Amber Archive Mar 2007 by author
406 messages
:
Starting
Sun Mar 04 2007 - 06:07:36 PST,
Ending
Sun Apr 01 2007 - 06:08:06 PDT
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A Box
AMBER: Amber9 Sander Error
(Thu Mar 29 2007 - 19:26:21 PDT)
Abhilash
Re: AMBER: Problem related simulation of dimer
(Thu Mar 15 2007 - 09:03:06 PDT)
Adrian Roitberg
Re: AMBER: qm/mm ti
(Fri Mar 02 2007 - 06:02:49 PST)
Akshay Patny
RE: AMBER: Problem with anisotropic pressure scaling
(Fri Mar 16 2007 - 09:37:22 PDT)
Alberto Perez
AMBER: dna forcefield: PARMBSC0
(Wed Mar 14 2007 - 00:14:36 PDT)
Amit Kumar
AMBER: vlimit error
(Fri Mar 16 2007 - 16:10:06 PDT)
Andrea Bortolato
Re: AMBER: is possible to compile pmemd using scali MPI?
(Fri Mar 30 2007 - 12:48:12 PDT)
AMBER: is possible to compile pmemd using scali MPI?
(Thu Mar 29 2007 - 09:17:05 PDT)
Andy Purkiss-Trew
Re: AMBER: Problem with anisotropic pressure scaling
(Fri Mar 16 2007 - 08:47:19 PDT)
Anju Sharma
AMBER: Problem while running Antechamber
(Wed Mar 21 2007 - 02:35:28 PDT)
AMBER: Problem while loading Pdb in xleap
(Tue Mar 20 2007 - 21:12:55 PDT)
AMBER: Problem!!
(Sun Mar 18 2007 - 23:38:15 PDT)
AMBER: Problem while creating structure in xLeap
(Sun Mar 18 2007 - 21:30:03 PDT)
AMBER: hi
(Sun Mar 18 2007 - 20:56:22 PDT)
AMBER: hi
(Fri Mar 16 2007 - 03:50:44 PDT)
AMBER: hii
(Thu Mar 15 2007 - 02:28:47 PDT)
AMBER: How to build organic compound in Amber
(Wed Mar 14 2007 - 21:24:09 PDT)
AMBER: Need help in Analysis
(Wed Mar 14 2007 - 02:13:03 PDT)
Re: AMBER: problem while analysing result
(Tue Mar 13 2007 - 23:27:20 PDT)
AMBER: problem while analysing result
(Tue Mar 13 2007 - 22:38:37 PDT)
AMBER: Problem Solved
(Tue Mar 13 2007 - 21:19:57 PDT)
Re: AMBER: problem while running minimisation
(Tue Mar 13 2007 - 21:19:03 PDT)
AMBER: problem while running minimisation
(Tue Mar 13 2007 - 21:10:15 PDT)
Re: AMBER: hi..
(Tue Mar 13 2007 - 05:29:28 PDT)
Re: AMBER: hi..
(Tue Mar 13 2007 - 05:28:23 PDT)
Re: AMBER: hi..
(Tue Mar 13 2007 - 05:15:27 PDT)
AMBER: hi..
(Tue Mar 13 2007 - 04:59:24 PDT)
AMBER: unable to run test
(Sun Mar 11 2007 - 22:14:03 PDT)
Austin B. Yongye
Re: AMBER: Trimannoside Problem
(Thu Mar 08 2007 - 06:09:48 PST)
AYTUG TUNCEL
AMBER: how to incorporate ismem =1 into mm_pbsa
(Mon Mar 05 2007 - 15:32:19 PST)
AMBER: mm_pbsa individual contributions of residues
(Mon Mar 05 2007 - 15:12:54 PST)
bala
AMBER: pbsa installation problem
(Mon Mar 05 2007 - 04:34:32 PST)
Beale, John
AMBER:
(Mon Mar 05 2007 - 09:51:29 PST)
AMBER:
(Mon Mar 05 2007 - 09:50:26 PST)
RE: AMBER: Disulfide Problem
(Thu Mar 01 2007 - 06:45:24 PST)
AMBER: Disulfide Problem
(Thu Mar 01 2007 - 05:49:22 PST)
Ben Sattelle
AMBER: qm/mm ti
(Fri Mar 02 2007 - 05:54:53 PST)
Benjamin Juhl
Re: AMBER: hii
(Thu Mar 15 2007 - 02:44:18 PDT)
bertrand russell
Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable)
(Thu Mar 29 2007 - 02:04:00 PDT)
Re: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable)
(Tue Mar 27 2007 - 23:36:17 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Tue Mar 27 2007 - 11:42:57 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Tue Mar 27 2007 - 11:39:28 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 22:57:31 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 10:12:57 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 10:10:12 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 02:03:56 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 01:56:06 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Sat Mar 24 2007 - 13:18:55 PDT)
AMBER: Error - must define AMBERHOME environment variable
(Fri Mar 23 2007 - 13:05:47 PDT)
Bill Ross
Re: AMBER: Can I measure improper torsion by ptarj?
(Tue Mar 13 2007 - 10:23:24 PDT)
brmeher.iitg.ernet.in
AMBER: TI calculation: charge is not zero in the perturbed state
(Sat Mar 03 2007 - 12:32:02 PST)
Carlos Simmerling
Re: AMBER: phe-phe simulation
(Tue Mar 27 2007 - 07:23:15 PDT)
Re: AMBER: Parameter file for Dipeptide
(Tue Mar 27 2007 - 07:20:55 PDT)
Re: AMBER: phe-phe simulation
(Mon Mar 26 2007 - 05:20:52 PDT)
Re: AMBER: restraint in minimization
(Mon Mar 26 2007 - 05:19:13 PDT)
Re: AMBER: ntt=1 or ntt= 3?
