Amber Archive Jun 2006 by author
360 messages
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Starting
Sun Jun 04 2006 - 06:07:09 PDT,
Ending
Wed Jul 19 2006 - 06:07:08 PDT
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AMBER: Minizsation strange error message! Please help.
(Mon Jun 26 2006 - 03:38:35 PDT)
AMBER: Can we submit jobs in sequences to amber?
(Mon Jun 26 2006 - 00:14:05 PDT)
AMBER: Tutorial 2: Minimise and equlibrium error NaN
(Fri Jun 23 2006 - 03:05:05 PDT)
AMBER: kill job command?
(Thu Jun 22 2006 - 00:47:51 PDT)
AMBER: Tutorial 2: Production MD.
(Wed Jun 21 2006 - 03:19:05 PDT)
Abhilash Mohan
AMBER: problems with cpinutil.pl
(Fri Jun 23 2006 - 10:00:36 PDT)
AMBER: problems with cpinutil.pl
(Wed Jun 21 2006 - 14:06:05 PDT)
Adam Pelzer
Re: AMBER: trouble adding mdcrd files together
(Sat Jun 03 2006 - 17:40:28 PDT)
AMBER: trouble adding mdcrd files together
(Fri Jun 02 2006 - 15:22:46 PDT)
Alik Widge
Re: AMBER: remlog option changed in amber9?
(Wed Jun 28 2006 - 14:24:07 PDT)
AMBER: remlog option changed in amber9?
(Wed Jun 28 2006 - 12:36:47 PDT)
Amber admin
Re: AMBER: pmemd_parallel_ins_prob
(Thu Jun 15 2006 - 12:08:46 PDT)
Ananda Rama Krishnan Selvaraj
Re: AMBER: calculating box dimensions during MD
(Tue Jun 06 2006 - 07:31:32 PDT)
Andrea Bortolato
AMBER: MM-PBSA and first solvation shell
(Mon Jun 05 2006 - 02:42:39 PDT)
Andrew Box
AMBER: MPICH and Sander
(Thu Jun 15 2006 - 19:07:11 PDT)
Angelo
Re: AMBER: Curves and Average Structures
(Tue Jun 27 2006 - 01:57:47 PDT)
Re: AMBER: offset?
(Thu Jun 01 2006 - 02:39:20 PDT)
anna ferrari
Re: AMBER: MM-PBSA and gaff atom types
(Wed Jun 28 2006 - 09:43:41 PDT)
AMBER: MM-PBSA and gaff atom types
(Tue Jun 27 2006 - 02:28:03 PDT)
anna.schrey.gmx.de
AMBER: Problems with restart file from pmemd sim.
(Sat Jun 17 2006 - 05:30:56 PDT)
Anthony Cruz
AMBER: GB simulation problem
(Fri Jun 30 2006 - 09:49:53 PDT)
Re: AMBER: Implicit solvent question
(Thu Jun 29 2006 - 09:44:54 PDT)
AMBER: Implicit solvent question
(Fri Jun 23 2006 - 06:49:22 PDT)
Asim Okur
Re: AMBER: REM test failures on IA-64 architecture
(Wed Jun 28 2006 - 13:09:08 PDT)
Atro Tossavainen
Re: AMBER: SGI compiler problems
(Wed Jun 21 2006 - 04:30:00 PDT)
Atsutoshi Okabe
RE: AMBER: Umbrella sampling
(Sun Jun 18 2006 - 03:14:10 PDT)
AMBER: Umbrella sampling
(Sat Jun 10 2006 - 03:42:34 PDT)
bala
AMBER: average struct.problem
(Thu Jun 22 2006 - 02:11:15 PDT)
Bill Ross
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!
(Fri Jun 30 2006 - 11:42:53 PDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!
(Thu Jun 29 2006 - 16:46:17 PDT)
Carlos Simmerling
Re: AMBER: remlog option changed in amber9?
(Wed Jun 28 2006 - 14:37:54 PDT)
Re: AMBER: remlog option changed in amber9?
(Wed Jun 28 2006 - 14:11:22 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 18:54:51 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 17:19:10 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 17:18:21 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 16:10:48 PDT)
Re: AMBER: Post-MD minimization
(Mon Jun 19 2006 - 07:27:37 PDT)
AMBER: GB and protein backbone parameters
(Thu Jun 08 2006 - 09:27:47 PDT)
Re: AMBER: problem with amber 9 and igb=5
(Wed Jun 07 2006 - 19:02:34 PDT)
Re: AMBER: trouble adding mdcrd files together
(Fri Jun 02 2006 - 16:45:16 PDT)
Re: AMBER: trouble adding mdcrd files together
(Fri Jun 02 2006 - 15:37:54 PDT)
Re: AMBER: Programes to calculate ligand RMSD
(Fri Jun 02 2006 - 04:45:17 PDT)
Cenk Andac
Re: AMBER: How to calculate binding free energy using MM-PBSA
(Fri Jun 30 2006 - 05:22:08 PDT)
Re: AMBER: How to calculate binding free energy using MM-PBSA
(Thu Jun 29 2006 - 03:38:11 PDT)
AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering
(Wed Jun 28 2006 - 03:46:49 PDT)
Cheng Luo, Ph.D.
