Amber Archive May 2009 by author
563 messages
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Starting
Wed May 20 2009 - 13:57:26 PDT,
Ending
Mon Jun 01 2009 - 01:11:52 PDT
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Adrian Roitberg
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 13:56:14 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:44:08 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:38:23 PDT)
Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
(Sat May 09 2009 - 11:07:08 PDT)
Alan
[AMBER] ligand QM/semi-empirical coords optmisation
(Tue May 26 2009 - 03:55:09 PDT)
[AMBER] Re: About Amber installations
(Tue May 26 2009 - 02:53:37 PDT)
Alessandro Nascimento
Re: [AMBER] Unit 8 Error on OPEN: prmtop
(Sun May 24 2009 - 11:28:26 PDT)
amit
Re: [AMBER] Protein with HETATM, am I doing the
(Mon May 25 2009 - 08:26:15 PDT)
Amit Bajaj
Re: [AMBER] Protein with HETATM, am I doing the
(Wed May 20 2009 - 22:26:49 PDT)
Andrew Purkiss-Trew
RE: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 08:16:40 PDT)
Re: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 07:30:14 PDT)
aneesh cna
Re: [AMBER] High energy during minimization
(Tue May 05 2009 - 22:58:00 PDT)
[AMBER] High energy during minimization
(Sat May 02 2009 - 21:26:16 PDT)
Atro Tossavainen
Re: [AMBER] Installation directory
(Mon May 25 2009 - 01:10:34 PDT)
Bala subramanian
[AMBER] secstruct with ptraj
(Fri May 15 2009 - 03:19:54 PDT)
Re: [OFFLIST] Re: [AMBER] amber9 in fedora10
(Thu May 14 2009 - 01:18:07 PDT)
[AMBER] amber9 in fedora10
(Wed May 13 2009 - 02:50:25 PDT)
[AMBER] ptraj netcdf
(Tue May 12 2009 - 05:04:00 PDT)
Barbault Florent
Re: [AMBER] Problem with MM-PBSA energy calculation
(Mon May 25 2009 - 11:57:19 PDT)
ben rodriguez
[AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'
(Fri May 15 2009 - 15:09:44 PDT)
Bill Ross
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration
(Thu May 28 2009 - 08:42:13 PDT)
Re: [AMBER] problem with MM-PBSA
(Wed May 27 2009 - 17:52:19 PDT)
Re: [AMBER] Modification of His
(Mon May 18 2009 - 13:06:16 PDT)
RE: [AMBER] What is the purpose to do the bond constraints?
(Mon May 18 2009 - 12:39:42 PDT)
Re: [AMBER] High energy during minimization
(Sun May 03 2009 - 11:00:32 PDT)
Bokun Cho
Re: [AMBER] RE: Listing gaff parameters in frcmod
(Thu May 07 2009 - 22:00:47 PDT)
[AMBER] RE: Listing gaff parameters in frcmod
(Thu May 07 2009 - 21:20:46 PDT)
Bradshaw, Richard
[AMBER] MM-PBSA and NetCDF
(Wed May 27 2009 - 08:38:13 PDT)
C Liu
[AMBER] QM/MM assigns Cd to C, Se to S
(Sat May 02 2009 - 19:09:27 PDT)
Carlos Simmerling
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 14:17:05 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 13:52:56 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 13:22:31 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:57:24 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:56:26 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:44:41 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:41:20 PDT)
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration
(Thu May 28 2009 - 11:15:09 PDT)
Re: [AMBER] Molecular simulation of a protein using special H2O cluster
(Tue May 26 2009 - 17:25:03 PDT)
Re: [AMBER] Molecular simulation of a protein using special H2O cluster
(Tue May 26 2009 - 04:45:50 PDT)
Re: [AMBER] Loading PDB of complex
(Thu May 21 2009 - 06:48:06 PDT)
Re: [AMBER] loadpdb atom type
(Tue May 19 2009 - 10:09:29 PDT)
Re: [AMBER] pmemd running very slow in amber10
(Thu May 14 2009 - 03:09:11 PDT)
Re: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 07:23:25 PDT)
Re: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 06:36:27 PDT)
Re: [AMBER] multiple chain specification in Sander
(Thu May 07 2009 - 03:19:09 PDT)
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Tue May 05 2009 - 10:32:42 PDT)
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Tue May 05 2009 - 09:39:52 PDT)
Re: [AMBER] Charge problem
(Tue May 05 2009 - 05:58:31 PDT)
Re: [AMBER] Suggestion for restraining chain of a protein
(Tue May 05 2009 - 05:27:05 PDT)
Re: [AMBER] Charge problem
(Tue May 05 2009 - 05:16:32 PDT)
Re: [AMBER] A confusion about tutorial B1
(Tue May 05 2009 - 03:11:43 PDT)
Re: [AMBER] Problem in production run
(Tue May 05 2009 - 03:07:11 PDT)
Re: [AMBER] Suggestion for restraining chain of a protein
(Tue May 05 2009 - 03:05:16 PDT)
Re: [AMBER] Number of processor in pmemd
(Mon May 04 2009 - 10:27:06 PDT)
Re: [AMBER] Parameter file not saved
(Mon May 04 2009 - 05:19:14 PDT)
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Sun May 03 2009 - 04:11:07 PDT)
Re: [AMBER] Amber FF and Glycam
(Fri May 01 2009 - 05:41:35 PDT)
Catein Catherine
[AMBER] AMBER for dual core processor?
(Thu May 07 2009 - 01:05:17 PDT)
[AMBER] Error in parallel run
(Wed May 06 2009 - 19:46:02 PDT)
[AMBER] Error message in "make test.sander" Is amber compatible with dual processors?
