pol3 water droplet
(Thu Feb 03 2011 - 13:29:51 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 12:24:56 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 12:07:26 PST)
Bongkeun Kim
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Fri Feb 18 2011 - 10:05:00 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Thu Feb 17 2011 - 10:26:19 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Wed Feb 16 2011 - 20:48:20 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Wed Feb 16 2011 - 09:03:37 PST)
[AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Tue Feb 15 2011 - 17:19:56 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Mon Feb 14 2011 - 13:57:13 PST)
[AMBER] max pairlist cutoff error on octahedral box
(Mon Feb 14 2011 - 11:11:50 PST)
[AMBER] ERROR IN SETPAR() when REMD running
(Fri Feb 11 2011 - 09:25:40 PST)
Brent Krueger
Re: [AMBER] Cluster considerations
(Fri Feb 11 2011 - 18:08:00 PST)
Carlos Simmerling
Re: [AMBER] restraints in Targeted Molecular dynamics
(Sat Feb 26 2011 - 12:00:37 PST)
Re: [AMBER] temperature setting in REMD
(Wed Feb 23 2011 - 18:57:27 PST)
Re: [AMBER] New to Amber
(Tue Feb 08 2011 - 04:11:52 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 09:17:26 PST)
Re: [AMBER] MOIL-view alternatives
(Fri Feb 04 2011 - 08:51:19 PST)
Re: [AMBER] MOIL-view alternatives
(Fri Feb 04 2011 - 08:45:57 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 08:45:07 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 08:23:55 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 07:23:13 PST)
Re: [AMBER] PMF problem
(Wed Feb 02 2011 - 07:45:21 PST)
case
Re: [AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal!
(Mon Feb 28 2011 - 10:56:26 PST)
Re: [AMBER] To fix dihedral angles during a simulation.
(Sat Feb 26 2011 - 13:47:44 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 12:42:30 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 10:54:44 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 06:28:53 PST)
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Sat Feb 26 2011 - 06:25:25 PST)
Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan
(Fri Feb 25 2011 - 12:46:42 PST)
Re: [AMBER] sqm out error
(Fri Feb 25 2011 - 09:25:03 PST)
Re: [AMBER] High temperature at the beginning
(Thu Feb 24 2011 - 04:51:31 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Thu Feb 17 2011 - 13:15:33 PST)
Re: [AMBER] Scale sander.MPI to 64 ncpus - Amber11
(Thu Feb 17 2011 - 12:47:20 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Thu Feb 17 2011 - 05:00:17 PST)
Re: [AMBER] Simple NAB script from manual segfaults at call to md()
(Thu Feb 17 2011 - 04:52:20 PST)
Re: [AMBER] FATAL ERROR
(Wed Feb 16 2011 - 09:28:53 PST)
Re: [AMBER] V5 dihedrals
(Wed Feb 16 2011 - 09:14:47 PST)
Re: [AMBER] AmberTools manual: AA residue names
(Wed Feb 16 2011 - 07:08:41 PST)
Re: [AMBER] FATAL ERROR
(Wed Feb 16 2011 - 07:06:59 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Wed Feb 16 2011 - 06:51:39 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 16:29:06 PST)
Re: [AMBER] xleap or rather ff10 bug? update
(Tue Feb 15 2011 - 14:56:04 PST)
Re: [AMBER] Fwd: ESURF term error in a one-step sander calculation
(Tue Feb 15 2011 - 12:49:54 PST)
[AMBER] cuda_DPDP problems; large cutoff radius problems
(Tue Feb 15 2011 - 09:17:17 PST)
Re: [AMBER] EVB with time-dependent coupling parameter?
(Tue Feb 15 2011 - 07:40:54 PST)
Re: [AMBER] ESURF term error in a one-step sander calculation
(Tue Feb 15 2011 - 06:08:48 PST)
Re: [AMBER] EVB with time-dependent coupling parameter?
(Tue Feb 15 2011 - 05:27:32 PST)
Re: [AMBER] Regarding AMBER help command and Ewald Namelist Variables Specifications
(Tue Feb 15 2011 - 05:24:28 PST)
Re: [AMBER] create urea molecule.
(Tue Feb 15 2011 - 04:52:30 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Tue Feb 15 2011 - 04:45:15 PST)
Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11
(Mon Feb 14 2011 - 11:54:52 PST)
Re: [AMBER] parametrization of acetyl-coa using antechamber
(Mon Feb 14 2011 - 09:30:44 PST)
Re: [AMBER] AMBER 9 install gfortran
(Mon Feb 14 2011 - 05:04:40 PST)
Re: [AMBER] problems with mm_pbsa on amber8
(Thu Feb 10 2011 - 05:03:51 PST)
Re: [AMBER] AMBER11 MMPBSA.py tutorial section 3.6
(Thu Feb 10 2011 - 04:55:24 PST)
Re: [AMBER] break down of simulation after approximately 60 ns
(Wed Feb 09 2011 - 11:52:36 PST)
Re: [AMBER] Distance restraints
(Mon Feb 07 2011 - 11:06:54 PST)
Re: [AMBER] Amber11 parallel testing error
(Thu Feb 03 2011 - 11:31:43 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 20:14:33 PST)
Re: [AMBER] Energy calculation with namdenergy and amber
(Wed Feb 02 2011 - 10:35:06 PST)
Re: [AMBER] frcmod.urea
(Tue Feb 01 2011 - 09:25:06 PST)
Catein Catherine
[AMBER] What is the unit for RMSF result?
(Mon Feb 21 2011 - 22:37:00 PST)
[AMBER] Large different between experimental and MM-GBSA absolute energy, any potential source of error?
(Mon Feb 21 2011 - 02:38:12 PST)
Re: [AMBER] MD simulation of protein with Calcium ion
(Mon Feb 21 2011 - 02:36:14 PST)
Cheng-I Lee
Re: [AMBER] Temperature generator of REMD in AMBER?
(Fri Feb 25 2011 - 21:31:41 PST)
Re: [AMBER] Temperature generator of REMD in AMBER?
(Fri Feb 25 2011 - 20:48:03 PST)
[AMBER] Temperature generator of REMD in AMBER?