AMBER: Ask for help in pbsa error in AMBER9
(Thu Jun 08 2006 - 09:08:10 PDT)
Chengwen Chen
Re: AMBER: problems about compiling a parallel version of AMBER 9
(Mon Jun 26 2006 - 21:41:05 PDT)
AMBER: problems about compiling a parallel version of AMBER 9
(Thu Jun 22 2006 - 00:25:11 PDT)
Chris Moth
Re: AMBER: How to calculate the mmpbsa for explicit MD ?
(Mon Jun 12 2006 - 12:23:01 PDT)
Christophe Guilbert
AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
(Thu Jun 29 2006 - 18:28:31 PDT)
Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!
(Thu Jun 29 2006 - 18:06:29 PDT)
AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!
(Thu Jun 29 2006 - 14:48:31 PDT)
AMBER: Antechamber poorly define atom angles of a five ring system which causes NH2 and C not to be planar as expected
(Mon Jun 19 2006 - 18:00:29 PDT)
AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand
(Fri Jun 16 2006 - 21:32:12 PDT)
Chunhu Tan
AMBER: Review.
(Mon Jun 26 2006 - 12:37:22 PDT)
AMBER: Problem of Ptraj in AMBER9
(Tue Jun 13 2006 - 15:24:26 PDT)
David A. Case
Re: AMBER: Second derivative matrix
(Tue Jun 27 2006 - 01:36:57 PDT)
Re: AMBER: help creating RNA
(Thu Jun 22 2006 - 14:08:45 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 14:36:49 PDT)
Re: AMBER: second derivative matrix
(Tue Jun 20 2006 - 14:37:01 PDT)
Re: AMBER: RMS FLUCTUATIONS
(Thu Jun 15 2006 - 21:09:53 PDT)
Re: AMBER: MPICH and Sander
(Thu Jun 15 2006 - 20:47:36 PDT)
Re: AMBER: parmchk error
(Wed Jun 14 2006 - 20:28:20 PDT)
Re: AMBER: saveamberparams error in Amber9
(Wed Jun 14 2006 - 20:15:05 PDT)
Re: AMBER: How to strip waters in trajectorie ?
(Mon Jun 12 2006 - 13:06:19 PDT)
Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ????
(Sat Jun 10 2006 - 11:24:29 PDT)
Re: AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied?
(Sat Jun 10 2006 - 10:06:49 PDT)
Re: AMBER: problem with amber 9 and igb=5
(Fri Jun 09 2006 - 14:58:02 PDT)
Re: AMBER: charmm force field in amber9
(Fri Jun 09 2006 - 07:02:03 PDT)
Re: AMBER: save coordinates during SANDER minimisation
(Thu Jun 08 2006 - 15:39:01 PDT)
Re: AMBER: software to visualize normal modes
(Thu Jun 08 2006 - 10:46:38 PDT)
Re: AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA.
(Wed Jun 07 2006 - 15:22:41 PDT)
Re: AMBER: compiler error for Amber9
(Wed Jun 07 2006 - 08:52:14 PDT)
Re: AMBER: Amber: Can't get sander to run
(Tue Jun 06 2006 - 13:31:56 PDT)
Re: AMBER: individual torsion/bond energies from a minimization
(Mon Jun 05 2006 - 07:21:40 PDT)
Re: AMBER: NMR restraint
(Fri Jun 02 2006 - 17:28:16 PDT)
Re: AMBER: some questions and problems about antechamber and divcon
(Fri Jun 02 2006 - 17:12:42 PDT)
Re: AMBER: trouble adding mdcrd files together
(Fri Jun 02 2006 - 16:30:20 PDT)
Re: AMBER: Namelists in input files
(Fri Jun 02 2006 - 13:48:42 PDT)
Re: AMBER: Installation of Amber8 on Fedora Core 5. .
(Fri Jun 02 2006 - 12:27:59 PDT)
AMBER: bugfix for frcmod.ff03 in Amber 9
(Fri Jun 02 2006 - 09:45:29 PDT)
Re: AMBER: Different results for TI calculation
(Thu Jun 01 2006 - 07:33:32 PDT)
David E. Konerding
Re: AMBER: Curves and Average Structures
(Mon Jun 26 2006 - 12:42:05 PDT)
David LeBard
Re: AMBER: AMD 64 Installation / configuration clarification
(Thu Jun 08 2006 - 16:52:57 PDT)
Re: AMBER: AMD 64 Installation / configuration clarification
(Thu Jun 08 2006 - 12:57:18 PDT)
David McGiven
Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test
(Wed Jun 21 2006 - 08:54:44 PDT)
AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test
(Wed Jun 21 2006 - 03:46:40 PDT)
David Mobley
AMBER: manual/prmtop/missing bonds section
(Mon Jun 26 2006 - 13:27:39 PDT)
AMBER: antechamber and FMN
(Tue Jun 06 2006 - 10:47:03 PDT)
Don.Bashford.stjude.org
Re: AMBER: Installation of Amber8 on Fedora Core 5. .