(Wed May 06 2009 - 06:08:49 PDT)
RE: [AMBER] Error message in "make test.sander"
(Tue May 05 2009 - 23:58:04 PDT)
RE: [AMBER] Error message in "make test.sander"
(Tue May 05 2009 - 22:40:54 PDT)
[AMBER] Error message in "make test.sander"
(Tue May 05 2009 - 19:52:26 PDT)
RE: [AMBER] QM/MM
(Tue May 05 2009 - 19:48:44 PDT)
[AMBER] Why the job idle before the sentence "| Running AMBER/MPI version on 2 nodes"?
(Mon May 04 2009 - 08:16:08 PDT)
RE: [AMBER] Error message for tutorial 1 (run in parallel)
(Mon May 04 2009 - 06:31:05 PDT)
[AMBER] Script for parallel runs 2
(Mon May 04 2009 - 02:41:58 PDT)
[AMBER] Script for parallel runs
(Mon May 04 2009 - 02:17:42 PDT)
[AMBER] Error message for tutorial 1 (run in parallel)
(Mon May 04 2009 - 02:05:17 PDT)
cgji
Re: [AMBER] How to take into account the charge in GAFF parameterization
(Thu May 28 2009 - 23:49:44 PDT)
chaitanya koppisetty
Re: [AMBER] normal modes calculation
(Thu May 14 2009 - 01:51:28 PDT)
CHAMI F.
RE: [AMBER] Amber/CHARMM summer school
(Thu May 21 2009 - 04:56:23 PDT)
Chih-Ying Lin
[AMBER] protein molecular weight?
(Fri May 29 2009 - 15:44:24 PDT)
Re: [AMBER] Why NaCl or KCl solution?
(Wed May 27 2009 - 19:11:21 PDT)
Re: RE: [AMBER] How to choose the counter ions for proteins?
(Sat May 23 2009 - 11:16:49 PDT)
[AMBER] Why NaCl or KCl solution?
(Sat May 23 2009 - 09:41:33 PDT)
[AMBER] How to choose the counter ions for proteins?
(Fri May 22 2009 - 22:42:40 PDT)
[AMBER] Why does protein carry charges?
(Fri May 22 2009 - 21:09:21 PDT)
[AMBER] What are the elements to speed up the simulation?
(Tue May 19 2009 - 15:17:07 PDT)
[AMBER] The protein swell?
(Sun May 17 2009 - 15:17:51 PDT)
[AMBER] What is the purpose to do the bond constraints?
(Sun May 17 2009 - 15:09:04 PDT)
[AMBER] How to setup the pH value?
(Sat May 16 2009 - 10:29:21 PDT)
[AMBER] how to make the different/specific displacement of ligand around protein?
(Fri May 15 2009 - 16:55:49 PDT)
Re: [AMBER] Protein Docking
(Thu May 14 2009 - 21:28:43 PDT)
[AMBER] Protein Docking
(Mon May 11 2009 - 13:21:45 PDT)
Chris Moth
Re: [AMBER] ptraj netcdf
(Tue May 12 2009 - 08:46:31 PDT)
Chunliyan
[AMBER] re: essential dynamics
(Wed May 13 2009 - 10:25:57 PDT)
[AMBER] essential dynamics
(Wed May 13 2009 - 09:23:23 PDT)
Cihan Aydin
Re: [AMBER] MM-PBSA tutorial
(Thu May 14 2009 - 18:19:04 PDT)
Collins Nganou
[AMBER] skip parallel test
(Tue May 05 2009 - 06:09:00 PDT)
[AMBER] make test.parallel.MM error
(Sun May 03 2009 - 14:20:51 PDT)
David A. Case
Re: [AMBER] broken Ligand
(Sun May 31 2009 - 05:50:57 PDT)
Re: [AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically
(Sat May 30 2009 - 06:11:59 PDT)
Re: [AMBER] QQD psuedoatom restraints
(Fri May 29 2009 - 12:26:27 PDT)
Re: [AMBER] QQD psuedoatom restraints
(Fri May 29 2009 - 08:18:29 PDT)
Re: [AMBER] broken Ligand
(Fri May 29 2009 - 07:45:20 PDT)
Re: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 14:52:29 PDT)
Re: [AMBER] xleap segmentation fault
(Thu May 28 2009 - 13:05:12 PDT)
Re: [AMBER] Minimization error on protonated system? Please help. Thanks!
(Thu May 28 2009 - 08:17:59 PDT)
Re: [AMBER] SANDER BOMB
(Thu May 28 2009 - 07:29:50 PDT)
Re: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels
(Wed May 27 2009 - 04:57:07 PDT)
Re: [AMBER] Tutorial 4 Please check the total charge and your -nc flag
(Wed May 27 2009 - 04:42:29 PDT)
Re: [AMBER] mdfil: Error unknown flag during sander minimization
(Tue May 26 2009 - 07:05:37 PDT)
Re: [AMBER] problem with program anal within Amber10
(Tue May 26 2009 - 05:03:01 PDT)
Re: [AMBER] ligand QM/semi-empirical coords optmisation
(Tue May 26 2009 - 04:41:25 PDT)
Re: [AMBER] problem with MM-PBSA
(Tue May 26 2009 - 04:37:31 PDT)
Re: [AMBER] file contains 2 atoms not in residue templates
(Sun May 24 2009 - 06:12:14 PDT)
Re: [AMBER] Protein with HETATM, am I doing the right thing
(Sat May 23 2009 - 05:13:01 PDT)
Re: [AMBER] Nab units ?