(Fri Feb 25 2011 - 18:22:28 PST)
[AMBER] temperature setting in REMD
(Wed Feb 23 2011 - 18:55:32 PST)
Re: [AMBER] REMD at constant pH
(Wed Feb 23 2011 - 18:48:57 PST)
Re: [AMBER] REMD at constant pH
(Wed Feb 23 2011 - 12:26:48 PST)
Re: [AMBER] REMD at constant pH
(Tue Feb 22 2011 - 20:50:39 PST)
[AMBER] Extracting replica trajectories
(Sun Feb 20 2011 - 01:11:04 PST)
Re: [AMBER] REMD at constant pH
(Wed Feb 16 2011 - 03:55:45 PST)
[AMBER] REMD at constant pH
(Tue Feb 15 2011 - 05:30:26 PST)
Chris King
[AMBER] Explanation of energy "genBorn" column in 3D-RISM calculation? Is solvation free energy computed?
(Thu Feb 24 2011 - 15:15:31 PST)
[AMBER] Simple NAB script from manual segfaults at call to md()
(Wed Feb 16 2011 - 14:35:26 PST)
cieplak.cgl.ucsf.edu
Re: [AMBER] parametrization of sugar modified nucleic acids
(Fri Feb 11 2011 - 11:25:19 PST)
Re: [AMBER] MMPBSA.py - dimer energy calculations
(Fri Feb 11 2011 - 11:15:34 PST)
colvin
Re: [AMBER] chamber - resend
(Mon Feb 28 2011 - 00:49:09 PST)
Re: [AMBER] chamber
(Thu Feb 24 2011 - 22:48:18 PST)
[AMBER] chamber
(Thu Feb 24 2011 - 04:15:39 PST)
Daniel Roe
Re: [AMBER] PTRAJ and segmentation faults
(Sun Feb 27 2011 - 12:12:30 PST)
Re: [AMBER] water mediated H-Bond analysis
(Fri Feb 25 2011 - 04:25:56 PST)
Re: [AMBER] center of mass motion
(Fri Feb 25 2011 - 04:05:55 PST)
Re: [AMBER] PTRAJ and segmentation faults
(Mon Feb 21 2011 - 20:25:23 PST)
Re: [AMBER] PTRAJ and segmentation faults
(Mon Feb 21 2011 - 14:07:47 PST)
Re: [AMBER] PTRAJ and segmentation faults
(Mon Feb 21 2011 - 13:00:25 PST)
Re: [AMBER] PMEMD and restraint problem
(Mon Feb 21 2011 - 07:57:28 PST)
Re: [AMBER] Fwd: About long simulation
(Thu Feb 17 2011 - 05:25:28 PST)
Re: [AMBER] ERROR IN SETPAR() upon atom distribution with FF03, 03.r1
(Thu Feb 17 2011 - 05:19:17 PST)
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 12:57:30 PST)
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 11:34:35 PST)
Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11
(Mon Feb 14 2011 - 11:23:34 PST)
Re: [AMBER] problem with analyzing trajectaries
(Sat Feb 12 2011 - 06:45:40 PST)
Re: [AMBER] Consistency between temperatures in mdout and mdcrd in REMD
(Fri Feb 11 2011 - 10:57:49 PST)
Re: [AMBER] compilation failure of amber 11 on Itanium2
(Tue Feb 08 2011 - 14:01:10 PST)
Re: [AMBER] Structural alignment & RMSD calculation
(Tue Feb 08 2011 - 08:10:41 PST)
Re: [AMBER] Ptraj Translate Error
(Tue Feb 08 2011 - 06:00:07 PST)
Re: [AMBER] Ptraj Translate Error
(Mon Feb 07 2011 - 21:09:51 PST)
Re: [AMBER] XMIN ERROR in LMOD calculation
(Mon Feb 07 2011 - 18:12:30 PST)
Re: [AMBER] clustering by attribute
(Mon Feb 07 2011 - 09:19:42 PST)
Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
(Sun Feb 06 2011 - 11:37:46 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 07:51:57 PST)
Re: [AMBER] Amber11 parallel testing error
(Wed Feb 02 2011 - 14:02:17 PST)
Re: [AMBER] Amber11 parallel configure error
(Wed Feb 02 2011 - 10:08:32 PST)
Re: [AMBER] Amber11 parallel testing error
(Wed Feb 02 2011 - 10:03:57 PST)
Daniel Sindhikara
Re: [AMBER] Extracting replica trajectories
(Sun Feb 20 2011 - 05:48:35 PST)
Re: [AMBER] center of mass motion
(Thu Feb 17 2011 - 18:57:33 PST)
Re: [AMBER] Consistency between temperatures in mdout and mdcrd in REMD
(Sat Feb 12 2011 - 00:20:12 PST)
[AMBER] Consistency between temperatures in mdout and mdcrd in REMD
(Fri Feb 11 2011 - 02:08:05 PST)
Re: [AMBER] PMF problem
(Tue Feb 01 2011 - 18:49:33 PST)
David A. Case
Re: [AMBER] nonbonding parameters
(Wed Feb 23 2011 - 06:55:13 PST)
Re: [AMBER] how to understand disappearing atoms no contribution to DVdl
(Wed Feb 23 2011 - 06:52:53 PST)
Re: [AMBER] Gasteiger parameter
(Tue Feb 22 2011 - 19:18:00 PST)
David Case
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Thu Feb 24 2011 - 19:20:18 PST)
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Thu Feb 24 2011 - 14:43:34 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 19:17:46 PST)
Re: [AMBER] parametrization of acetyl-coa using antechamber
(Sat Feb 12 2011 - 14:19:49 PST)
Re: [AMBER] nab problems: compile and use on different machines
(Sat Feb 12 2011 - 14:15:43 PST)
Re: [AMBER] AmberTools 1.4 parallel programs
(Tue Feb 08 2011 - 16:48:54 PST)
Re: [AMBER] AmberTools 1.4 parallel programs
(Tue Feb 08 2011 - 09:39:57 PST)
david condon
Re: [AMBER] PTRAJ and segmentation faults
(Mon Feb 21 2011 - 15:10:05 PST)
Dean Cuebas
[AMBER] A bit off-topic? Comments
(Tue Feb 22 2011 - 17:28:53 PST)
Re: [AMBER] parametrization of acetyl-coa using antechamber
(Sun Feb 13 2011 - 12:09:20 PST)
dhacademic
Re: [AMBER] PMF problem
(Wed Feb 02 2011 - 07:40:26 PST)
[AMBER] PMF problem
(Tue Feb 01 2011 - 12:55:30 PST)
Dmitry Nilov
[AMBER] Use of semiempirical QM/MM method in Amber to obtain free energy profile of a reaction
(Tue Feb 22 2011 - 08:11:29 PST)
Re: [AMBER] MD of protein with NADPH
(Wed Feb 16 2011 - 02:24:07 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 22:09:26 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 12:15:22 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 11:59:39 PST)
Eliac Brown
Re: [AMBER] Gasteiger parameter
(Wed Feb 23 2011 - 11:15:51 PST)
[AMBER] Gasteiger parameter
(Tue Feb 22 2011 - 16:45:57 PST)
[AMBER] Two fragments minimization
(Sun Feb 13 2011 - 13:23:00 PST)