(Thu Jun 01 2006 - 09:23:11 PDT)
Douali, Latifa
AMBER: software to visualize normal modes
(Thu Jun 08 2006 - 10:03:26 PDT)
Eric Hu
AMBER: general question about hydrogen bond energy vs electrostatic energy
(Thu Jun 29 2006 - 17:58:24 PDT)
AMBER: repeat use of a trimer lib file
(Thu Jun 15 2006 - 16:35:39 PDT)
Evan Kelly
Re: AMBER: parmchk error
(Mon Jun 12 2006 - 22:42:16 PDT)
AMBER: parmchk error
(Sat Jun 10 2006 - 20:30:11 PDT)
AMBER: compile error with pgf90
(Thu Jun 01 2006 - 22:33:21 PDT)
Fabian Boes
Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband
(Thu Jun 29 2006 - 10:53:23 PDT)
AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband
(Thu Jun 29 2006 - 08:58:26 PDT)
Fabien Cailliez
AMBER: switching function for electrostatic interactions
(Mon Jun 12 2006 - 04:38:22 PDT)
FyD
Re: AMBER: Having trouble getting Iron parameters for QM/MM
(Thu Jun 29 2006 - 13:55:14 PDT)
Re: AMBER: Leap: neutralising the charge
(Tue Jun 27 2006 - 04:19:08 PDT)
Re: AMBER: how to create 2'-5' RNA
(Fri Jun 23 2006 - 23:29:43 PDT)
Re: AMBER: RESP charge fitting problems with capping group
(Thu Jun 22 2006 - 11:51:13 PDT)
Re: AMBER: LEaP error : unbalanced charge
(Mon Jun 19 2006 - 00:03:38 PDT)
Re: AMBER: LEaP Warning ... when do NH2-neutral fragment
(Tue Jun 13 2006 - 12:20:52 PDT)
Re: Fwd: AMBER: How to build N-terminal of alanine : NH2
(Thu Jun 08 2006 - 23:45:27 PDT)
Re: AMBER: How to build N-terminal of alanine : NH2
(Thu Jun 08 2006 - 01:27:58 PDT)
Giovanni
AMBER: problems on mm_pbsa
(Wed Jun 14 2006 - 05:05:03 PDT)
Glass, Kevin A
AMBER: REM test failures on IA-64 architecture
(Wed Jun 28 2006 - 08:28:07 PDT)
Guillaume Bollot
AMBER: Restraint internal coordinates in Amber 8.0
(Thu Jun 22 2006 - 02:00:03 PDT)
Gustavo Seabra
Re: AMBER: Fully QM periodic runs
(Wed Jun 14 2006 - 10:44:37 PDT)
Re: AMBER: How to strip waters in trajectorie ?
(Mon Jun 12 2006 - 12:57:30 PDT)
Hannes Barsch
AMBER: save coordinates during SANDER minimisation
(Thu Jun 08 2006 - 02:34:51 PDT)
Hannes Loeffler
AMBER: ions+proteins
(Mon Jun 19 2006 - 18:45:57 PDT)
Hashem Taha
AMBER: xleap problem
(Tue Jun 06 2006 - 11:29:31 PDT)
hayden
AMBER: RESP charge fitting problems with capping group
(Thu Jun 22 2006 - 02:51:52 PDT)
hbluo
AMBER: periodic boundary condition in the X and Y dimensions only
(Mon Jun 26 2006 - 15:15:51 PDT)
AMBER: periodic boundary condition in the X and Y dimensions only
(Mon Jun 26 2006 - 14:58:00 PDT)
Heike.Meiselbach.chemie.uni-erlangen.de
Re: AMBER: MMPBSA error
(Tue Jun 13 2006 - 08:27:22 PDT)
Ilyas Yildirim
Re: AMBER: how to create 2'-5' RNA
(Mon Jun 26 2006 - 15:52:10 PDT)
Re: AMBER: Can we submit jobs in sequences to amber?
(Mon Jun 26 2006 - 00:22:00 PDT)
Re: AMBER: help creating RNA
(Thu Jun 22 2006 - 12:29:49 PDT)
RE: AMBER: Umbrella sampling
(Sun Jun 18 2006 - 09:57:09 PDT)
Re: Fwd: Fwd: AMBER: LEaP error : unbalanced charge
(Sun Jun 18 2006 - 00:53:58 PDT)
Re: AMBER: Antechamber - NH2 and C not planar when it should be on one of my ligand
(Sat Jun 17 2006 - 01:28:55 PDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
(Wed Jun 14 2006 - 11:46:22 PDT)
Re: AMBER: LEaP Warning ... when do NH2-neutral fragment
(Tue Jun 13 2006 - 14:23:18 PDT)
Re: AMBER: Difficulty loading a pdb file
(Tue Jun 13 2006 - 14:25:27 PDT)
Re: AMBER: Umbrella sampling
(Sat Jun 10 2006 - 07:53:41 PDT)
Re: AMBER: save coordinates during SANDER minimisation
(Thu Jun 08 2006 - 03:22:24 PDT)
Re: AMBER: xleap problem
(Tue Jun 06 2006 - 23:49:04 PDT)
Re: AMBER: Thermodynamic integration using the amber 9
(Fri Jun 02 2006 - 13:12:18 PDT)
Jiang Jianwen
RE: AMBER: RMS FLUCTUATIONS
(Fri Jun 16 2006 - 00:01:10 PDT)
AMBER: RMS FLUCTUATIONS
(Thu Jun 15 2006 - 04:37:24 PDT)
jitrayut jitonnom
Fwd: Fwd: Fwd: AMBER: LEaP error : unbalanced charge
(Sun Jun 18 2006 - 06:17:57 PDT)
Fwd: Fwd: AMBER: LEaP error : unbalanced charge
(Sat Jun 17 2006 - 13:37:46 PDT)
AMBER: charge in LEaP step
(Sat Jun 17 2006 - 11:14:24 PDT)
Fwd: Fwd: AMBER: LEaP error : unbalanced charge
(Fri Jun 16 2006 - 10:28:08 PDT)
Fwd: AMBER: LEaP error : unbalanced charge
(Fri Jun 16 2006 - 09:34:42 PDT)
AMBER: LEaP error : unbalanced charge
(Fri Jun 16 2006 - 06:52:33 PDT)
Fwd: Fwd: AMBER: MMPBSA error
(Wed Jun 14 2006 - 04:27:51 PDT)
AMBER: LEaP Warning ... when do NH2-neutral fragment
(Tue Jun 13 2006 - 11:40:47 PDT)
Fwd: AMBER: MMPBSA error
(Tue Jun 13 2006 - 09:28:43 PDT)
AMBER: MMPBSA error
(Tue Jun 13 2006 - 07:52:08 PDT)
AMBER: How to strip waters in trajectorie ?