(Fri May 22 2009 - 18:33:34 PDT)
Re: [AMBER] Installation directory
(Thu May 21 2009 - 11:19:28 PDT)
Re: [AMBER] Protein with HETATM, am I doing the right thing
(Thu May 21 2009 - 05:39:14 PDT)
Re: [AMBER] Problem with Nmode
(Thu May 21 2009 - 05:29:06 PDT)
Re: [AMBER] errors when add ions
(Thu May 21 2009 - 05:23:08 PDT)
Re: [AMBER] Problem with Nmode
(Wed May 20 2009 - 11:02:44 PDT)
[AMBER] Amber/CHARMM summer school
(Wed May 20 2009 - 05:40:39 PDT)
Re: [AMBER] gaff and aromatic compounds
(Wed May 20 2009 - 05:04:05 PDT)
Re: [AMBER] How to setup the pH value?
(Tue May 19 2009 - 12:08:53 PDT)
Re: [AMBER] loadpdb atom type
(Tue May 19 2009 - 11:19:44 PDT)
Re: [AMBER] gaff and aromatic compounds
(Tue May 19 2009 - 09:07:29 PDT)
Re: [AMBER] Problem with nonstandard residues
(Tue May 19 2009 - 08:22:15 PDT)
Re: [AMBER] Problem with nonstandard residues
(Tue May 19 2009 - 05:54:14 PDT)
Re: [AMBER] makeDIST_RST: no map function for ambiguous restraint
(Tue May 19 2009 - 05:35:31 PDT)
Re: [AMBER] Amber - Leap- SolvateBox help
(Tue May 19 2009 - 04:48:39 PDT)
Re: [AMBER] problem with parmchk
(Mon May 18 2009 - 13:00:07 PDT)
Re: [AMBER] problem with parmchk
(Mon May 18 2009 - 07:19:54 PDT)
Re: [AMBER] Modification of His
(Mon May 18 2009 - 05:31:33 PDT)
Re: [AMBER] Modification of His
(Mon May 18 2009 - 04:58:34 PDT)
Re: [AMBER] parallel amber on cluster
(Mon May 18 2009 - 04:54:18 PDT)
Re: [AMBER] FE: unexpected coordination 4 - using nonstandard tree type '4'
(Fri May 15 2009 - 16:56:34 PDT)
Re: [AMBER] Amber - Leap- SolvateBox help
(Fri May 15 2009 - 16:57:00 PDT)
Re: [AMBER] xleap reading hydrogens giving error
(Fri May 15 2009 - 09:25:11 PDT)
Re: [AMBER] xleap reading hydrogens giving error
(Fri May 15 2009 - 07:17:04 PDT)
Re: [AMBER] molecular crystal simulation
(Wed May 13 2009 - 15:28:37 PDT)
Re: [AMBER] re: essential dynamics
(Wed May 13 2009 - 10:48:42 PDT)
Re: [AMBER] essential dynamics
(Wed May 13 2009 - 10:15:50 PDT)
Re: [AMBER] building quadruplex with NAB
(Wed May 13 2009 - 04:48:38 PDT)
Re: [AMBER] Adding non standard residues
(Mon May 11 2009 - 10:30:56 PDT)
Re: [AMBER] molsurf and probe radius
(Mon May 11 2009 - 08:03:10 PDT)
Re: [AMBER] The resonable way to create single strand DNA with NAB ?
(Mon May 11 2009 - 04:34:16 PDT)
Re: [AMBER] Problems in the result of MM_PBSA
(Fri May 08 2009 - 05:45:19 PDT)
Re: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 07:09:55 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Thu May 07 2009 - 04:33:20 PDT)
Re: [AMBER] xleap input pdb problem
(Wed May 06 2009 - 19:16:10 PDT)
Re: [AMBER] difference in temperature
(Wed May 06 2009 - 05:08:01 PDT)
Re: [AMBER] A confusion about tutorial B1
(Tue May 05 2009 - 08:41:54 PDT)
Re: [AMBER] skip parallel test
(Tue May 05 2009 - 08:34:14 PDT)
Re: [AMBER] creating new residue adds none wanted ter
(Tue May 05 2009 - 05:07:53 PDT)
Re: [AMBER] creating new residue adds none wanted ter
(Mon May 04 2009 - 11:27:58 PDT)
Re: [AMBER] normal mode analysis
(Mon May 04 2009 - 11:06:32 PDT)
Re: [AMBER] normal mode analysis
(Mon May 04 2009 - 06:37:02 PDT)
Re: [AMBER] creating new residue adds none wanted ter
(Mon May 04 2009 - 06:35:41 PDT)
Re: [AMBER] Error message for tutorial 1 (run in parallel)
(Mon May 04 2009 - 05:40:36 PDT)
Re: [AMBER] High energy during minimization
(Sun May 03 2009 - 06:40:22 PDT)
Re: [AMBER] charge of Fe-heme
(Fri May 01 2009 - 15:52:45 PDT)
David Watson
[AMBER] molsurf and probe radius
(Sat May 09 2009 - 10:32:43 PDT)
Dechang Li
Re: [AMBER] J coupling constant calculation
(Thu May 28 2009 - 22:31:06 PDT)
Dmitry Osolodkin
Re: [AMBER] MM-PBSA nmode statistics
(Sat May 30 2009 - 10:25:46 PDT)
Re: [AMBER] MM-PBSA nmode statistics
(Fri May 29 2009 - 03:53:27 PDT)
[AMBER] MM-PBSA nmode statistics
(Thu May 28 2009 - 04:54:18 PDT)
[AMBER] Non-zero internal energy in single trajectory MM-PBSA calculations
(Mon May 04 2009 - 02:24:59 PDT)
Dong Xu
[AMBER] MM-GBSA energy decomposition and pairwise decomposition question
(Fri May 15 2009 - 15:05:52 PDT)
[AMBER] LCPO or Molsurf?
(Sat May 02 2009 - 20:14:55 PDT)
E.M.
[AMBER] anal output: Entalphy or Free Energy?
(Tue May 12 2009 - 15:25:41 PDT)
Edward M
[AMBER] anal output: Entalphy or Free Energy?