(Thu Mar 22 2007 - 14:47:26 PDT)
Re: AMBER: ntt=1 or ntt= 3?
(Thu Mar 22 2007 - 14:30:05 PDT)
Re: AMBER: restraint in minimization
(Thu Mar 22 2007 - 04:14:22 PDT)
Re: AMBER: ntt=1 or ntt= 3?
(Wed Mar 21 2007 - 10:40:20 PDT)
Re: AMBER: How to reimage the trajectories of LES calculations?
(Wed Mar 21 2007 - 10:04:03 PDT)
Re: AMBER: MMPBSA with water molecule in active site
(Sun Mar 18 2007 - 11:07:14 PDT)
Re: AMBER: MMPBSA with water molecule in active site
(Sun Mar 18 2007 - 10:43:44 PDT)
Re: AMBER: targeted MD problem
(Sat Mar 17 2007 - 05:27:28 PDT)
Re: AMBER: hi
(Fri Mar 16 2007 - 04:14:15 PDT)
Re: AMBER: solvate shell
(Thu Mar 15 2007 - 09:36:52 PDT)
Re: AMBER: Problem related simulation of dimer
(Thu Mar 15 2007 - 04:38:57 PDT)
Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)
(Wed Mar 14 2007 - 18:47:23 PDT)
Re: AMBER: torsion angle
(Wed Mar 14 2007 - 05:27:02 PDT)
Re: AMBER: hi..
(Tue Mar 13 2007 - 05:20:40 PDT)
Re: AMBER: hi..
(Tue Mar 13 2007 - 05:08:47 PDT)
Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly
(Mon Mar 12 2007 - 04:51:38 PDT)
Re: AMBER: addles
(Mon Mar 12 2007 - 04:28:20 PDT)
Re: AMBER: rmsd calculation in ptraj
(Sat Mar 10 2007 - 06:26:34 PST)
Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat?
(Fri Mar 09 2007 - 04:07:48 PST)
Re: AMBER: Amber 9, sander imin = 5, -y flag
(Wed Mar 07 2007 - 11:15:22 PST)
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 10:56:46 PST)
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 09:39:40 PST)
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 04:08:27 PST)
Re: AMBER: coordinate changes using ptraj
(Sun Mar 04 2007 - 06:19:33 PST)
Re: AMBER: coordinate changes using ptraj
(Sat Mar 03 2007 - 16:44:00 PST)
Re: AMBER: calculate RMSD of only chain C
(Sat Mar 03 2007 - 06:51:34 PST)
Re: AMBER: reproducibility between software
(Fri Mar 02 2007 - 08:43:04 PST)
Re: AMBER: restraints during MD
(Fri Mar 02 2007 - 08:27:50 PST)
Re: AMBER: Restart Files
(Fri Mar 02 2007 - 07:32:46 PST)
Re: AMBER: Disulfide Problem
(Fri Mar 02 2007 - 06:54:42 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Fri Mar 02 2007 - 04:14:20 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 14:42:31 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 08:07:51 PST)
Re: AMBER: Disulfide Problem
(Thu Mar 01 2007 - 06:15:22 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 04:10:55 PST)
Cenk Andac
Re: AMBER: water density
(Fri Mar 23 2007 - 16:13:16 PDT)
Re: AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 19 2007 - 06:30:00 PDT)
Re: AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 19 2007 - 06:16:42 PDT)
Re: AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 12 2007 - 07:03:03 PDT)
AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 12 2007 - 02:13:56 PDT)
AMBER: Question about translational and rotational degree of freedom in MM-PBSA v9 computations
(Sun Mar 04 2007 - 04:06:22 PST)
Chengwen Chen
Re: AMBER: Can I measure improper torsion by ptarj?
(Mon Mar 12 2007 - 21:18:24 PDT)
AMBER: Can I measure improper torsion by ptarj?
(Mon Mar 12 2007 - 09:21:55 PDT)
Re: AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat?
(Fri Mar 09 2007 - 23:37:06 PST)
AMBER: van der Waals parameters and 6-12 potential parameters of NB in parm99.dat?
(Fri Mar 09 2007 - 00:04:00 PST)
Cyril Bauvais
AMBER: problem decomposing energies (MMPBSA)
(Tue Mar 20 2007 - 04:15:29 PDT)
AMBER: problem decomposing energies (MMPBSA)
(Thu Mar 15 2007 - 02:27:57 PDT)
David A. Case
Re: AMBER: Distance restraint to centre of mass
(Sat Mar 31 2007 - 21:13:48 PDT)
Re: AMBER: Problem with PCSHIFT module
(Sat Mar 31 2007 - 21:13:12 PDT)
Re: AMBER: Some problems during the testing of Amber.
(Sat Mar 31 2007 - 21:13:38 PDT)
Re: AMBER: DISAVE value1
(Fri Mar 30 2007 - 08:24:27 PDT)
Re: AMBER: Amber9 Sander Error
(Fri Mar 30 2007 - 07:04:40 PDT)
Re: AMBER: Please check the total charge and your -nc flag
(Tue Mar 27 2007 - 15:29:32 PDT)
Re: AMBER: Amber 9 TI Details
(Tue Mar 27 2007 - 15:23:34 PDT)
Re: AMBER: amber 9: fortran/test failures
(Tue Mar 27 2007 - 15:15:50 PDT)
Re: AMBER: amber 9 - output of forces
(Fri Mar 23 2007 - 22:10:21 PDT)
Re: AMBER: Holding NA Base syn during annealing
(Thu Mar 22 2007 - 08:41:30 PDT)
Re: AMBER: xLeAP: TI calculation: the perturbed charge is not integral
(Wed Mar 21 2007 - 12:33:33 PDT)
Re: AMBER: ntt=1 or ntt= 3?