Elisa Frezza
[AMBER] Protonation of C terminal residue
(Thu Feb 24 2011 - 02:55:46 PST)
Emanuele G
Re: [AMBER] MOIL-view alternatives
(Fri Feb 04 2011 - 08:49:47 PST)
[AMBER] MOIL-view alternatives
(Fri Feb 04 2011 - 08:29:07 PST)
Emanuele Galletta
[AMBER] PMEMD and restraint problem
(Mon Feb 21 2011 - 00:46:55 PST)
FCUP
[AMBER] TI problem - Antechamber changes the atom order
(Tue Feb 15 2011 - 03:27:31 PST)
Re: [AMBER] TI in vacuum
(Wed Feb 09 2011 - 03:11:30 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 08 2011 - 08:34:25 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 08 2011 - 01:43:24 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 01 2011 - 09:08:22 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 01 2011 - 09:02:40 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 01 2011 - 08:28:14 PST)
[AMBER] TI in vacuum
(Tue Feb 01 2011 - 06:36:55 PST)
federica de leo
Re: [AMBER] Probelm with antechamber for resp charge derivation
(Sat Feb 19 2011 - 21:02:32 PST)
Francesco Pietra
[AMBER] Fwd: reimaging failure
(Sun Feb 20 2011 - 13:30:46 PST)
[AMBER] reimaging failure
(Sun Feb 20 2011 - 09:29:53 PST)
[AMBER] restraining protons with pmemd
(Wed Feb 16 2011 - 10:11:50 PST)
Fredrick Devadoss
Re: [AMBER] increasing rmsd value
(Tue Feb 15 2011 - 05:17:52 PST)
FyD
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Sat Feb 26 2011 - 06:14:52 PST)
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Sat Feb 26 2011 - 00:51:09 PST)
Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan
(Fri Feb 25 2011 - 12:18:06 PST)
Re: [AMBER] Protonation of C terminal residue
(Thu Feb 24 2011 - 04:12:06 PST)
Re: [AMBER] REDserver {urea molecule}
(Wed Feb 23 2011 - 06:56:37 PST)
Re: [AMBER] developing parameters for Zn-binding site
(Wed Feb 23 2011 - 00:16:58 PST)
Re: [AMBER] Probelm with antechamber for resp charge derivation
(Tue Feb 22 2011 - 23:59:13 PST)
Re: [AMBER] developing parameters for Zn-binding site
(Tue Feb 22 2011 - 14:28:47 PST)
Re: [AMBER] Probelm with antechamber for resp charge derivation
(Sun Feb 20 2011 - 08:52:57 PST)
Re: [AMBER] Probelm with antechamber for resp charge derivation
(Sat Feb 19 2011 - 02:42:23 PST)
Re: [AMBER] problem with parametrization of an organo-metallic cluster using RED server
(Thu Feb 17 2011 - 12:37:43 PST)
Re: [AMBER] xleap does not want to impose my dihedrals
(Tue Feb 15 2011 - 13:20:42 PST)
Re: [AMBER] Create EtOHbox
(Mon Feb 14 2011 - 01:41:37 PST)
Re: [AMBER] create urea molecule.
(Sat Feb 12 2011 - 08:28:53 PST)
Re: [AMBER] create urea molecule.
(Fri Feb 11 2011 - 23:38:15 PST)
Re: [AMBER] Create EtOHbox
(Sat Feb 05 2011 - 01:03:14 PST)
Re: [AMBER] Create EtOHbox
(Wed Feb 02 2011 - 00:26:05 PST)
George Tzotzos
Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G
(Tue Feb 15 2011 - 09:45:47 PST)
[AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G
(Tue Feb 15 2011 - 08:40:00 PST)
gromacs
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 19:27:00 PST)
[AMBER] AMBER 9 install gfortran, If i install xorg-dev package, there will be error; However if i did not install xorg-dev, i cannot pass the test of tleap.
(Mon Feb 14 2011 - 19:17:39 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 18:47:17 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 17:41:16 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 17:20:11 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 17:04:24 PST)
[AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 16:20:24 PST)
[AMBER] AMBER 9 install gfortran
(Sun Feb 13 2011 - 23:15:07 PST)
Gustavo Seabra
Re: [AMBER] Use of semiempirical QM/MM method in Amber to obtain free energy profile of a reaction
(Tue Feb 22 2011 - 09:53:31 PST)
haris p
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 13:13:34 PST)
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 13:08:30 PST)
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 12:08:23 PST)
[AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 07:47:19 PST)
Hirdesh Kumar
Re: [AMBER] pdb error
(Tue Feb 22 2011 - 23:03:54 PST)
[AMBER] Query regarding atom type using xleap
(Wed Feb 16 2011 - 22:37:28 PST)
Re: [AMBER] Ptraj Translate Error
(Mon Feb 07 2011 - 21:23:40 PST)
[AMBER] Ptraj Translate Error
(Mon Feb 07 2011 - 21:02:58 PST)
[AMBER] Membrane Protein Simulation
(Thu Feb 03 2011 - 20:44:25 PST)
Re: [AMBER] Can anyone suggest me solution
(Thu Feb 03 2011 - 00:38:53 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 19:47:35 PST)
Re: [AMBER] Regarding NVIDIA Graphics Card
(Wed Feb 02 2011 - 00:32:51 PST)
[AMBER] Regarding NVIDIA Graphics Card
(Tue Feb 01 2011 - 09:05:19 PST)
Igor Marques
Re: [AMBER] New to Amber
(Tue Feb 08 2011 - 04:15:25 PST)
Ivan Gladich
Re: [AMBER] No energy conservation in NVE ensemble amber 11
(Fri Feb 25 2011 - 02:50:23 PST)
[AMBER] No energy conservation in NVE ensemble amber 11
(Thu Feb 24 2011 - 03:49:18 PST)
Jagur Lambix
[AMBER] MM-PBSA error: Missing BELE for MM in residue 1
(Thu Feb 24 2011 - 16:03:38 PST)
[AMBER] MM-PBSA error
(Fri Feb 04 2011 - 15:39:09 PST)
Jakob Luchner
[AMBER] break down of simulation after approximately 60 ns
(Wed Feb 09 2011 - 11:36:25 PST)
[AMBER] Energy calculation with namdenergy and amber
(Wed Feb 02 2011 - 09:15:46 PST)
Jason Swails
Re: [AMBER] Temperature generator of REMD in AMBER?