(Tue May 12 2009 - 17:14:37 PDT)
Elodie Laine
[AMBER] Question about Thermal Integration with Softcore
(Wed May 13 2009 - 02:13:22 PDT)
Fernando Martín García
RE: [AMBER] dftb_disper problem
(Mon May 11 2009 - 05:34:01 PDT)
Re: [AMBER] dftb_disper problem
(Fri May 08 2009 - 05:43:19 PDT)
Re: [Barracuda SPAM] Re: [AMBER] dftb_disper problem
(Thu May 07 2009 - 06:32:06 PDT)
[AMBER] dftb_disper problem
(Thu May 07 2009 - 05:30:25 PDT)
fmgarcia.cbm.uam.es
RE: [AMBER] dftb_disper problem
(Fri May 08 2009 - 09:27:30 PDT)
FyD
Re: [AMBER] can I get partial charge for lipid membrane with Antechamber and RESP
(Sun May 31 2009 - 05:51:50 PDT)
Re: [AMBER] unnatural amino acid
(Thu May 28 2009 - 11:46:27 PDT)
Re: [AMBER] partial charge and topology of intrastrand cross-link DNA
(Tue May 26 2009 - 22:27:40 PDT)
[AMBER] resp charge
(Wed May 20 2009 - 00:42:07 PDT)
Re: [AMBER] adding a standard amino acid as ligand
(Fri May 15 2009 - 06:39:18 PDT)
Re: [AMBER] Can I use only a single point calculation to derive RESP charges?
(Sat May 09 2009 - 23:52:12 PDT)
Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
(Sat May 09 2009 - 22:49:55 PDT)
Re: [AMBER] Can I use only a single point calculation to derive RESP charges?
(Fri May 08 2009 - 23:00:36 PDT)
Re: [AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber
(Sat May 02 2009 - 09:06:28 PDT)
Re: [AMBER] charge of Fe-heme
(Sat May 02 2009 - 09:02:48 PDT)
Gabriel Urquiza
[AMBER] Targeted MD and QM/MM
(Fri May 29 2009 - 13:09:31 PDT)
German Erlenkamp
Re: [AMBER] Problems with PMEMD installation for AMBER10
(Thu May 07 2009 - 00:18:36 PDT)
Re: [AMBER] Problems with PMEMD installation for AMBER10
(Tue May 05 2009 - 06:07:13 PDT)
[AMBER] Problems with PMEMD installation for AMBER10
(Tue May 05 2009 - 05:40:56 PDT)
Gustavo Seabra
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 10:28:35 PDT)
Re: [AMBER] dftb_disper problem
(Fri May 08 2009 - 09:34:39 PDT)
Re: [AMBER] dftb_disper problem
(Thu May 07 2009 - 06:01:42 PDT)
Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander?
(Tue May 05 2009 - 10:28:10 PDT)
Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander?
(Tue May 05 2009 - 10:04:37 PDT)
Re: [AMBER] Script for parallel runs
(Tue May 05 2009 - 09:31:38 PDT)
Hannes Loeffler
Re: [AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated?
(Thu May 07 2009 - 00:47:23 PDT)
Re: [AMBER] Amber FF and Glycam
(Fri May 01 2009 - 01:33:34 PDT)
Hannes Wallnoefer
Re: [AMBER] normal mode analysis
(Mon May 04 2009 - 08:56:11 PDT)
[AMBER] normal mode analysis
(Mon May 04 2009 - 02:39:16 PDT)
Hemant Kumar
[AMBER] Number of processor in pmemd
(Mon May 04 2009 - 10:17:13 PDT)
Hopkins, Robert
RE: [AMBER] Running PTRAJ command line scripts in background
(Mon May 18 2009 - 15:50:06 PDT)
RE: [AMBER] Running PTRAJ command line scripts in background
(Sun May 17 2009 - 09:55:48 PDT)
[AMBER] Running PTRAJ command line scripts in background
(Sat May 16 2009 - 17:47:38 PDT)
[AMBER] Amber 10 install parallel problem
(Sat May 16 2009 - 17:38:16 PDT)
RE: [Subject Filtered] [AMBER] hbond-error in amber9 8%
(Thu Apr 30 2009 - 17:02:34 PDT)
Houyang Chen
RE: [AMBER] A confusion about tutorial B1
(Tue May 05 2009 - 10:39:18 PDT)
RE: [AMBER] A confusion about tutorial B1
(Mon May 04 2009 - 22:24:39 PDT)
[AMBER] A confusion about tutorial B1
(Mon May 04 2009 - 22:01:31 PDT)
Jack Colis
Re: [AMBER] MMPBSA- interaction energy for every frame
(Tue May 05 2009 - 01:22:35 PDT)
[AMBER] MMPBSA- interaction energy for every frame
(Mon May 04 2009 - 07:38:38 PDT)
jacky zhao
Re: [AMBER] Re: About Amber installations
(Tue May 26 2009 - 04:18:25 PDT)
Jayalakshmi Sridhar
Re: [AMBER] xleap segmentation fault
(Fri May 29 2009 - 08:45:25 PDT)
[AMBER] xleap segmentation fault
(Thu May 28 2009 - 09:29:47 PDT)
[AMBER] xleap segmentation fault