(Mon Jun 12 2006 - 12:50:02 PDT)
Fwd: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?
(Mon Jun 12 2006 - 12:15:06 PDT)
Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?
(Mon Jun 12 2006 - 11:37:49 PDT)
AMBER: How to calculate the mmpbsa for explicit MD ?
(Mon Jun 12 2006 - 09:41:52 PDT)
AMBER: MMPBSA problem
(Fri Jun 09 2006 - 02:48:50 PDT)
AMBER: Problem with Leap
(Thu Jun 08 2006 - 21:40:52 PDT)
Fwd: AMBER: How to build N-terminal of alanine : NH2
(Thu Jun 08 2006 - 05:32:22 PDT)
AMBER: How to build N-terminal of alanine : NH2
(Thu Jun 08 2006 - 00:59:34 PDT)
John Mongan
Re: AMBER: Implicit solvent question
(Fri Jun 23 2006 - 09:09:49 PDT)
Re: AMBER: problem with amber 9 and igb=5
(Wed Jun 07 2006 - 19:04:59 PDT)
JunJun Liu
Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl
(Thu Jun 29 2006 - 16:56:34 PDT)
Re: AMBER: kill job command?
(Thu Jun 22 2006 - 06:13:04 PDT)
Re: AMBER: What's the meaning of NTYPES?
(Wed Jun 21 2006 - 13:59:23 PDT)
AMBER: What's the meaning of NTYPES?
(Wed Jun 21 2006 - 13:27:51 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 18:08:32 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 16:45:52 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 15:55:09 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 14:37:52 PDT)
AMBER: why has "ELE " a large fluctuation in MMPBSA?
(Tue Jun 20 2006 - 06:56:25 PDT)
Re: Fwd: AMBER: MMPBSA error
(Tue Jun 13 2006 - 08:51:58 PDT)
Re: AMBER: Nmode memory allocation problem
(Tue Jun 13 2006 - 08:08:25 PDT)
AMBER: Nmode memory allocation problem
(Mon Jun 12 2006 - 16:45:14 PDT)
Junmei Wang
AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected
(Mon Jun 19 2006 - 20:08:56 PDT)
RE: AMBER: parmchk error
(Thu Jun 15 2006 - 08:16:10 PDT)
AMBER: RE: antechamber and FMN
(Wed Jun 07 2006 - 13:39:48 PDT)
Kara Di Giorgio
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
(Thu Jun 15 2006 - 09:27:45 PDT)
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
(Wed Jun 14 2006 - 10:20:40 PDT)
AMBER: Difficulty loading a pdb file
(Tue Jun 13 2006 - 11:20:41 PDT)
Kateryna Miroshnychenko
Re: AMBER: problems about compiling a parallel version of AMBER 9
(Tue Jun 27 2006 - 01:41:21 PDT)
Ken Merz
Re: AMBER: Having trouble getting Iron parameters for QM/MM
(Thu Jun 29 2006 - 12:54:45 PDT)
Re: AMBER: Fully QM periodic runs
(Thu Jun 15 2006 - 07:10:13 PDT)
Kenley Barrett
AMBER: rgbmax--something wrong with my input file?
(Tue Jun 27 2006 - 14:10:27 PDT)
khn _
AMBER: COM
(Thu Jun 08 2006 - 17:13:27 PDT)
Knut Langsetmo
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
(Wed Jun 14 2006 - 12:55:56 PDT)
Lauren O'Neil
AMBER: Curves and Average Structures
(Mon Jun 26 2006 - 10:26:46 PDT)
linfu
Re: Re: AMBER:it seems that The SAS in MMPBSA is SES , not SAS. ????
(Sat Jun 10 2006 - 20:27:20 PDT)
AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ????
(Fri Jun 09 2006 - 20:25:24 PDT)
AMBER: does the Amber8 or Amber9 contains Br,I and Sulfur parameter for MM-PBSA or MM-GBSA.