(Sat Feb 26 2011 - 07:35:59 PST)
Re: [AMBER] Temperature generator of REMD in AMBER?
(Fri Feb 25 2011 - 19:40:08 PST)
Re: [AMBER] REMD at constant pH
(Wed Feb 23 2011 - 16:59:49 PST)
Re: [AMBER] REMD at constant pH
(Wed Feb 23 2011 - 05:36:54 PST)
Re: [AMBER] nonbonding parameters
(Wed Feb 23 2011 - 05:35:19 PST)
Re: [AMBER] binding energy calculation problem
(Tue Feb 22 2011 - 08:47:25 PST)
Re: [AMBER] How to generate MM/PBSA statistics from recovered Job
(Tue Feb 22 2011 - 06:59:57 PST)
Re: [AMBER] binding energy calculation problem
(Tue Feb 22 2011 - 06:54:27 PST)
Re: [AMBER] How to generate MM/PBSA statistics from recovered Job
(Mon Feb 21 2011 - 11:05:45 PST)
Re: [AMBER] Large different between experimental and MM-GBSA absolute energy, any potential source of error?
(Mon Feb 21 2011 - 09:58:23 PST)
Re: [AMBER] How to generate MM/PBSA statistics from recovered Job
(Mon Feb 21 2011 - 09:08:22 PST)
Re: [AMBER] MD simulation of protein with Calcium ion
(Fri Feb 18 2011 - 05:27:19 PST)
Re: [AMBER] binding energy calculation problem
(Thu Feb 17 2011 - 09:27:12 PST)
Re: [AMBER] Fwd: About long simulation
(Wed Feb 16 2011 - 16:18:44 PST)
Re: [AMBER] R: Re: V5 dihedrals
(Wed Feb 16 2011 - 11:04:24 PST)
Re: [AMBER] V5 dihedrals
(Wed Feb 16 2011 - 10:10:46 PST)
Re: [AMBER] 回复： 回复： 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Wed Feb 16 2011 - 05:25:20 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 17:52:00 PST)
Re: [AMBER] 回复： 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 15 2011 - 17:47:19 PST)
Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G
(Tue Feb 15 2011 - 11:18:07 PST)
Re: [AMBER] MMPBSA.py: Factoring in the contribution of individual HOH molecules to delta G
(Tue Feb 15 2011 - 09:03:03 PST)
Re: [AMBER] 回复： 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 15 2011 - 06:46:42 PST)
Re: [AMBER] REMD at constant pH
(Tue Feb 15 2011 - 05:41:29 PST)
Re: [AMBER] AMBER 9 install gfortran, If i install xorg-dev package, there will be error; However if i did not install xorg-dev, i cannot pass the test of tleap.
(Mon Feb 14 2011 - 19:40:05 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 17:53:13 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 17:48:59 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 17:47:39 PST)
Re: [AMBER] AMBER 9 install gfortran, not need AmberTool
(Mon Feb 14 2011 - 16:42:54 PST)
Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11
(Mon Feb 14 2011 - 12:20:22 PST)
Re: [AMBER] AMBER 9 install gfortran
(Mon Feb 14 2011 - 04:41:27 PST)
Re: [AMBER] nab problems: compile and use on different machines
(Sun Feb 13 2011 - 16:05:26 PST)
Re: [AMBER] nab problems: compile and use on different machines
(Sat Feb 12 2011 - 21:29:38 PST)
Re: [AMBER] AMBER11 MMPBSA.py tutorial section 3.6
(Wed Feb 09 2011 - 18:46:25 PST)
Re: [AMBER] AmberTools 1.4 parallel programs
(Mon Feb 07 2011 - 14:45:39 PST)
Re: [AMBER] Ionic strength in MM-PBSA
(Mon Feb 07 2011 - 14:40:27 PST)
Re: [AMBER] Ionic strength in MM-PBSA
(Mon Feb 07 2011 - 14:37:51 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Mon Feb 07 2011 - 10:27:12 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Mon Feb 07 2011 - 08:27:52 PST)
Re: [AMBER] Kindly help me out for the following errors during installation of AmberTools
(Mon Feb 07 2011 - 06:38:09 PST)
Re: [AMBER] pdb error
(Sun Feb 06 2011 - 06:44:26 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Sat Feb 05 2011 - 11:47:11 PST)
Re: [AMBER] Amber11 parallel testing error
(Thu Feb 03 2011 - 11:33:27 PST)
Re: [AMBER] Dielectric constant for solute
(Thu Feb 03 2011 - 06:59:46 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 14:07:04 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 11:50:10 PST)
Re: [AMBER] frcmod.urea
(Wed Feb 02 2011 - 07:12:00 PST)
Re: [AMBER] MMPBSA printres syntax
(Tue Feb 01 2011 - 06:46:33 PST)
Re: [AMBER] 回复： 回复： 回复： 回复： MM-PBSA error about protein + Mg2+
(Tue Feb 01 2011 - 06:44:35 PST)
Jesper Sørensen
[AMBER] MMPBSA.py keep_files
(Thu Feb 24 2011 - 03:03:04 PST)
[AMBER] MMPBSA printres syntax
(Tue Feb 01 2011 - 01:30:29 PST)
Jiri Sponer
Re: [AMBER] Simulation of DNA using generalized Born model
(Tue Feb 15 2011 - 03:01:41 PST)
Jorge Iulek
[AMBER] Calculation of molecular surface for calcium
(Wed Feb 23 2011 - 11:14:27 PST)
[AMBER] Calculation of molecular surface for calcium
(Wed Feb 23 2011 - 03:55:30 PST)
Jorgen Simonsen
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Sat Feb 26 2011 - 04:37:58 PST)
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Sat Feb 26 2011 - 00:19:37 PST)
Re: [AMBER] (UNKNOWN ATOM TYPE: UA)
(Thu Feb 24 2011 - 15:18:11 PST)
[AMBER] (UNKNOWN ATOM TYPE: UA)
(Thu Feb 24 2011 - 13:00:11 PST)
Re: [AMBER] nonbonding parameters
(Wed Feb 23 2011 - 06:28:37 PST)
Re: [AMBER] nonbonding parameters
(Wed Feb 23 2011 - 03:37:26 PST)
Re: [AMBER] developing parameters for Zn-binding site
(Tue Feb 22 2011 - 23:41:58 PST)
[AMBER] nonbonding parameters
(Tue Feb 22 2011 - 23:14:51 PST)
[AMBER] developing parameters for Zn-binding site
(Tue Feb 22 2011 - 09:44:10 PST)
Jose Borreguero
Re: [AMBER] EVB with time-dependent coupling parameter?