(Mon May 04 2009 - 08:50:06 PDT)
[AMBER] unable to start xleap
(Fri May 01 2009 - 11:32:27 PDT)
Jia Xu
Re: [AMBER] ptraj questions
(Sat May 23 2009 - 22:06:10 PDT)
[AMBER] ptraj questions
(Wed May 20 2009 - 07:39:13 PDT)
Re: [AMBER] Running PTRAJ command line scripts in background
(Sun May 17 2009 - 00:16:49 PDT)
john smith
Re: [AMBER] Radius for Bromine in MMPBSA calculation
(Mon May 25 2009 - 22:00:52 PDT)
Re: [AMBER] Radius for Bromine in MMPBSA calculation
(Sun May 24 2009 - 21:52:48 PDT)
[AMBER] Radius for Bromine in MMPBSA calculation
(Wed May 20 2009 - 22:24:05 PDT)
Re: [AMBER] pmemd compilation error
(Tue May 05 2009 - 04:20:08 PDT)
Jorgen Simonsen
Re: [AMBER] Modification of His
(Mon May 18 2009 - 05:16:10 PDT)
[AMBER] Modification of His
(Mon May 18 2009 - 03:51:50 PDT)
Re: [AMBER] xleap reading hydrogens giving error
(Fri May 15 2009 - 08:54:17 PDT)
[AMBER] xleap reading hydrogens giving error
(Fri May 15 2009 - 00:47:10 PDT)
Re: [AMBER] Adding non standard residues
(Mon May 11 2009 - 14:11:49 PDT)
[AMBER] Adding non standard residues
(Mon May 11 2009 - 01:54:25 PDT)
[AMBER] Modifying a water molecule
(Sat May 09 2009 - 06:16:54 PDT)
Re: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 11:29:41 PDT)
[AMBER] ambertools for NAMD
(Thu May 07 2009 - 05:35:24 PDT)
Re: [AMBER] creating new residue adds none wanted ter
(Tue May 05 2009 - 02:57:29 PDT)
Re: [AMBER] creating new residue adds none wanted ter
(Mon May 04 2009 - 07:09:08 PDT)
[AMBER] creating new residue adds none wanted ter
(Mon May 04 2009 - 00:49:47 PDT)
Josmar R. da Rocha
Re: [AMBER] Can I use only a single point calculation to derive RESP charges?
(Sat May 09 2009 - 08:19:07 PDT)
[AMBER] Can I use only a single point calculation to derive RESP charges?
(Fri May 08 2009 - 17:08:54 PDT)
[AMBER] help with RESP tutorial using antechamber and gaussian
(Sun May 03 2009 - 10:59:23 PDT)
Re: [AMBER] chain restrain x TI
(Sat May 02 2009 - 10:09:53 PDT)
Junmei Wang
Re: [AMBER] gaff and aromatic compounds
(Tue May 26 2009 - 09:03:53 PDT)
Re: [AMBER] gaff and aromatic compounds
(Thu May 21 2009 - 18:24:52 PDT)
Karen Callahan
[AMBER] Question about &dipoles printing in AMBER 8
(Mon May 25 2009 - 16:46:00 PDT)
Kshatresh Dutta Dubey
Re: [AMBER] MM-PBSA nmode statistics
(Thu May 28 2009 - 22:13:34 PDT)
[AMBER] Segmentation error in Ptraj
(Fri May 22 2009 - 00:17:27 PDT)
Re: [AMBER] Problem with Nmode
(Wed May 20 2009 - 22:14:50 PDT)
[AMBER] Problem with Nmode
(Mon May 18 2009 - 21:25:05 PDT)
[AMBER] Problem in Nmode
(Sun May 17 2009 - 23:07:52 PDT)
Lachele Foley (Lists)
Re: [AMBER] Cyclodextrin forcefield
(Fri May 01 2009 - 08:23:37 PDT)
liuhui
Re: [AMBER] Error running MM _PBSA.pl script
(Tue May 19 2009 - 19:20:26 PDT)
Re: [AMBER] Error running MM _PBSA.pl script
(Tue May 19 2009 - 09:15:24 PDT)
Re: [AMBER] Error running MM _PBSA.pl script
(Tue May 19 2009 - 07:29:23 PDT)
Mahmoud A. A. Ibrahim
Re: [AMBER] Can bond clevage & formation conducted by qm/mm via sander?
(Tue May 05 2009 - 10:15:18 PDT)
Majeed Shaik
[AMBER] xleap input pdb problem
(Wed May 06 2009 - 11:47:45 PDT)
manoj singh
[AMBER] Choice of force field
(Sun May 31 2009 - 13:39:13 PDT)
[AMBER] Choice of force feild
(Sun May 31 2009 - 10:12:23 PDT)
[AMBER] Parameter file content
(Sat May 30 2009 - 18:53:37 PDT)
Re: [AMBER] Changing bond length
(Thu May 28 2009 - 10:00:14 PDT)
[AMBER] Changing bond length
(Wed May 27 2009 - 20:47:52 PDT)
Marek Maly
[AMBER] PARMCAL calculation ?
(Wed May 27 2009 - 07:19:48 PDT)
Re: [AMBER] Nab units ?
(Fri May 22 2009 - 18:43:41 PDT)
[AMBER] Nab units ?
(Fri May 22 2009 - 17:20:14 PDT)
Marek Malý
Re: [AMBER] The resonable way to create single strand DNA with NAB ?
(Mon May 11 2009 - 05:18:06 PDT)
[AMBER] The resonable way to create single strand DNA with NAB ?