(Mon Jun 05 2006 - 19:24:17 PDT)
Re: AMBER: manual docking
(Sat Jun 03 2006 - 00:39:44 PDT)
Lwin, ThuZar
AMBER: problem with pattern searching in mm_pbsa_calceneent.pm, Amber8, when salt>0 using delphi version 4
(Wed Jun 28 2006 - 17:58:14 PDT)
AMBER: terms in mm-pbsa
(Wed Jun 21 2006 - 08:48:37 PDT)
M. Scott Shell
Re: AMBER: problem with amber 9 and igb=5
(Sat Jun 10 2006 - 11:40:05 PDT)
Re: AMBER: problem with amber 9 and igb=5
(Thu Jun 08 2006 - 22:15:56 PDT)
Re: AMBER: problem with amber 9 and igb=5
(Thu Jun 08 2006 - 09:05:10 PDT)
Re: AMBER: problem with amber 9 and igb=5
(Thu Jun 08 2006 - 08:55:36 PDT)
AMBER: problem with amber 9 and igb=5
(Wed Jun 07 2006 - 18:06:02 PDT)
Marcela Madrid
AMBER: ptraj
(Fri Jun 09 2006 - 14:19:54 PDT)
Marie Brut
AMBER: second derivative matrix
(Tue Jun 20 2006 - 05:28:02 PDT)
Martin LEPSIK
AMBER: GBSA of nonstandard cations
(Thu Jun 15 2006 - 15:46:16 PDT)
Martin Peters
Re: AMBER: some questions and problems about antechamber and divcon
(Fri Jun 02 2006 - 06:07:03 PDT)
mathew k varghese
AMBER: manual docking
(Fri Jun 02 2006 - 20:50:03 PDT)
AMBER: manual docking
(Fri Jun 02 2006 - 20:39:13 PDT)
mbrut.laas.fr
AMBER: Second derivative matrix
(Sat Jun 24 2006 - 04:21:27 PDT)
Mengjuei Hsieh
Re: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
(Sun Jun 25 2006 - 21:15:26 PDT)
Miguel Ferreira
AMBER: MM-PBSA questions
(Wed Jun 28 2006 - 18:26:14 PDT)
AMBER: Leap: neutralising the charge
(Tue Jun 27 2006 - 02:49:36 PDT)
AMBER: MD stopped
(Sat Jun 10 2006 - 02:33:05 PDT)
Mingfeng Yang
Re: AMBER: ptraj: rms per residue
(Wed Jun 14 2006 - 13:28:07 PDT)
Myunggi Yi
Re: AMBER: Amber minimization with multiple restraints
(Wed Jun 28 2006 - 12:53:12 PDT)
Re: AMBER: Amber minimization with multiple restraints
(Wed Jun 28 2006 - 12:56:49 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 14:55:05 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 13:07:36 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 11:20:53 PDT)
AMBER: ptraj vector
(Tue Jun 20 2006 - 09:13:54 PDT)
Re: AMBER: antechamber
(Wed Jun 07 2006 - 09:31:46 PDT)
Re: AMBER: xleap problem
(Wed Jun 07 2006 - 07:22:12 PDT)
Re: AMBER: xleap problem
(Tue Jun 06 2006 - 16:42:34 PDT)
Re: AMBER: xleap problem
(Tue Jun 06 2006 - 16:32:16 PDT)
Re: AMBER: NMR restraint
(Sat Jun 03 2006 - 06:25:26 PDT)
Re: AMBER: NMR restraint
(Fri Jun 02 2006 - 12:23:28 PDT)
Re: AMBER: NMR restraint
(Fri Jun 02 2006 - 12:15:41 PDT)
AMBER: NMR restraint
(Fri Jun 02 2006 - 11:11:51 PDT)
AMBER: distance restraints
(Fri Jun 02 2006 - 08:06:38 PDT)
nag raj
AMBER: Non bond list overflow in amber8.0 program.
(Sun Jun 18 2006 - 21:54:04 PDT)
AMBER: Programes to calculate ligand RMSD
(Fri Jun 02 2006 - 03:59:04 PDT)
Navnit Kumar Mishra
Re: AMBER: mm_pbsa calculation for calcium
(Tue Jun 13 2006 - 10:26:56 PDT)
Re: AMBER: mm_pbsa calculation for calcium
(Tue Jun 13 2006 - 00:45:32 PDT)
AMBER: mm_pbsa calculation for calcium
(Sun Jun 11 2006 - 22:59:06 PDT)
AMBER: process_mdout
(Mon Jun 05 2006 - 05:00:40 PDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system?
(Mon Jun 05 2006 - 02:22:33 PDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in a complex system?