(Wed Mar 21 2007 - 12:29:45 PDT)
Re: AMBER: Problem while loading Pdb in xleap
(Tue Mar 20 2007 - 22:31:42 PDT)
Re: AMBER: vlimit error
(Mon Mar 19 2007 - 16:11:57 PDT)
Re: AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 19 2007 - 08:02:41 PDT)
Re: AMBER: antechamber
(Sun Mar 18 2007 - 16:50:00 PDT)
Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)
(Fri Mar 16 2007 - 13:51:14 PDT)
Re: AMBER: Problem with anisotropic pressure scaling
(Fri Mar 16 2007 - 08:55:51 PDT)
Re: AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap
(Fri Mar 16 2007 - 08:24:16 PDT)
Re: AMBER: solvate shell
(Thu Mar 15 2007 - 12:36:04 PDT)
Re: AMBER: van der waals parameters.
(Thu Mar 15 2007 - 12:30:34 PDT)
Re: AMBER: Problem related simulation of dimer
(Thu Mar 15 2007 - 10:09:52 PDT)
Re: AMBER: AMBER hydrophobic Box : script
(Wed Mar 14 2007 - 09:22:41 PDT)
Re: AMBER: AMBER hydrophobic Box : script
(Wed Mar 14 2007 - 08:29:47 PDT)
Re: AMBER: poor performance of sander on a quad-core linux machine
(Tue Mar 13 2007 - 10:42:48 PDT)
Re: AMBER: Can I measure improper torsion by ptarj?
(Tue Mar 13 2007 - 09:55:13 PDT)
Re: AMBER: Can I measure improper torsion by ptarj?
(Mon Mar 12 2007 - 09:36:07 PDT)
Re: AMBER: unable to run test
(Sun Mar 11 2007 - 23:54:34 PDT)
Re: AMBER: rmsd calculation in ptraj II
(Sat Mar 10 2007 - 21:55:32 PST)
Re: AMBER: problem with ptraj with calculating auto time correlation functions
(Sat Mar 10 2007 - 09:34:32 PST)
Re: AMBER: problem with ptraj with calculating auto time correlation functions
(Fri Mar 09 2007 - 17:01:44 PST)
Re: AMBER: Topology file problem in TI !
(Thu Mar 08 2007 - 07:59:22 PST)
Re: AMBER: DHAS_10_12 compilation aborted for egb.f
(Wed Mar 07 2007 - 10:11:21 PST)
Re: AMBER: addles segmentation fault
(Wed Mar 07 2007 - 09:23:21 PST)
Re: AMBER: how is the standard deviations calculated in mm-pbsa?
(Tue Mar 06 2007 - 17:13:55 PST)
Re: AMBER: how to modify map.DG-AMBER file?
(Tue Mar 06 2007 - 17:06:57 PST)
Re: AMBER: DHAS_10_12 compilation aborted for egb.f
(Tue Mar 06 2007 - 08:31:10 PST)
Re: AMBER: prep file limit exceeding
(Mon Mar 05 2007 - 21:25:20 PST)
Re: AMBER: pbsa installation problem
(Mon Mar 05 2007 - 09:48:13 PST)
Re: AMBER: Restraints on modified NA's
(Mon Mar 05 2007 - 08:44:56 PST)
Re: AMBER: coordinate changes using ptraj
(Mon Mar 05 2007 - 08:41:42 PST)
Re: AMBER: TI calculation: charge is not zero in the perturbed state
(Sat Mar 03 2007 - 13:11:52 PST)
Re: AMBER: Amber 9 make parallel fails with mpich
(Fri Mar 02 2007 - 09:59:50 PST)
Re: AMBER: OpenMPI on MacBook Pro -- problems
(Fri Mar 02 2007 - 09:36:28 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 10:42:31 PST)
AMBER: [rsachdeva.imtech.res.in: A query]
(Thu Mar 01 2007 - 09:02:27 PST)
Re: AMBER: Disulfide Problem
(Thu Mar 01 2007 - 09:00:31 PST)
Re: AMBER: momentum and periodic boundary condition
(Thu Mar 01 2007 - 08:52:00 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 08:47:19 PST)
David LeBard
Re: AMBER: Question about loadMol2
(Tue Mar 27 2007 - 15:53:21 PDT)
Re: AMBER: Question about loadMol2
(Tue Mar 27 2007 - 13:49:10 PDT)
AMBER: Question about loadMol2
(Tue Mar 27 2007 - 11:31:56 PDT)
David Mobley
Re: AMBER: Question about loadMol2
(Tue Mar 27 2007 - 13:15:26 PDT)
Re: AMBER: Combining RESP with AM1-BCC
(Fri Mar 23 2007 - 16:17:50 PDT)
deepti nayar
AMBER: RST can not be opened
(Fri Mar 30 2007 - 02:21:58 PDT)
Re: AMBER: minimization energy query
(Fri Mar 30 2007 - 02:03:24 PDT)
AMBER: minimization + simulation
(Fri Mar 30 2007 - 00:54:03 PDT)
Re: AMBER: minimization energy query
(Fri Mar 30 2007 - 00:50:56 PDT)
Re: AMBER: minimization energy query
(Thu Mar 29 2007 - 04:35:45 PDT)
AMBER: minimization energy query
(Thu Mar 29 2007 - 03:55:39 PDT)
Re: AMBER: minimization not running
(Thu Mar 29 2007 - 03:51:26 PDT)