(Sun May 10 2009 - 10:12:09 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 18:36:49 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 18:05:40 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 16:37:28 PDT)
[AMBER] Re:
(Fri May 08 2009 - 12:12:39 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 12:10:41 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 11:27:20 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 11:02:53 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 10:57:36 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 09:38:27 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 05:54:57 PDT)
Re: [AMBER] Error in PMEMD run
(Thu May 07 2009 - 16:59:23 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 14:27:17 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 14:25:02 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 13:26:58 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 13:02:11 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 12:48:26 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 11:51:03 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 11:42:36 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 11:30:43 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 08:58:33 PDT)
Re: [AMBER] Error in PMEMD run
(Mon May 04 2009 - 19:19:20 PDT)
[AMBER] Error in PMEMD run
(Mon May 04 2009 - 18:23:33 PDT)
Marina Grabar
[AMBER] problem with program anal within Amber10
(Tue May 26 2009 - 04:48:38 PDT)
Mark M Huntress
[AMBER] heating advice
(Wed May 27 2009 - 13:44:26 PDT)
RE: [AMBER] loadpdb atom type
(Tue May 19 2009 - 11:15:02 PDT)
[AMBER] loadpdb atom type
(Tue May 19 2009 - 09:20:20 PDT)
[AMBER] RE: xleap, mac number problem
(Sat May 09 2009 - 15:29:50 PDT)
[AMBER] xleap, mac number problem
(Sat May 09 2009 - 12:46:46 PDT)
[AMBER] prmtop
(Sun May 03 2009 - 16:20:39 PDT)
Maryam Hamzehee
[AMBER] problem with MM-PBSA
(Mon May 25 2009 - 21:52:29 PDT)
[AMBER] problem with MM-PBSA
(Sat May 23 2009 - 21:48:05 PDT)
mathew k varghese
[AMBER] Fw: MM-PBSA with explicit water
(Thu May 14 2009 - 23:43:46 PDT)
[AMBER] MM-PBSA with explicit water
(Thu May 14 2009 - 23:45:23 PDT)
Matthew Tessier
RE: [AMBER] Conformation of sulfated Glucosamine
(Wed May 06 2009 - 08:19:22 PDT)
Matthew Wilce
[AMBER] ntf, ntc with softcore potentials and TI in amber10
(Tue May 05 2009 - 18:33:28 PDT)
moitrayee.mbu.iisc.ernet.in
Re: [AMBER] Problem with nonstandard residues
(Tue May 19 2009 - 09:47:38 PDT)
Re: [AMBER] Problem with nonstandard residues
(Tue May 19 2009 - 06:10:00 PDT)
[AMBER] Problem with nonstandard residues
(Tue May 19 2009 - 04:48:33 PDT)
Musa Ozboyaci
[AMBER] MM-PBSA statistics
(Sun May 10 2009 - 03:00:19 PDT)
Myunggi Yi
Re: [AMBER] ptraj questions
(Fri May 22 2009 - 06:57:08 PDT)
Re: [AMBER] lipid membrane(dppc) in amber
(Fri May 22 2009 - 06:45:20 PDT)
Nancy
[AMBER] how to use two dimensions periodic boundary ?
(Wed May 20 2009 - 18:32:50 PDT)
[AMBER] no equilibrium
(Mon May 18 2009 - 19:44:03 PDT)
[AMBER] no equilibrium
(Mon May 18 2009 - 19:32:01 PDT)
[AMBER] please help me out
(Sun May 10 2009 - 00:56:33 PDT)
Naser Alijabbari
Re: [AMBER] nanoseconds of simulation with nscm=0
(Sun May 24 2009 - 12:56:28 PDT)
[AMBER] nanoseconds of simulation with nscm=0
(Sun May 24 2009 - 10:20:18 PDT)
Re: [AMBER] difference in temperature
(Wed May 06 2009 - 05:29:48 PDT)
[AMBER] difference in temperature
(Tue May 05 2009 - 17:02:28 PDT)
Neha Gandhi
[AMBER] J coupling constant calculation
(Thu May 28 2009 - 22:24:37 PDT)
[AMBER] scee term
(Fri May 15 2009 - 02:03:48 PDT)
[AMBER] normal modes calculation
(Wed May 13 2009 - 20:12:13 PDT)
[AMBER] Conformation of sulfated Glucosamine
(Wed May 06 2009 - 02:54:31 PDT)
nicholus bhattacharjee
Re: [AMBER] how to know that adequate equilibration from rmsd curve of equilibration
(Thu May 28 2009 - 11:08:52 PDT)
[AMBER] how to know that adequate equilibration from rmsd curve of equilibration
(Thu May 28 2009 - 06:37:29 PDT)
[AMBER] Re: How to know that the md is stable in equilibration run
(Mon May 25 2009 - 09:11:39 PDT)
[AMBER] How to know that the md is stable in equilibration run
(Mon May 25 2009 - 04:54:25 PDT)
Re: [AMBER] Protein with HETATM, am I doing the right thing
(Thu May 21 2009 - 09:28:52 PDT)
[AMBER] Protein with HETATM, am I doing the right thing
(Thu May 21 2009 - 04:21:15 PDT)
Re: [AMBER] Protein with HETATM, am I doing the
(Wed May 20 2009 - 23:43:37 PDT)
[AMBER] Protein with HETATM, am I doing the
(Wed May 20 2009 - 21:48:42 PDT)
Re: [AMBER] Suggestion for restraining chain of a protein
(Tue May 05 2009 - 05:20:44 PDT)
[AMBER] Suggestion for restraining chain of a protein
(Mon May 04 2009 - 23:29:54 PDT)
[AMBER] Problem in production run
(Mon May 04 2009 - 22:50:07 PDT)
Niel Henriksen
RE: [AMBER] re: essential dynamics
(Wed May 13 2009 - 11:28:22 PDT)
Patrick Gedeon
[AMBER] ptraj PCA - Highest Eigenvalues or First 2 Calculated?