(Tue Feb 15 2011 - 06:09:37 PST)
[AMBER] EVB with time-dependent coupling parameter?
(Sat Feb 12 2011 - 11:15:59 PST)
João Henriques
Re: [AMBER] cluster using ptraj
(Wed Feb 16 2011 - 20:29:26 PST)
Julia Romanowska
[AMBER] MMPBSA.py - dimer energy calculations
(Fri Feb 11 2011 - 03:34:02 PST)
Junjian Miao
[AMBER] how to understand disappearing atoms no contribution to DVdl
(Wed Feb 23 2011 - 06:13:45 PST)
[AMBER] how to simulate solute in vacuum with TI
(Tue Feb 22 2011 - 17:34:19 PST)
[AMBER] How to simulate hydration free energy with thermodynamic integration?
(Fri Feb 18 2011 - 05:45:49 PST)
[AMBER] How to simulate hydration free energy with thermodynamic integration?
(Fri Feb 18 2011 - 05:32:18 PST)
kala
Re: [AMBER] sqm out error
(Sat Feb 26 2011 - 08:52:34 PST)
[AMBER] sqm out error
(Fri Feb 25 2011 - 07:42:02 PST)
Kamali Sripathi
Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
(Fri Feb 11 2011 - 07:40:46 PST)
Re: [AMBER] ptraj (AT 1.4) hiccups with gzipped trajectory files
(Sun Feb 06 2011 - 09:51:22 PST)
Katharina Lang
[AMBER] Open MPI invalid message type 10
(Thu Feb 24 2011 - 08:21:47 PST)
Knut Jørgen Bjuland
Re: [AMBER] parametrization of acetyl-coa using antechamber
(Sun Feb 13 2011 - 01:00:02 PST)
[AMBER] parametrization of acetyl-coa using antechamber
(Sat Feb 12 2011 - 10:29:24 PST)
Lachele Foley (Lists)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Wed Feb 09 2011 - 09:39:14 PST)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Wed Feb 09 2011 - 08:08:57 PST)
Re: [AMBER] compilation failure of amber 11 on Itanium2
(Tue Feb 08 2011 - 14:12:30 PST)
Lane Votapka
[AMBER] Fwd: [ics.uci.edu #33898] Fwd: Amber11 download instructions
(Tue Feb 22 2011 - 09:30:40 PST)
Leong Wye Kit Damien
Re: [AMBER] Scale sander.MPI to 64 ncpus - Amber11
(Thu Feb 17 2011 - 18:22:51 PST)
[AMBER] Scale sander.MPI to 64 ncpus - Amber11
(Thu Feb 17 2011 - 09:05:09 PST)
Mahmoud A. A. Ibrahim
[AMBER] Antechamber - bug
(Wed Feb 23 2011 - 19:25:30 PST)
manikanthan bhavaraju
Re: [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small
(Tue Feb 22 2011 - 11:02:49 PST)
[AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small
(Mon Feb 21 2011 - 18:02:22 PST)
Marek Maly
Re: [AMBER] Simultaneous calculations on one GPU ?
(Tue Feb 22 2011 - 18:57:36 PST)
[AMBER] Simultaneous calculations on one GPU ?
(Tue Feb 22 2011 - 18:22:42 PST)
Re: [AMBER] Memory problem with NPT simulation of 124K atoms on GeForce GTX 470 ...
(Fri Feb 18 2011 - 21:40:00 PST)
Re: [AMBER] Cluster considerations
(Fri Feb 18 2011 - 20:42:59 PST)
[AMBER] Memory problem with NPT simulation of 124K atoms on GeForce GTX 470 ...