AMBER: minimization not running
(Thu Mar 29 2007 - 02:57:15 PDT)
AMBER: specifying psi and phi for a dipeptide
(Wed Mar 28 2007 - 04:50:28 PDT)
Re: AMBER: phe-phe simulation
(Wed Mar 28 2007 - 04:28:51 PDT)
Re: AMBER: phe-phe simulation
(Tue Mar 27 2007 - 05:48:01 PDT)
Re: AMBER: phe-phe simulation
(Mon Mar 26 2007 - 22:12:03 PDT)
Re: AMBER: restraint in minimization
(Mon Mar 26 2007 - 22:10:50 PDT)
AMBER: phe-phe simulation
(Mon Mar 26 2007 - 00:25:19 PDT)
AMBER: restraint in minimization
(Thu Mar 22 2007 - 01:21:32 PDT)
Re: AMBER: torsion angle
(Wed Mar 14 2007 - 23:13:43 PDT)
AMBER: torsion angle
(Wed Mar 14 2007 - 05:03:08 PDT)
AMBER: NEB tutorial and addles
(Tue Mar 13 2007 - 21:28:20 PDT)
Re: AMBER: addles
(Mon Mar 12 2007 - 04:37:27 PDT)
AMBER: NEB tutorial
(Mon Mar 12 2007 - 03:03:17 PDT)
AMBER: addles
(Sun Mar 11 2007 - 23:29:37 PDT)
Re: AMBER: addles segmentation fault
(Thu Mar 08 2007 - 01:35:43 PST)
AMBER: addles segmentation fault
(Tue Mar 06 2007 - 23:18:39 PST)
AMBER: psi , phi angles
(Mon Mar 05 2007 - 03:07:41 PST)
Edoardo Saccenti
AMBER: Problem with PCSHIFT module
(Fri Mar 30 2007 - 04:20:37 PDT)
Eric Shamay
Re: AMBER: amber 9 - output of forces
(Tue Mar 27 2007 - 13:36:34 PDT)
Re: AMBER: amber 9 - output of forces
(Mon Mar 26 2007 - 15:08:58 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Sat Mar 24 2007 - 17:32:40 PDT)
Re: AMBER: Error - must define AMBERHOME environment variable
(Fri Mar 23 2007 - 15:26:02 PDT)
Re: AMBER: amber 9 - output of forces
(Fri Mar 23 2007 - 23:27:41 PDT)
AMBER: amber 9 - output of forces
(Fri Mar 23 2007 - 16:00:39 PDT)
Re: AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)
(Wed Mar 14 2007 - 19:18:55 PDT)
AMBER: Segmentation fault (iforrtoccurs during minimization (Amber 9)
(Wed Mar 14 2007 - 18:12:49 PDT)
Esther Brugger
AMBER: water density
(Fri Mar 23 2007 - 15:47:33 PDT)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 15:58:50 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 11:15:51 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 09:03:34 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 08:40:16 PST)
Re: AMBER: solvent accessible surface area (SASA)
(Thu Mar 01 2007 - 07:23:04 PST)
Evan Kelly
AMBER: Distance restraint to centre of mass
(Fri Mar 30 2007 - 15:41:32 PDT)
Fenghui Fan
AMBER: simulation of the phosphorylated protein
(Wed Mar 07 2007 - 17:20:09 PST)
FyD
Re: AMBER: Combining RESP with AM1-BCC
(Sat Mar 24 2007 - 02:03:37 PDT)
Re: AMBER: Generating structure of polyethylene glycol in AMBER
(Thu Mar 22 2007 - 15:57:55 PDT)
Re: AMBER: Generating structure of polyethylene glycol in AMBER
(Thu Mar 22 2007 - 15:11:07 PDT)
Re: AMBER: basis set for RESP calculation
(Wed Mar 21 2007 - 10:17:44 PDT)
Re: AMBER: Modified Nucleic Acid Problem
(Wed Mar 21 2007 - 07:20:34 PDT)
Re: AMBER: Modified Nucleic Acid Problem
(Wed Mar 21 2007 - 07:19:09 PDT)
Re: AMBER: basis set for RESP calculation
(Wed Mar 21 2007 - 01:03:15 PDT)
Gianluca Degliesposti
AMBER: mmpbsa free energy pairwise decomposition
(Wed Mar 14 2007 - 11:54:32 PDT)
gurpreet singh
AMBER: Fwd: problem regarding water handling in explicit simu
(Fri Mar 30 2007 - 02:36:52 PDT)
AMBER: problem regarding water handling in explicit simu
(Fri Mar 30 2007 - 02:35:49 PDT)
AMBER: problem in implcit simulation
(Wed Mar 28 2007 - 21:25:53 PDT)
AMBER: targetedMD problem
(Sun Mar 18 2007 - 06:32:40 PDT)
AMBER: targeted MD problem
(Sat Mar 17 2007 - 05:17:27 PDT)
AMBER: rmsd calculation in ptraj II
(Sat Mar 10 2007 - 20:37:10 PST)
AMBER: rmsd calculation in ptraj
(Sat Mar 10 2007 - 05:38:28 PST)
AMBER: rmsd calculation in ptraj
(Sat Mar 10 2007 - 05:24:50 PST)
AMBER: prep file limit exceeding
(Sun Mar 04 2007 - 23:52:49 PST)
Gustavo Seabra
Re: AMBER: is possible to compile pmemd using scali MPI?