(Mon Jun 05 2006 - 01:08:12 PDT)
opitz.che.udel.edu
AMBER: Amber7-CHARMM22-TRIPOS force fields
(Mon Jun 19 2006 - 08:37:24 PDT)
pang zhao
AMBER: use ptraj and two differenct prmtop file to analyze LES trajectory
(Fri Jun 09 2006 - 01:56:57 PDT)
AMBER: How to analyze the trajectory generated by LES simulation
(Fri Jun 02 2006 - 00:08:03 PDT)
Peter Gannett
AMBER: SGI compiler problems
(Tue Jun 13 2006 - 05:46:18 PDT)
pkb bioinfo
AMBER: How to submit a job in cluster
(Tue Jun 06 2006 - 01:46:21 PDT)
pkmukher
Re: AMBER: pmemd_parallel_ins_prob
(Thu Jun 08 2006 - 11:09:00 PDT)
AMBER: pmemd_parallel_ins_prob
(Wed Jun 07 2006 - 14:00:20 PDT)
priya priya
AMBER: can i use unusual amino acid
(Thu Jun 22 2006 - 02:15:55 PDT)
Qingning Shu
AMBER: Amber minimization with multiple restraints
(Mon Jun 26 2006 - 10:23:33 PDT)
Ray Luo
Re: AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl
(Thu Jun 29 2006 - 17:47:13 PDT)
Re: AMBER: MM-PBSA questions
(Thu Jun 29 2006 - 22:56:42 PDT)
Re: AMBER: MM-PBSA and gaff atom types
(Tue Jun 27 2006 - 19:47:51 PDT)
Re: AMBER: problems on mm_pbsa
(Tue Jun 13 2006 - 22:04:28 PDT)
Re: AMBER: is seems that The SAS in MMPBSA is SES , not SAS. ????
(Sat Jun 10 2006 - 10:45:17 PDT)
Re: AMBER: Ask for help in pbsa error in AMBER9
(Thu Jun 08 2006 - 12:01:06 PDT)
Ricardo J. F. Branco
Re: AMBER: references
(Fri Jun 23 2006 - 03:47:50 PDT)
AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8
(Fri Jun 23 2006 - 00:36:44 PDT)
Robert Duke
Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband
(Thu Jun 29 2006 - 11:24:14 PDT)
Re: AMBER: Strange problems with PMEMD on Intel Xeons with Infiniband
(Thu Jun 29 2006 - 09:37:53 PDT)
Re: AMBER: Problems with restart file from pmemd sim.
(Sat Jun 17 2006 - 06:10:24 PDT)
Re: AMBER: pmemd_parallel_ins_prob
(Wed Jun 07 2006 - 14:21:28 PDT)
Re: AMBER: compiler error for Amber9
(Wed Jun 07 2006 - 08:03:15 PDT)
Robert Konecny
AMBER: ANN: APBS/Amber interface released
(Thu Jun 22 2006 - 23:23:35 PDT)
Roberto Gomperts
Re: AMBER: Can we submit jobs in sequences to amber?
(Mon Jun 26 2006 - 03:25:03 PDT)
Re: AMBER: SGI compiler problems
(Wed Jun 21 2006 - 08:09:54 PDT)
Re: AMBER: Amber9 under SGI Prism (Altix) with Intel 8.0 error in pbpgb test
(Wed Jun 21 2006 - 07:10:44 PDT)
Ross Walker
RE: AMBER: Having trouble getting Iron parameters for QM/MM
(Fri Jun 30 2006 - 01:54:28 PDT)
RE: AMBER: rgbmax--something wrong with my input file?
(Tue Jun 27 2006 - 15:52:06 PDT)
RE: AMBER: constant pressure equillibration
(Fri Jun 23 2006 - 08:53:17 PDT)
RE: AMBER: Post-MD minimization
(Fri Jun 23 2006 - 05:19:14 PDT)
RE: AMBER: Ptraj reimage truncated octahedral box simulation with AMBER8
(Fri Jun 23 2006 - 04:34:47 PDT)
RE: AMBER: references
(Fri Jun 23 2006 - 04:32:57 PDT)
RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN
(Fri Jun 23 2006 - 04:28:17 PDT)
RE: AMBER: Post-MD minimization
(Mon Jun 19 2006 - 08:20:25 PDT)
RE: AMBER: Difficulty loading a pdb file (Modified by Kara Di Giorgio)
(Wed Jun 14 2006 - 13:06:49 PDT)
RE: AMBER: Fully QM periodic runs
(Wed Jun 14 2006 - 09:41:58 PDT)
RE: AMBER: Difficulty loading a pdb file
(Wed Jun 14 2006 - 07:05:34 PDT)
RE: AMBER: Nmode memory allocation problem
(Mon Jun 12 2006 - 18:34:24 PDT)
RE: AMBER: MD stopped
(Mon Jun 12 2006 - 08:50:34 PDT)
RE: AMBER: parmchk error
(Mon Jun 12 2006 - 08:31:59 PDT)
RE: AMBER: switching function for electrostatic interactions
(Mon Jun 12 2006 - 08:28:19 PDT)
RE: AMBER: problem with amber 9 and igb=5
(Sat Jun 10 2006 - 12:31:26 PDT)
RE: AMBER: software to visualize normal modes
(Thu Jun 08 2006 - 10:07:41 PDT)
RE: AMBER: antechamber
(Wed Jun 07 2006 - 09:56:01 PDT)
RE: AMBER: compiler error for Amber9
(Wed Jun 07 2006 - 08:34:20 PDT)
RE: AMBER: Amber: Segfault while running sander
(Mon Jun 05 2006 - 11:31:35 PDT)
RE: AMBER: process_mdout
(Mon Jun 05 2006 - 08:19:47 PDT)
RE: AMBER: compile error with pgf90
(Fri Jun 02 2006 - 08:15:01 PDT)
RE: AMBER: Another Installation Problem
(Thu Jun 01 2006 - 22:02:03 PDT)
RE: AMBER: Amber 8 QMMM tests fail on AIX
(Thu Jun 01 2006 - 09:27:24 PDT)