(Fri Feb 18 2011 - 18:46:50 PST)
[AMBER] Positive value of DELTA INT using one trajectory approach
(Wed Feb 16 2011 - 11:31:34 PST)
Mark Santer
[AMBER] ncsu-umbrella-slice utility in AMBER11
(Mon Feb 07 2011 - 04:07:15 PST)
Mark Williamson
Re: [AMBER] chamber
(Thu Feb 24 2011 - 11:10:44 PST)
Re: [AMBER] No energy conservation in NVE ensemble amber 11
(Thu Feb 24 2011 - 03:37:02 PST)
Martin M. Ossowski
Re: [AMBER] AmberTools 1.4 parallel programs
(Tue Feb 08 2011 - 13:21:58 PST)
Re: [AMBER] compilation failure of amber 11 on Itanium2
(Tue Feb 08 2011 - 12:37:09 PST)
Re: [AMBER] AmberTools 1.4 parallel programs
(Tue Feb 08 2011 - 08:23:52 PST)
[AMBER] AmberTools 1.4 parallel programs
(Mon Feb 07 2011 - 13:44:13 PST)
Massimiliano Porrini
[AMBER] Principal COORDINATES analysis
(Wed Feb 23 2011 - 04:33:00 PST)
Re: [AMBER] cluster using ptraj
(Wed Feb 16 2011 - 04:42:59 PST)
Re: [AMBER] clustering by attribute
(Mon Feb 07 2011 - 10:06:08 PST)
[AMBER] Fwd: clustering by attribute
(Mon Feb 07 2011 - 07:58:26 PST)
[AMBER] clustering by attribute
(Wed Feb 02 2011 - 15:20:22 PST)
Mattei, Alessandra
Re: [AMBER] Create EtOHbox
(Fri Feb 04 2011 - 11:12:59 PST)
[AMBER] Create EtOHbox
(Tue Feb 01 2011 - 14:43:45 PST)
mish
Re: [AMBER] How to generate MM/PBSA statistics from recovered Job
(Tue Feb 22 2011 - 01:51:43 PST)
Re: [AMBER] How to generate MM/PBSA statistics from recovered Job
(Mon Feb 21 2011 - 10:18:46 PST)
[AMBER] How to generate MM/PBSA statistics from recovered Job
(Mon Feb 21 2011 - 07:38:24 PST)
Re: [AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Wed Feb 09 2011 - 09:18:39 PST)
[AMBER] How to rename GLYCAM residue names of a sugar to the same name for one complete sugar (in tleap or xleap)
(Wed Feb 09 2011 - 07:30:02 PST)
[AMBER] Dielectric constant for solute
(Thu Feb 03 2011 - 06:31:22 PST)
moacyr comar
[AMBER] Problems with mmpbsa
(Tue Feb 22 2011 - 05:15:23 PST)
moitrayee.mbu.iisc.ernet.in
[AMBER] problem with parametrization of an organo-metallic cluster using RED server
(Thu Feb 17 2011 - 00:18:13 PST)
[AMBER] parameters for CO2+
(Mon Feb 14 2011 - 22:05:31 PST)
Naveen Samala
[AMBER] Regarding AMBER help command and Ewald Namelist Variables Specifications
(Mon Feb 14 2011 - 11:06:34 PST)
Niel Henriksen
Re: [AMBER] softcore TI with more than 2 procs?
(Tue Feb 08 2011 - 15:34:31 PST)
[AMBER] softcore TI with more than 2 procs?
(Mon Feb 07 2011 - 10:40:26 PST)
Nitu Bansal
Re: [AMBER] Energy Calculation Problem
(Thu Feb 24 2011 - 04:08:43 PST)
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 22:47:36 PST)
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 22:12:01 PST)
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 20:54:03 PST)
[AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 08:33:07 PST)
peker milas
Re: [AMBER] Cluster considerations
(Fri Feb 18 2011 - 19:29:18 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 16:44:13 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 16:20:38 PST)
[AMBER] Cluster considerations
(Fri Feb 11 2011 - 16:33:39 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 11:58:01 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 11:38:29 PST)
Peter Schmidtke
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Tue Feb 08 2011 - 17:21:30 PST)
poll.chemie.uni-hamburg.de
Re: [AMBER] binding energy calculation problem
(Thu Feb 24 2011 - 05:09:00 PST)
Re: [AMBER] binding energy calculation problem
(Thu Feb 24 2011 - 02:27:28 PST)
Re: [AMBER] binding energy calculation problem
(Tue Feb 22 2011 - 08:16:57 PST)
Re: [AMBER] binding energy calculation problem
(Tue Feb 22 2011 - 06:26:07 PST)
Re: [AMBER] binding energy calculation problem
(Thu Feb 17 2011 - 08:38:07 PST)
[AMBER] binding energy calculation problem
(Thu Feb 17 2011 - 07:13:25 PST)
py
[AMBER] How to defining a bond between the Cβ of the substrate and the Cα of the catalytic serine
(Sun Feb 27 2011 - 21:34:48 PST)
Rahul Banerjee
[AMBER] Structural alignment & RMSD calculation
(Mon Feb 07 2011 - 10:50:14 PST)
Rajesh Raju
Re: [AMBER] Probelm with antechamber for resp charge derivation
(Tue Feb 22 2011 - 14:27:30 PST)
Re: [AMBER] Probelm with antechamber for resp charge derivation
(Sat Feb 19 2011 - 11:15:33 PST)
[AMBER] Probelm with antechamber for resp charge derivation
(Fri Feb 18 2011 - 09:52:50 PST)
Ray Luo, Ph.D.
Re: [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small
(Tue Feb 22 2011 - 17:40:30 PST)
Re: [AMBER] MM-PBSA: PB bomb in pb_reslist(): maxnbr too small
(Mon Feb 21 2011 - 19:17:38 PST)
Re: [AMBER] Ionic strength in MM-PBSA
(Mon Feb 07 2011 - 14:56:02 PST)
Re: [AMBER] Ionic strength in MM-PBSA
(Mon Feb 07 2011 - 14:33:53 PST)
Robert Elder
[AMBER] Ionic strength in MM-PBSA
(Mon Feb 07 2011 - 13:14:28 PST)
Ross Walker
Re: [AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent
(Mon Feb 28 2011 - 16:37:35 PST)
[AMBER] AMBER specific GPU test drive.
(Wed Feb 23 2011 - 18:13:15 PST)
Re: [AMBER] Simultaneous calculations on one GPU ?
(Tue Feb 22 2011 - 18:59:41 PST)
Re: [AMBER] Memory problem with NPT simulation of 124K atoms on GeForce GTX 470 ...
(Fri Feb 18 2011 - 21:03:48 PST)
[AMBER] AMBER Workshop in Barcelona, Spain, May 3rd to 6th 2011.