(Fri Mar 30 2007 - 13:21:39 PDT)
Re: AMBER: sander/topology problem
(Fri Mar 23 2007 - 08:15:21 PDT)
Re: AMBER: Need help in Analysis
(Wed Mar 14 2007 - 03:39:51 PDT)
Re: AMBER: The parallel test fails while sander.MPI seems to be installed correctly
(Mon Mar 12 2007 - 06:23:50 PDT)
Re: AMBER: Restart Files
(Fri Mar 02 2007 - 13:28:26 PST)
Re: AMBER: Restart Files
(Fri Mar 02 2007 - 10:06:16 PST)
Heike.Meiselbach.chemie.uni-erlangen.de
Re: AMBER: Need help in Analysis
(Wed Mar 14 2007 - 03:35:34 PDT)
Hu, Shaowen \(JSC-SK\)[USRA]
RE: AMBER: ntt=1 or ntt= 3?
(Thu Mar 22 2007 - 14:40:09 PDT)
RE: AMBER: ntt=1 or ntt= 3?
(Thu Mar 22 2007 - 14:24:10 PDT)
Ignacio Faustino
AMBER: TI calculation: the perturbed charge is not integral
(Wed Mar 21 2007 - 12:21:52 PDT)
AMBER: xLeAP: TI calculation: the perturbed charge is not integral
(Wed Mar 21 2007 - 12:17:12 PDT)
Ilyas Yildirim
Re: AMBER: Combining RESP with AM1-BCC
(Fri Mar 23 2007 - 17:27:07 PDT)
AMBER: Combining RESP with AM1-BCC
(Fri Mar 23 2007 - 14:41:04 PDT)
AMBER: antechamber
(Sun Mar 18 2007 - 10:56:00 PDT)
AMBER: antechamber error
(Fri Mar 16 2007 - 23:44:57 PDT)
Re: AMBER: Topology file problem in TI !
(Wed Mar 07 2007 - 10:09:39 PST)
Re: AMBER: psi , phi angles
(Tue Mar 06 2007 - 04:10:32 PST)
j j
Re: AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit
(Tue Mar 27 2007 - 11:43:49 PDT)
AMBER: The ring number exceeds MAXRING, increase MAXRING and recompile the programs, exit
(Tue Mar 27 2007 - 07:04:48 PDT)
Re: AMBER: Restart from restart file obtained from ptraj with added velocities
(Thu Mar 01 2007 - 09:43:13 PST)
AMBER: Restart from restart file obtained from ptraj with added velocities
(Thu Mar 01 2007 - 08:17:41 PST)
janavi raghavan
Re: AMBER: Problem related simulation of dimer
(Thu Mar 15 2007 - 10:28:32 PDT)
Re: AMBER: solvate shell
(Thu Mar 15 2007 - 10:27:42 PDT)
Re: AMBER: Problem related simulation of dimer
(Thu Mar 15 2007 - 10:24:23 PDT)
AMBER: solvate shell
(Thu Mar 15 2007 - 09:33:13 PDT)
Jerome.GOLEBIOWSKI.unice.fr
Re: AMBER: Minimization
(Wed Mar 28 2007 - 01:48:35 PDT)
Jesus Angulo
RE: AMBER: DHAS_10_12 compilation aborted for egb.f
(Tue Mar 06 2007 - 09:41:37 PST)
AMBER: DHAS_10_12 compilation aborted for egb.f
(Tue Mar 06 2007 - 06:31:28 PST)
Jin-Soo Kim
Re: AMBER: Problem while creating structure in xLeap
(Sat Mar 24 2007 - 04:53:29 PDT)
AMBER: Does Sander.MPI support coupling effect between different molecules at the same area at the same temperature in the mixture?
(Sat Mar 24 2007 - 04:40:26 PDT)
Re: AMBER: sander/topology problem
(Sat Mar 24 2007 - 04:17:51 PDT)
Re: AMBER: sander/topology problem
(Fri Mar 23 2007 - 07:31:00 PDT)
Jiri Sponer
Re: AMBER: MMPBSA with water molecule in active site
(Sun Mar 18 2007 - 11:21:17 PDT)
Re: AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 12 2007 - 07:44:08 PDT)
Re: AMBER: Essential ions and water molecules in MMPBSA computations
(Mon Mar 12 2007 - 06:05:49 PDT)
Re: AMBER: denaturing salt conditions
(Sat Mar 03 2007 - 16:28:28 PST)
Kailee
Re: AMBER: How to reimage the trajectories of LES calculations?
(Wed Mar 21 2007 - 10:32:34 PDT)
AMBER: How to reimage the trajectories of LES calculations?
(Wed Mar 21 2007 - 06:35:06 PDT)
Kara Di Giorgio
AMBER: Question about Boron
(Wed Mar 14 2007 - 10:15:22 PDT)
Kateryna Miroshnychenko
Re:AMBER: Problem while running Antechamber
(Wed Mar 21 2007 - 04:06:15 PDT)
kepa koldo burusco
AMBER: Dipolar and Inertia Moments
(Thu Mar 15 2007 - 04:46:17 PDT)
kkirschn.hamilton.edu
Re: AMBER: Trimannoside Problem
(Thu Mar 08 2007 - 05:37:27 PST)
Re: AMBER: Trimannoside Problem
(Tue Mar 06 2007 - 10:13:43 PST)
Kristina Furse
RE: AMBER: Disulfide Problem
(Thu Mar 01 2007 - 08:19:17 PST)
Kyle L. Brown
AMBER: DISAVE value1
(Wed Mar 28 2007 - 14:42:16 PDT)
AMBER: DNA Flat Angle Restraints
(Mon Mar 26 2007 - 10:04:09 PDT)
Lachele Foley (Lists)
AMBER: Amber 9 TI Details
(Tue Mar 27 2007 - 14:03:20 PDT)
Laura McDriscoll
AMBER: Segmentation Fault when saving prmtop and inpcrd files in xleap
(Thu Mar 15 2007 - 22:59:33 PDT)
Lei Jia
AMBER: Calcium parameters
(Fri Mar 02 2007 - 11:58:27 PST)
Liang, Lei
AMBER: Some problems during the testing of Amber.