(Wed May 06 2009 - 21:12:39 PDT)
Peter Gannett
Re: [AMBER] Unit 8 Error on OPEN: prmtop
(Sun May 24 2009 - 12:29:58 PDT)
Re: [AMBER] Unit 8 Error on OPEN: prmtop
(Sun May 24 2009 - 10:46:47 PDT)
Peter Varnai
Re: [AMBER] xmin
(Sun May 17 2009 - 17:58:00 PDT)
[AMBER] makeDIST_RST: no map function for ambiguous restraint
(Sun May 17 2009 - 11:41:24 PDT)
[AMBER] xmin
(Thu May 14 2009 - 14:29:09 PDT)
[AMBER] building quadruplex with NAB
(Sun May 10 2009 - 16:27:38 PDT)
PRADEEP VENKATARAMAN
[AMBER] SANDER BOMB
(Wed May 27 2009 - 19:39:56 PDT)
R. A.
[AMBER] resp charge
(Tue May 19 2009 - 19:35:25 PDT)
Rajesh Raju
Re: [AMBER] Cyclodextrin forcefield
(Fri May 01 2009 - 10:21:21 PDT)
[AMBER] Cyclodextrin forcefield
(Fri May 01 2009 - 07:51:17 PDT)
Ray Luo
RE: [AMBER] MM-PBSA nmode statistics
(Sun May 31 2009 - 10:32:49 PDT)
RE: [AMBER] MM-PBSA nmode statistics
(Fri May 29 2009 - 11:01:36 PDT)
RE: [AMBER] Radius for Bromine in MMPBSA calculation
(Tue May 26 2009 - 12:02:27 PDT)
RE: [AMBER] problem with MM-PBSA
(Tue May 26 2009 - 09:44:14 PDT)
RE: [AMBER] Radius for Bromine in MMPBSA calculation
(Mon May 25 2009 - 14:10:41 PDT)
RE: [AMBER] Radius for Bromine in MMPBSA calculation
(Thu May 21 2009 - 09:32:41 PDT)
RE: [AMBER] Error running MM _PBSA.pl script
(Mon May 18 2009 - 10:43:30 PDT)
RE: [AMBER] Error in binding energy (MM PBSA)
(Mon May 11 2009 - 11:14:20 PDT)
RE: [AMBER] Problems in the result of MM_PBSA
(Mon May 11 2009 - 10:55:12 PDT)
RE: [AMBER] Error in binding energy (MM PBSA)
(Sat May 09 2009 - 18:39:05 PDT)
RE: [AMBER] Problems in the result of MM_PBSA
(Sat May 09 2009 - 18:36:04 PDT)
RE: [AMBER] Error in binding energy (MM PBSA)
(Fri May 08 2009 - 09:42:58 PDT)
RE: [AMBER] Problems in the result of MM_PBSA
(Thu May 07 2009 - 19:02:58 PDT)
RE: [AMBER] Error in binding energy (MM PBSA)
(Thu May 07 2009 - 11:12:18 PDT)
rebeca
Re: [AMBER] gaff and aromatic compounds
(Fri May 22 2009 - 02:04:45 PDT)
[AMBER] gaff and aromatic compounds
(Wed May 20 2009 - 01:54:43 PDT)
[AMBER] gaff and aromatic compounds
(Tue May 19 2009 - 08:50:02 PDT)
Re: [AMBER] problem with parmchk
(Mon May 18 2009 - 07:34:31 PDT)
[AMBER] problem with parmchk
(Mon May 18 2009 - 06:59:51 PDT)
Remya S R
Re: [AMBER] Amber - Leap- SolvateBox help
(Mon May 18 2009 - 23:22:12 PDT)
Re: [AMBER] Charge problem
(Tue May 05 2009 - 05:19:51 PDT)
[AMBER] Charge problem
(Tue May 05 2009 - 04:43:47 PDT)
[AMBER] Parameter file not saved
(Mon May 04 2009 - 05:03:08 PDT)
[AMBER] Parameter file not saved
(Sun May 03 2009 - 23:30:19 PDT)
[AMBER] "Parameter file not generated"
(Sun May 03 2009 - 23:17:23 PDT)
Rilei Yu
Re: [AMBER] Molecular simulation of a protein using special H2O cluster
(Tue May 26 2009 - 17:21:15 PDT)
[AMBER] Molecular simulation of a protein using special H2O cluster
(Tue May 26 2009 - 01:20:56 PDT)
Re: [AMBER] Influence about HIS-HIE-HIS-HIP
(Thu Apr 30 2009 - 17:37:17 PDT)
Robert Duke
Re: [AMBER] pmemd running very slow in amber10
(Thu May 14 2009 - 06:38:29 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 18:26:37 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 17:01:23 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 12:44:08 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 11:24:35 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 11:14:12 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 11:06:17 PDT)
Re: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 06:29:48 PDT)
Re: [AMBER] Error in PMEMD run
(Thu May 07 2009 - 17:11:25 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 16:04:10 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 13:40:29 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 13:08:56 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 12:58:29 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 12:55:49 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 12:29:41 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 12:20:37 PDT)
Re: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 10:30:43 PDT)
Re: [AMBER] Problems with PMEMD installation for AMBER10
(Tue May 05 2009 - 06:48:06 PDT)
Re: [AMBER] Problems with PMEMD installation for AMBER10
(Tue May 05 2009 - 06:00:54 PDT)
Re: [AMBER] Error in PMEMD run
(Mon May 04 2009 - 21:08:37 PDT)
Re: [AMBER] Error in PMEMD run
(Mon May 04 2009 - 18:35:54 PDT)
Re: [AMBER] Number of processor in pmemd
(Mon May 04 2009 - 10:28:11 PDT)
Rose Tamil
[AMBER] Error: cannot run prepgen
(Tue May 05 2009 - 08:20:52 PDT)
Ross Walker
[AMBER] FW: About Amber10 installation "Possible Failure"
(Thu May 28 2009 - 07:06:31 PDT)
RE: [AMBER] Changing bond length
(Wed May 27 2009 - 21:38:59 PDT)
RE: [AMBER] Tutorial 4 Parameter file was not saved
(Wed May 27 2009 - 10:31:30 PDT)
[AMBER] RE: About Amber10 installation "Possible Failure"
(Tue May 26 2009 - 08:38:19 PDT)
RE: [AMBER] How to choose the counter ions for proteins?