(Wed Feb 16 2011 - 12:16:01 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Tue Feb 15 2011 - 12:50:58 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Mon Feb 14 2011 - 13:36:45 PST)
Re: [AMBER] Cluster considerations
(Fri Feb 11 2011 - 20:12:15 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Wed Feb 09 2011 - 22:37:09 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Tue Feb 08 2011 - 19:29:08 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Tue Feb 08 2011 - 19:26:43 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Tue Feb 08 2011 - 17:27:14 PST)
Re: [AMBER] Kindly help me out for the following errors during installation of AmberTools
(Sun Feb 06 2011 - 22:26:15 PST)
Re: [AMBER] Regarding NVIDIA Graphics Card
(Tue Feb 01 2011 - 17:05:40 PST)
Sangita Kachhap
[AMBER] how to decide water mediated interaction betwen
(Sun Feb 27 2011 - 20:44:31 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 23:37:38 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 23:24:47 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 09:59:14 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 09:55:56 PST)
Re: [AMBER] water mediated H-Bond analysis
(Sat Feb 26 2011 - 02:19:14 PST)
[AMBER] water mediated H-Bond analysis
(Fri Feb 25 2011 - 00:32:10 PST)
Re: [AMBER] MD simulation of protein with Calcium ion
(Fri Feb 18 2011 - 00:47:38 PST)
Re: [AMBER] MD simulation of protein with Calcium ion
(Thu Feb 17 2011 - 21:55:14 PST)
Re: [AMBER] FATAL ERROR
(Wed Feb 16 2011 - 09:39:02 PST)
Re: [AMBER] FATAL ERROR
(Wed Feb 16 2011 - 09:32:23 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 22:50:08 PST)
Re: [AMBER] increasing rmsd value
(Tue Feb 15 2011 - 21:56:15 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Mon Feb 07 2011 - 10:53:17 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Mon Feb 07 2011 - 10:20:09 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Mon Feb 07 2011 - 07:50:40 PST)
Re: [AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Sun Feb 06 2011 - 07:28:31 PST)
[AMBER] measruement of effect of perticular water molecule on affinity and specificity
(Fri Feb 04 2011 - 23:13:31 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 21:06:53 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 09:41:13 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 09:02:28 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 08:43:24 PST)
Re: [AMBER] REMD production run restart
(Fri Feb 04 2011 - 08:21:18 PST)
[AMBER] REMD production run restart
(Fri Feb 04 2011 - 07:21:28 PST)
Re: [AMBER] REMD equilibration restart
(Mon Jan 31 2011 - 19:35:22 PST)
Re: [AMBER] REMD equilibration restart
(Mon Jan 31 2011 - 19:28:21 PST)
Sasha Buzko
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Thu Feb 10 2011 - 10:13:11 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Wed Feb 09 2011 - 09:24:08 PST)
[AMBER] pmemd.cuda issues on Tesla S2050
(Tue Feb 08 2011 - 16:57:37 PST)
Scott Brozell
[AMBER] sleap bugfixes
(Wed Feb 23 2011 - 13:34:03 PST)
Scott Le Grand
Re: [AMBER] cuda_DPDP problems; large cutoff radius problems
(Thu Feb 17 2011 - 08:28:13 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Wed Feb 16 2011 - 08:47:49 PST)
Re: [AMBER] cuda_DPDP problems; large cutoff radius problems
(Tue Feb 15 2011 - 09:39:56 PST)
Re: [AMBER] max pairlist cutoff error on octahedral box
(Tue Feb 15 2011 - 08:24:36 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Thu Feb 10 2011 - 07:01:25 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Thu Feb 10 2011 - 06:51:21 PST)
Re: [AMBER] pmemd.cuda issues on Tesla S2050
(Tue Feb 08 2011 - 17:22:37 PST)
[AMBER] 3 GB GTX580s
(Fri Feb 04 2011 - 14:29:33 PST)
Seibold, Stephen
Re: [AMBER] PTRAJ and segmentation faults
(Sun Feb 27 2011 - 10:53:29 PST)
Re: [AMBER] PTRAJ and segmentation faults
(Mon Feb 21 2011 - 13:18:25 PST)
[AMBER] PTRAJ and segmentation faults
(Mon Feb 21 2011 - 12:56:03 PST)
serena_leone.libero.it
[AMBER] R: Re: V5 dihedrals
(Wed Feb 16 2011 - 10:29:00 PST)
[AMBER] V5 dihedrals
(Wed Feb 16 2011 - 08:21:50 PST)
setyanto md
Re: [AMBER] Create EtOHbox
(Mon Feb 14 2011 - 02:51:03 PST)
Re: [AMBER] Create EtOHbox
(Mon Feb 14 2011 - 00:03:04 PST)
Re: [AMBER] sander on amber12
(Mon Jan 31 2011 - 18:58:42 PST)
siddesh southekal
Re: [AMBER] center of mass motion
(Fri Feb 25 2011 - 03:31:56 PST)
[AMBER] restraints in Targeted Molecular dynamics
(Tue Feb 22 2011 - 02:20:52 PST)
[AMBER] center of mass motion
(Thu Feb 17 2011 - 05:09:28 PST)
Sidney Elmer
Re: [AMBER] improper dihedral torsion parameters for fused rings on tryptophan
(Mon Feb 28 2011 - 10:22:10 PST)
[AMBER] improper dihedral torsion parameters for fused rings on tryptophan
(Fri Feb 25 2011 - 10:37:23 PST)
Siti Mohamad
Re: [AMBER] increasing rmsd value
(Tue Feb 15 2011 - 17:13:57 PST)
[AMBER] increasing rmsd value
(Tue Feb 15 2011 - 05:07:04 PST)
snoze pa
Re: [AMBER] parametrization of acetyl-coa using antechamber
(Sat Feb 12 2011 - 22:55:53 PST)
steinbrt.rci.rutgers.edu
Re: [AMBER] TI with softcores: size of scmask and crgmask
(Fri Feb 25 2011 - 00:35:27 PST)
Re: [AMBER] how to simulate solute in vacuum with TI
(Wed Feb 23 2011 - 00:39:59 PST)
Re: [AMBER] How to simulate hydration free energy with thermodynamic integration?
(Fri Feb 18 2011 - 07:11:31 PST)
Re: [AMBER] binding energy calculation problem
(Thu Feb 17 2011 - 07:21:43 PST)
[AMBER] xleap or rather ff10 bug? update
(Tue Feb 15 2011 - 10:47:25 PST)
[AMBER] xleap does not want to impose my dihedrals
(Tue Feb 15 2011 - 10:27:27 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 08 2011 - 09:43:29 PST)
Re: [AMBER] New to Amber
(Tue Feb 08 2011 - 04:14:43 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 08 2011 - 01:57:30 PST)
Re: [AMBER] softcore TI with more than 2 procs?