(Fri Mar 30 2007 - 11:12:50 PDT)
Lili Peng
Re: AMBER: Generating structure of polyethylene glycol in AMBER
(Thu Mar 22 2007 - 15:17:22 PDT)
AMBER: Generating structure of polyethylene glycol in AMBER
(Thu Mar 22 2007 - 14:35:07 PDT)
Lillian chong
AMBER: poor performance of sander on a quad-core linux machine
(Tue Mar 13 2007 - 10:27:31 PDT)
Linda Prengaman
AMBER: Problem with anisotropic pressure scaling
(Fri Mar 16 2007 - 07:23:30 PDT)
luckyang.gmail.com
Re: AMBER: Generating structure of polyethylene glycol in AMBER
(Thu Mar 22 2007 - 15:38:02 PDT)
M. L. Dodson
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 09:42:13 PST)
Magne Olufsen
AMBER: how is the standard deviations calculated in mm-pbsa?
(Tue Mar 06 2007 - 04:58:17 PST)
Mark Williamson
Re: AMBER: basis set for RESP calculation
(Wed Mar 21 2007 - 10:36:40 PDT)
mathew k varghese
Re: AMBER: RESP calculation of modified nucleotides
(Fri Mar 02 2007 - 03:35:41 PST)
Re: AMBER: RESP calculation of modified nucleotides
(Thu Mar 01 2007 - 19:22:43 PST)
Re: AMBER: RESP calculation of modified nucleotides
(Thu Mar 01 2007 - 06:33:00 PST)
Michel Becker
AMBER: basis set for RESP calculation
(Tue Mar 20 2007 - 13:43:10 PDT)
Mike Summers
AMBER: coordinate changes using ptraj
(Sat Mar 03 2007 - 16:34:24 PST)
Re: AMBER: coordinate changes using ptraj
(Sat Mar 03 2007 - 17:39:28 PST)
Re: AMBER: OpenMPI on MacBook Pro -- problems
(Sat Mar 03 2007 - 08:07:28 PST)
Re: AMBER: OpenMPI on MacBook Pro -- problems
(Fri Mar 02 2007 - 12:36:07 PST)
Re: AMBER: OpenMPI on MacBook Pro -- problems
(Fri Mar 02 2007 - 12:04:17 PST)
AMBER: OpenMPI on MacBook Pro -- problems
(Fri Mar 02 2007 - 08:48:49 PST)
Mingfeng Yang
Re: AMBER: problem regarding water handling in explicit simu
(Fri Mar 30 2007 - 12:50:00 PDT)
AMBER: rms and rmsf in ptraj
(Wed Mar 28 2007 - 14:06:02 PDT)
Mostafa Sadighi
AMBER: The parallel test fails while sander.MPI seems to be installed correctly
(Mon Mar 12 2007 - 04:43:14 PDT)
nag raj
AMBER: Lipid bilayer
(Wed Mar 14 2007 - 20:51:19 PDT)
Neelanjana Sengupta
AMBER: Parameter file for Dipeptide
(Mon Mar 26 2007 - 22:23:32 PDT)
Pankaj R. Daga
AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished
(Thu Mar 29 2007 - 20:59:08 PDT)
AMBER: abnormal termination of tleap
(Fri Mar 09 2007 - 14:24:37 PST)
Piotr Cieplak
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 11:27:13 PST)
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 10:30:46 PST)
Re: AMBER: psi , phi angles
(Mon Mar 05 2007 - 09:29:30 PST)
Pradipta Bandyopadhyay
Re: AMBER: Topology file problem in TI !
(Thu Mar 08 2007 - 08:18:58 PST)
Re: AMBER: Topology file problem in TI !
(Wed Mar 07 2007 - 21:55:26 PST)
AMBER: Topology file problem in TI !
(Wed Mar 07 2007 - 03:08:39 PST)
priya priya
Re: AMBER: Problem related simulation of dimer
(Mon Mar 19 2007 - 03:38:59 PDT)
Re: AMBER: Problem related simulation of dimer
(Sun Mar 18 2007 - 22:35:42 PDT)
AMBER: Problem related simulation of dimer
(Thu Mar 15 2007 - 04:23:31 PDT)
puneet kacker
Re: AMBER: problem while analysing result
(Tue Mar 13 2007 - 23:46:22 PDT)
Re: AMBER: problem while analysing result
(Tue Mar 13 2007 - 22:59:20 PDT)
Qing Zhang
Re: AMBER: Calcium parameters
(Fri Mar 02 2007 - 15:10:24 PST)
r. a.
AMBER: distance calculation!
(Mon Mar 05 2007 - 00:43:45 PST)
Rafi Ahmad
AMBER: Regarding counter ions
(Wed Mar 14 2007 - 13:00:59 PDT)
RE: AMBER: hi..
(Tue Mar 13 2007 - 05:32:18 PDT)
RE: AMBER: hi..
(Tue Mar 13 2007 - 05:20:28 PDT)
Raviprasad Aduri
Re: AMBER: RESP calculation of modified nucleotides
(Fri Mar 02 2007 - 09:16:39 PST)
Re: AMBER: RESP calculation of modified nucleotides
(Thu Mar 01 2007 - 10:12:54 PST)
Rene Salmon
AMBER: Amber 9 make parallel fails with mpich
(Fri Mar 02 2007 - 09:45:37 PST)
Rita Cassia
AMBER: pdb file produced by vmd
(Mon Mar 26 2007 - 09:04:19 PDT)
Robert Duke
Re: AMBER: is possible to compile pmemd using scali MPI?