S.Sundar Raman
AMBER: compiler requirement for SGI Fuel To install AMBER9
(Tue Jun 13 2006 - 23:45:40 PDT)
sangeeta.bioinfo.ernet.in
AMBER:Checkoverlap query
(Mon Jun 26 2006 - 05:12:56 PDT)
RE: AMBER: Post-MD minimization
(Thu Jun 22 2006 - 23:09:31 PDT)
AMBER: MMTSB: phi-pdi-based clustering
(Wed Jun 21 2006 - 05:37:39 PDT)
RE: AMBER: checkoverlap doubt [was: Post-MD minimization]
(Tue Jun 20 2006 - 06:21:11 PDT)
AMBER: Post-MD minimization
(Mon Jun 19 2006 - 04:33:58 PDT)
Scott Brozell
AMBER: Re: Problem in compiling sander with MMTSB
(Thu Jun 15 2006 - 16:28:27 PDT)
AMBER: Re: Problem in compiling sander with MMTSB
(Wed Jun 14 2006 - 20:29:57 PDT)
Scott Pendley
Re: AMBER: mm_pbsa calculation for calcium
(Tue Jun 13 2006 - 13:03:17 PDT)
Re: AMBER: mm_pbsa calculation for calcium
(Tue Jun 13 2006 - 09:20:42 PDT)
Re: AMBER: mm_pbsa calculation for calcium
(Mon Jun 12 2006 - 14:42:59 PDT)
Re: AMBER: Another Installation Problem
(Fri Jun 02 2006 - 09:21:09 PDT)
Seth Lilavivat
AMBER: Creating an Intercalation site
(Sat Jun 17 2006 - 12:25:59 PDT)
AMBER: Compiling / Installing Amber 8 on SUSE 10.1
(Tue Jun 13 2006 - 20:23:25 PDT)
AMBER: Another Installation Problem
(Thu Jun 01 2006 - 16:01:13 PDT)
sethl.gatech.edu
AMBER: NAMOT
(Fri Jun 30 2006 - 12:17:46 PDT)
AMBER: creating RNA, nucgen / leap
(Mon Jun 26 2006 - 13:59:46 PDT)
Re: AMBER: help creating RNA
(Mon Jun 26 2006 - 08:42:00 PDT)
AMBER: how to create 2'-5' RNA
(Fri Jun 23 2006 - 14:13:57 PDT)
AMBER: help creating RNA
(Thu Jun 22 2006 - 12:14:06 PDT)
AMBER: help with custom RNA molecule
(Mon Jun 19 2006 - 11:55:59 PDT)
AMBER: best way to customize linkages
(Wed Jun 14 2006 - 13:25:07 PDT)
Re: AMBER: AMD 64 Installation / configuration clarification
(Thu Jun 08 2006 - 13:23:51 PDT)
AMBER: AMD 64 Installation / configuration clarification
(Thu Jun 08 2006 - 12:09:50 PDT)
AMBER: Amber: Can't get sander to run
(Tue Jun 06 2006 - 11:15:14 PDT)
AMBER: Amber: Segfault while running sander
(Mon Jun 05 2006 - 11:19:33 PDT)
Shan-ho Tsai
RE: AMBER: Amber 8 QMMM tests fail on AIX
(Thu Jun 01 2006 - 10:31:08 PDT)
AMBER: Amber 8 QMMM tests fail on AIX
(Thu Jun 01 2006 - 08:08:26 PDT)
simon whitehead
Re: AMBER: references
(Fri Jun 23 2006 - 04:46:22 PDT)
AMBER: constant pressure equillibration
(Fri Jun 23 2006 - 02:17:35 PDT)
AMBER: references
(Fri Jun 23 2006 - 03:35:56 PDT)
AMBER: ptraj: rms per residue
(Wed Jun 14 2006 - 07:14:28 PDT)
Re: AMBER: How to strip waters in trajectorie ?
(Tue Jun 13 2006 - 01:24:37 PDT)
sishi.tang.utoronto.ca
AMBER: about GBSA
(Sun Jun 25 2006 - 11:45:11 PDT)
snoze pa
AMBER: openmpi
(Wed Jun 21 2006 - 10:28:28 PDT)
AMBER: amber9 hostfile
(Tue Jun 20 2006 - 17:12:50 PDT)
Re: AMBER: manual docking
(Sun Jun 04 2006 - 21:46:05 PDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB
(Thu Jun 01 2006 - 08:41:02 PDT)
soo
AMBER: charmm force field in amber9
(Thu Jun 08 2006 - 21:23:26 PDT)
Steve Seibold
AMBER: antechamber
(Wed Jun 07 2006 - 09:16:47 PDT)
Steven Winfield
AMBER: Fully QM periodic runs
(Wed Jun 14 2006 - 09:03:43 PDT)
Thomas Cheatham
Re: AMBER: Question about ptraj setup for phase angles (P) of ribose sugar puckering
(Wed Jun 28 2006 - 09:22:42 PDT)
Re: AMBER: average struct.problem
(Thu Jun 22 2006 - 07:35:45 PDT)
Re: AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 16:48:54 PDT)
RE: AMBER: checkoverlap doubt [was: Post-MD minimization]
(Tue Jun 20 2006 - 15:28:36 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 15:13:06 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 14:59:50 PDT)
Re: AMBER: ptraj vector
(Tue Jun 20 2006 - 12:32:17 PDT)
Re: AMBER: switching function for electrostatic interactions
(Mon Jun 12 2006 - 09:12:28 PDT)
Re: AMBER: COM
(Thu Jun 08 2006 - 17:34:03 PDT)
Re: AMBER: MM-PBSA and first solvation shell
(Mon Jun 05 2006 - 10:23:58 PDT)
Re: AMBER: AMBER mdcrd file bigger than 2GB
(Thu Jun 01 2006 - 09:25:19 PDT)
Thomas Pochapsky
AMBER: individual torsion/bond energies from a minimization
(Fri Jun 02 2006 - 06:25:33 PDT)
Thomas Steinbrecher
Re: AMBER: Tutorial 2: Production MD.