(Tue Feb 08 2011 - 00:31:59 PST)
Re: [AMBER] TI in vacuum
(Wed Feb 02 2011 - 01:17:29 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 01 2011 - 08:31:54 PST)
Re: [AMBER] TI in vacuum
(Tue Feb 01 2011 - 06:46:03 PST)
Stephane Abel
Re: [AMBER] parametrization of sugar modified nucleic acids
(Fri Feb 11 2011 - 05:43:05 PST)
subrata paul
[AMBER] REDserver {urea molecule}
(Wed Feb 23 2011 - 03:20:47 PST)
[AMBER] pdb error
(Tue Feb 22 2011 - 22:46:02 PST)
Re: [AMBER] create urea molecule.
(Tue Feb 15 2011 - 04:24:33 PST)
Re: [AMBER] create urea molecule.
(Sat Feb 12 2011 - 03:53:22 PST)
[AMBER] create urea molecule.
(Fri Feb 11 2011 - 23:22:54 PST)
[AMBER] pdb error
(Sat Feb 05 2011 - 21:27:09 PST)
Re: [AMBER] frcmod.urea
(Wed Feb 02 2011 - 07:02:48 PST)
[AMBER] frcmod.urea
(Tue Feb 01 2011 - 07:07:49 PST)
Sushil Mishra
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 23:01:49 PST)
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 22:39:55 PST)
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 21:38:05 PST)
Re: [AMBER] Energy Calculation Problem
(Tue Feb 22 2011 - 11:06:53 PST)
Re: [AMBER] How to generate MM/PBSA statistics from recovered Job
(Tue Feb 22 2011 - 02:54:17 PST)
Tan Yaw Sing
[AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11
(Mon Feb 14 2011 - 10:23:29 PST)
thomas.fox.boehringer-ingelheim.com
[AMBER] TI with softcores: size of scmask and crgmask
(Thu Feb 24 2011 - 23:06:10 PST)
tommaso.casalini.mail.polimi.it
[AMBER] Problem with dihedral angles
(Wed Feb 23 2011 - 10:09:03 PST)
[AMBER] Angle setting
(Sun Feb 20 2011 - 06:37:30 PST)
[AMBER] Polymeric lattice building
(Fri Feb 11 2011 - 03:45:18 PST)
Re: [AMBER] Create EtOHbox
(Thu Feb 03 2011 - 09:27:22 PST)
Tyler Luchko
Re: [AMBER] Explanation of energy "genBorn" column in 3D-RISM calculation? Is solvation free energy computed?
(Thu Feb 24 2011 - 18:48:19 PST)
vani panguluri
Re: [AMBER] FATAL ERROR
(Wed Feb 16 2011 - 08:38:53 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 20:44:09 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 18:04:16 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 16:40:06 PST)
Re: [AMBER] FATAL ERROR
(Tue Feb 15 2011 - 16:36:51 PST)
[AMBER] FATAL ERROR
(Tue Feb 15 2011 - 16:02:09 PST)
[AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 11:33:16 PST)
Re: [AMBER] Can anyone suggest me solution
(Wed Feb 02 2011 - 11:44:44 PST)
Vijay Manickam Achari
Re: [AMBER] installing ambertools1.4
(Tue Feb 01 2011 - 23:57:43 PST)
vitor.felix.ua.pt
[AMBER] NPT simulation crash using a GPU CARD for a simulation carried out in a organic explicit solvent
(Mon Feb 28 2011 - 01:05:25 PST)
Waqas Nasir
[AMBER] problems with mm_pbsa on amber8
(Thu Feb 10 2011 - 04:22:59 PST)
Wong, Sergio E.
Re: [AMBER] XMIN ERROR in LMOD calculation
(Tue Feb 08 2011 - 17:46:21 PST)
[AMBER] XMIN ERROR in LMOD calculation
(Mon Feb 07 2011 - 16:34:18 PST)
Wook Lee
[AMBER] Problem with QMMM umbrella sampling
(Mon Feb 14 2011 - 02:06:19 PST)
Xioling Chuang
[AMBER] parameter "ISTRNG" in PBSA script does not work properly (2nd post)
(Wed Feb 16 2011 - 22:13:53 PST)
[AMBER] ISTRNG in PBSA script does not work properly
(Sun Feb 13 2011 - 23:24:05 PST)
Yao-Chi Chen
Re: [AMBER] MM-PBSA error: Missing BELE for MM in residue 1
(Thu Feb 24 2011 - 17:54:57 PST)
[AMBER] Fwd: ESURF term error in a one-step sander calculation
(Tue Feb 15 2011 - 10:10:31 PST)
[AMBER] ESURF term error in a one-step sander calculation
(Mon Feb 14 2011 - 18:01:45 PST)
[AMBER] ESURF term error in a one-step sander calculation
(Mon Feb 14 2011 - 18:00:44 PST)
Yokota_Akihiro.takeda.co.jp
Re: [AMBER] AMBER11 MMPBSA.py tutorial section 3.6
(Wed Feb 09 2011 - 22:04:56 PST)
[AMBER] AMBER11 MMPBSA.py tutorial section 3.6
(Sun Feb 06 2011 - 23:54:11 PST)
Yubo Fan
[AMBER] compilation failure of amber 11 on Itanium2
(Tue Feb 08 2011 - 12:18:48 PST)
[AMBER] pol3 water droplet
(Thu Feb 03 2011 - 13:11:30 PST)
[AMBER] pol3 water droplet
(Wed Feb 02 2011 - 12:33:22 PST)
Zhu, James
Re: [AMBER] Amber11 parallel testing error
(Thu Feb 03 2011 - 11:19:14 PST)
Re: [AMBER] Amber11 parallel testing error
(Thu Feb 03 2011 - 10:37:24 PST)
Re: [AMBER] Amber11 parallel testing error
(Wed Feb 02 2011 - 12:53:46 PST)
[AMBER] Amber11 parallel configure error
(Wed Feb 02 2011 - 09:53:10 PST)
[AMBER] Amber11 parallel testing error
(Tue Feb 01 2011 - 08:36:18 PST)
Last message date
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Mon Feb 28 2011 - 17:00:04 PST
Archived on
: Fri Nov 22 2024 - 05:54:11 PST
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