(Thu Mar 29 2007 - 09:36:01 PDT)
Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up)
(Thu Mar 29 2007 - 08:53:56 PDT)
Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up)
(Thu Mar 29 2007 - 06:57:26 PDT)
Re: AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 10:16:08 PDT)
Re: AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 08:26:22 PDT)
Re: AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 06:25:36 PDT)
Re: AMBER: Problem with anisotropic pressure scaling
(Fri Mar 16 2007 - 08:46:58 PDT)
Re: AMBER: reproducibility between software
(Fri Mar 02 2007 - 09:49:01 PST)
Roberto Gomperts
Re: AMBER: Problems with QMMM tests on Altix
(Thu Mar 08 2007 - 15:39:14 PST)
Ross Walker
RE: AMBER: RST can not be opened
(Fri Mar 30 2007 - 08:42:45 PDT)
RE: AMBER: Sander error : Coordinate resetting (SHAKE) cannot be accomplished
(Thu Mar 29 2007 - 21:33:37 PDT)
RE: AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable)
(Thu Mar 29 2007 - 15:43:21 PDT)
RE: AMBER: problem in implcit simulation
(Wed Mar 28 2007 - 22:02:28 PDT)
AMBER: SGI Altix Compilation Problems (Was: Error - must define AMBERHOME environment variable)
(Tue Mar 27 2007 - 12:14:28 PDT)
RE: AMBER: Error - must define AMBERHOME environment variable
(Tue Mar 27 2007 - 08:31:26 PDT)
RE: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 10:56:25 PDT)
RE: AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 10:46:48 PDT)
RE: AMBER: Error - must define AMBERHOME environment variable
(Mon Mar 26 2007 - 09:31:08 PDT)
RE: AMBER: Error - must define AMBERHOME environment variable
(Sat Mar 24 2007 - 21:06:23 PDT)
RE: AMBER: Problem!!
(Mon Mar 19 2007 - 08:23:40 PDT)
RE: AMBER: hi
(Sun Mar 18 2007 - 22:09:56 PDT)
RE: AMBER: NEB tutorial and addles
(Thu Mar 15 2007 - 09:21:29 PDT)
S.Sundar Raman
Re: AMBER: Amber 9, sander imin = 5, -y flag
(Wed Mar 07 2007 - 10:05:19 PST)
Sandeep Kaushik
Re: AMBER: restraint in minimization
(Mon Mar 26 2007 - 02:21:27 PDT)
Re: AMBER: Problem while loading Pdb in xleap
(Thu Mar 22 2007 - 03:07:13 PDT)
Re: AMBER: Problem related simulation of dimer
(Mon Mar 19 2007 - 04:16:39 PDT)
Re: AMBER: Problem related simulation of dimer
(Mon Mar 19 2007 - 00:47:49 PDT)
Re: AMBER: Trimannoside Problem
(Mon Mar 19 2007 - 00:02:54 PDT)
Re: AMBER: Problem related simulation of dimer
(Fri Mar 16 2007 - 03:32:20 PDT)
Re: AMBER: Trimannoside Problem
(Wed Mar 07 2007 - 23:02:02 PST)
AMBER: Trimannoside Problem
(Tue Mar 06 2007 - 04:44:20 PST)
saurabh agrawal
Re: AMBER: MMPBSA with water molecule in active site
(Sun Mar 18 2007 - 11:30:31 PDT)
Re: AMBER: MMPBSA with water molecule in active site
(Sun Mar 18 2007 - 11:03:21 PDT)
AMBER: MMPBSA with water molecule in active site
(Sun Mar 18 2007 - 10:25:44 PDT)
Scott Brozell
Re: AMBER: rms and rmsf in ptraj
(Thu Mar 29 2007 - 08:57:43 PDT)
Re: AMBER: Question about loadMol2
(Tue Mar 27 2007 - 15:11:02 PDT)
Re: AMBER: Question about loadMol2
(Tue Mar 27 2007 - 12:49:25 PDT)
Sean Rathlef
AMBER: denaturing salt conditions
(Sat Mar 03 2007 - 14:35:45 PST)
Sergey Samsonov
AMBER: MM-GBSA residues decomposition comparison
(Tue Mar 20 2007 - 07:17:26 PDT)
Seth Lilavivat
AMBER: anneal algorthm
(Fri Mar 23 2007 - 12:33:42 PDT)
AMBER: Holding NA Base syn during annealing
(Thu Mar 22 2007 - 08:23:20 PDT)
AMBER: how to modify map.DG-AMBER file?
(Tue Mar 06 2007 - 12:55:40 PST)
AMBER: Restraints on modified NA's
(Fri Mar 02 2007 - 13:56:07 PST)
AMBER: restraints during MD
(Fri Mar 02 2007 - 08:16:05 PST)
SHARAD gupta
AMBER: Modified Nucleic Acid Problem
(Wed Mar 21 2007 - 06:22:10 PDT)
Sisir Das
AMBER: any general approach to create SiO2 wall
(Mon Mar 05 2007 - 20:46:42 PST)
snoze pa
AMBER: Please check the total charge and your -nc flag
(Sun Mar 25 2007 - 21:54:52 PDT)
Sophie Barbe
Re: AMBER: Minimization
(Wed Mar 28 2007 - 02:27:27 PDT)
AMBER: Minimization
(Wed Mar 28 2007 - 01:36:35 PDT)
Re: AMBER: AMBER hydrophobic Box : script
(Wed Mar 14 2007 - 09:00:30 PDT)
AMBER: AMBER hydrophobic Box : script
(Wed Mar 14 2007 - 03:48:50 PDT)
Stefano Tonzani
AMBER: van der waals parameters.