(Wed Jun 21 2006 - 08:37:51 PDT)
Re: AMBER: LEaP error : unbalanced charge
(Fri Jun 16 2006 - 07:59:50 PDT)
Re: AMBER: saveamberparams error in Amber9
(Wed Jun 14 2006 - 08:07:28 PDT)
Re: Fwd: AMBER: How to calculate the mmpbsa for explicit MD ?
(Mon Jun 12 2006 - 11:50:30 PDT)
Re: AMBER: How to calculate the mmpbsa for explicit MD ?
(Mon Jun 12 2006 - 09:58:33 PDT)
Re: AMBER: MMPBSA problem
(Fri Jun 09 2006 - 08:06:34 PDT)
tmarch.coin.org
Re: AMBER: rgbmax--something wrong with my input file?
(Wed Jun 28 2006 - 14:37:19 PDT)
Tonda March
AMBER: offset?
(Wed May 31 2006 - 23:12:19 PDT)
Vlad Cojocaru
Re: AMBER: help creating RNA
(Fri Jun 23 2006 - 01:14:24 PDT)
AMBER: calculating box dimensions during MD
(Tue Jun 06 2006 - 07:13:14 PDT)
Re: AMBER: How to analyze the trajectory generated by LES simulation
(Fri Jun 02 2006 - 02:54:20 PDT)
Wei Zhang
Re: AMBER: problems about compiling a parallel version of AMBER 9
(Thu Jun 22 2006 - 09:21:32 PDT)
Re: AMBER: What's the meaning of NTYPES?
(Thu Jun 22 2006 - 09:18:38 PDT)
Re: AMBER: Fully QM periodic runs
(Wed Jun 14 2006 - 09:58:51 PDT)
Weihua Li
Re: AMBER: saveamberparams error in Amber9
(Wed Jun 14 2006 - 23:48:52 PDT)
Re: AMBER: saveamberparams error in Amber9
(Wed Jun 14 2006 - 19:15:03 PDT)
AMBER: saveamberparams error in Amber9
(Wed Jun 14 2006 - 06:28:43 PDT)
AMBER: compiler error for Amber9
(Wed Jun 07 2006 - 07:34:49 PDT)
Xioling Chuang
Re: AMBER: How to calculate binding free energy using MM-PBSA
(Thu Jun 29 2006 - 21:16:48 PDT)
AMBER: How to calculate binding free energy using MM-PBSA
(Thu Jun 29 2006 - 02:38:58 PDT)
Yong Duan
RE: AMBER: RMS FLUCTUATIONS
(Thu Jun 15 2006 - 07:49:16 PDT)
Yongmei Pan
AMBER: Why the energy from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied?
(Fri Jun 09 2006 - 19:57:42 PDT)
AMBER: Why the result from sander minimization (epsilon=4r) is not same with that from nmode, when restraint is applied?
(Fri Jun 09 2006 - 20:03:26 PDT)
yxiong99
AMBER: inconsistence in MM_PBSA between mm_pbsa .pl and mm_pbsa_statistics.pl
(Thu Jun 29 2006 - 13:49:50 PDT)
AMBER: why has "ELE " a large fluctuation in MMP BSA?
(Tue Jun 20 2006 - 06:47:44 PDT)
zachary hartman
AMBER: Having trouble getting Iron parameters for QM/MM
(Thu Jun 29 2006 - 12:23:06 PDT)
Zhihong Yu
AMBER: How to simplify this big system rationally to perform MD studies
(Wed Jun 14 2006 - 03:43:59 PDT)
Re: AMBER: How to use the prmtop and inpcrd files of ligand in acomplex system?
(Mon Jun 05 2006 - 01:57:44 PDT)
AMBER: How to use the prmtop and inpcrd files of ligand in a complex system?
(Sat Jun 03 2006 - 00:00:23 PDT)
AMBER: attachments for my last mail
(Fri Jun 02 2006 - 00:30:30 PDT)
AMBER: some questions and problems about antechamber and divcon
(Fri Jun 02 2006 - 00:11:22 PDT)
Егоров Д.А.
AMBER: Bond Force Conctants in Amber Force Fields
(Wed May 31 2006 - 22:22:01 PDT)
Last message date
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Wed Jul 19 2006 - 06:07:08 PDT
Archived on
: Mon May 06 2024 - 05:53:22 PDT
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