(Thu Mar 15 2007 - 10:52:09 PDT)
Stern, Julie
AMBER: residue types for GLY/high pH
(Tue Mar 27 2007 - 13:19:47 PDT)
AMBER: amber 9: fortran/test failures
(Tue Mar 27 2007 - 11:55:43 PDT)
AMBER: amber 9 install: patch reject
(Tue Mar 27 2007 - 11:50:33 PDT)
AMBER: constraint pdb file
(Mon Mar 05 2007 - 13:06:47 PST)
AMBER: reproducibility between software
(Fri Mar 02 2007 - 08:34:32 PST)
Steve Seibold
RE: AMBER: Restart Files
(Fri Mar 02 2007 - 11:52:39 PST)
RE: AMBER: Restart Files
(Fri Mar 02 2007 - 09:01:19 PST)
AMBER: Restart Files
(Fri Mar 02 2007 - 07:26:03 PST)
Steven Winfield
Re: AMBER: SCF convergence issues
(Fri Mar 02 2007 - 05:43:58 PST)
Stéphane Téletchéa
AMBER: DNA Helicoïdal Plots over time
(Mon Mar 12 2007 - 05:31:02 PDT)
Swarup Gupta
AMBER: sander.MPI vs MPICH2 problem!!!
(Fri Mar 23 2007 - 19:33:44 PDT)
Syed Tarique Moin
Re: AMBER: problem while analysing result
(Tue Mar 13 2007 - 23:43:59 PDT)
Terry Lang
Re: AMBER: problem with ptraj with calculating auto time correlation functions
(Sat Mar 10 2007 - 07:59:09 PST)
AMBER: problem with ptraj with calculating auto time correlation functions
(Fri Mar 09 2007 - 10:36:14 PST)
Therese Malliavin
AMBER: ntt=1 or ntt= 3?
(Wed Mar 21 2007 - 10:32:07 PDT)
Thomas Cheatham
Re: AMBER: rms and rmsf in ptraj
(Wed Mar 28 2007 - 17:01:13 PDT)
Thomas Cheatham III
Re: AMBER: reproducibility between software
(Fri Mar 02 2007 - 09:32:35 PST)
Re: AMBER: Restart from restart file obtained from ptraj with added velocities
(Thu Mar 01 2007 - 08:51:28 PST)
Thomas Steinbrecher
Re: AMBER: Amber 9 TI Details
(Tue Mar 27 2007 - 14:58:55 PDT)
Re: AMBER: Question about loadMol2
(Tue Mar 27 2007 - 13:24:55 PDT)
Re: AMBER: Topology file problem in TI !
(Wed Mar 07 2007 - 11:35:29 PST)
Re: AMBER: Topology file problem in TI !
(Wed Mar 07 2007 - 08:48:10 PST)
Viktor Hornak
Re: AMBER: [rsachdeva.imtech.res.in: A query]
(Thu Mar 01 2007 - 10:56:40 PST)
Vitor Felix
Re: AMBER: DNA Helicoïdal Plots over time
(Mon Mar 12 2007 - 05:51:12 PDT)
Vlad Cojocaru
Re: AMBER: RST can not be opened
(Fri Mar 30 2007 - 02:45:55 PDT)
Re: AMBER: minimization energy query
(Fri Mar 30 2007 - 01:28:03 PDT)
Re: AMBER: minimization + simulation
(Fri Mar 30 2007 - 01:19:55 PDT)
Re: AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up)
(Thu Mar 29 2007 - 08:25:59 PDT)
Re: AMBER: minimization energy query
(Thu Mar 29 2007 - 04:00:02 PDT)
Re: AMBER: minimization not running
(Thu Mar 29 2007 - 03:15:36 PDT)
AMBER: benchmarking pmemd and sander (pmemd segmentation fault problem follow up)
(Thu Mar 29 2007 - 02:50:29 PDT)
Re: AMBER: pmemd segmentation fault
(Tue Mar 27 2007 - 05:25:26 PDT)
Re: AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 09:43:52 PDT)
Re: AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 07:29:12 PDT)
AMBER: pmemd segmentation fault
(Mon Mar 26 2007 - 02:14:50 PDT)
Wang, Xuelin
AMBER: mm_pbsa error
(Fri Mar 30 2007 - 09:21:50 PDT)
AMBER: PDB file with charge and size in mm_pbsa calculations
(Fri Mar 30 2007 - 08:13:58 PDT)
WANG,YING
AMBER: A question about biomineral simulation, help!!
(Fri Mar 30 2007 - 14:36:02 PDT)
xiaoqin huang
Re: AMBER: Disulfide Problem
(Fri Mar 02 2007 - 06:48:14 PST)
Yong Duan
RE: AMBER: ntt=1 or ntt= 3?
(Thu Mar 22 2007 - 03:42:37 PDT)
RE: AMBER: ntt=1 or ntt= 3?
(Wed Mar 21 2007 - 11:00:56 PDT)
Youyi Peng
AMBER: ptraj average structure strip water
(Fri Mar 02 2007 - 11:52:02 PST)
Yves Boulard
AMBER: problem with mm_pbsa
(Tue Mar 13 2007 - 07:21:22 PDT)
Zhenyu Lu
AMBER: distcovar in ptraj
(Mon Mar 26 2007 - 21:00:13 PDT)
赵亚雪
AMBER: calculate RMSD of only chain C
(Fri Mar 02 2007 - 18:21:33 PST)
Last message date
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Sun Apr 01 2007 - 06:08:06 PDT
Archived on
: Mon Dec 23 2024 - 05:53:30 PST
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