(Sat May 23 2009 - 11:09:27 PDT)
RE: [AMBER] Why does protein carry charges?
(Sat May 23 2009 - 11:06:57 PDT)
[AMBER] RE: add magnesium
(Wed May 20 2009 - 14:30:09 PDT)
RE: [AMBER] resp charge
(Wed May 20 2009 - 08:05:20 PDT)
RE: [AMBER] Amber - Leap- SolvateBox help
(Tue May 19 2009 - 22:20:50 PDT)
RE: [AMBER] What is the purpose to do the bond constraints?
(Sun May 17 2009 - 20:38:52 PDT)
RE: [AMBER] Running PTRAJ command line scripts in background
(Sun May 17 2009 - 20:35:09 PDT)
RE: [AMBER] scee term
(Fri May 15 2009 - 08:02:09 PDT)
RE: [AMBER] pmemd running very slow in amber10
(Thu May 14 2009 - 05:57:43 PDT)
RE: [AMBER] Amber - Leap- SolvateBox help
(Thu May 14 2009 - 05:28:36 PDT)
RE: [AMBER] amber9 in fedora10
(Wed May 13 2009 - 16:22:20 PDT)
RE: [AMBER] Error in PMEMD run
(Fri May 08 2009 - 11:11:19 PDT)
RE: [AMBER] dftb_disper problem
(Fri May 08 2009 - 08:47:39 PDT)
RE: [AMBER] QM/MM assigns Cd to C, Se to S
(Fri May 08 2009 - 00:16:09 PDT)
RE: [AMBER] RE: Listing gaff parameters in frcmod
(Thu May 07 2009 - 21:34:08 PDT)
RE: [AMBER] AMBER for dual core processor?
(Thu May 07 2009 - 08:26:09 PDT)
RE: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 14:53:07 PDT)
RE: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 13:36:36 PDT)
RE: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 12:41:10 PDT)
RE: [AMBER] Error in PMEMD run
(Wed May 06 2009 - 10:07:01 PDT)
RE: [AMBER] Error message in "make test.sander"
(Tue May 05 2009 - 23:28:01 PDT)
RE: [AMBER] High energy during minimization
(Tue May 05 2009 - 23:24:30 PDT)
RE: [AMBER] Error message in "make test.sander"
(Tue May 05 2009 - 20:37:28 PDT)
RE: [AMBER] QM/MM
(Tue May 05 2009 - 15:16:26 PDT)
RE: [AMBER] skip parallel test
(Tue May 05 2009 - 08:43:34 PDT)
RE: [AMBER] A confusion about tutorial B1
(Tue May 05 2009 - 08:29:23 PDT)
RE: [AMBER] A confusion about tutorial B1
(Mon May 04 2009 - 22:18:43 PDT)
RE: [AMBER] QM/MM
(Mon May 04 2009 - 10:47:21 PDT)
RE: [AMBER] Script for parallel runs 2
(Mon May 04 2009 - 08:39:27 PDT)
RE: [AMBER] problem with cutoff
(Mon May 04 2009 - 08:35:40 PDT)
RE: [AMBER] problem with cutoff
(Sun May 03 2009 - 22:02:04 PDT)
RE: [AMBER] prmtop
(Sun May 03 2009 - 19:18:04 PDT)
RE: [AMBER] QM/MM assigns Cd to C, Se to S
(Sat May 02 2009 - 21:45:41 PDT)
Rubben Torella
[AMBER] Minimization on MM-PBSA
(Thu May 28 2009 - 08:23:07 PDT)
Re: [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber
(Tue May 26 2009 - 15:33:18 PDT)
Re: [AMBER] Problem with MM-PBSA energy calculation
(Tue May 26 2009 - 04:24:56 PDT)
[AMBER] Problem with MM-PBSA energy calculation
(Mon May 25 2009 - 08:58:41 PDT)
S.Sundar Raman
[AMBER] Issue related to saving the vector in ptraj
(Sat May 16 2009 - 05:41:10 PDT)
[AMBER] Issue related to vector saving
(Fri May 15 2009 - 06:35:01 PDT)
Scott Brozell
Re: [AMBER] xmin
(Mon May 18 2009 - 13:30:17 PDT)
Re: [AMBER] xmin
(Sun May 17 2009 - 13:45:27 PDT)
Sean Zhao
Re: [AMBER] Problems in the result of MM_PBSA
(Sun May 10 2009 - 01:23:19 PDT)
Re: [AMBER] Problems in the result of MM_PBSA
(Fri May 08 2009 - 20:44:29 PDT)
[AMBER] Problems in the result of MM_PBSA
(Thu May 07 2009 - 18:30:24 PDT)
[AMBER] MM_PBSA problem in Amber 9
(Mon May 04 2009 - 02:09:14 PDT)
Sergey Samsonov
Re: [AMBER] AMBER 10 output
(Tue May 19 2009 - 07:53:41 PDT)
[AMBER] AMBER 10 output
(Tue May 19 2009 - 00:33:21 PDT)
sheerychen
[AMBER] adding a standard amino acid as ligand
(Fri May 15 2009 - 02:37:51 PDT)
Shuang Ding
[AMBER] partial charge and topology of intrastrand cross-link DNA
(Mon May 25 2009 - 19:27:43 PDT)
Shubhra Gupta
Re: [AMBER] broken Ligand
(Fri May 29 2009 - 23:35:46 PDT)
[AMBER] broken Ligand
(Fri May 29 2009 - 06:28:22 PDT)
Re: [AMBER] mdfil: Error unknown flag during sander minimization
(Tue May 26 2009 - 21:07:25 PDT)
Re: [AMBER] Amber - Leap- SolvateBox help
(Mon May 18 2009 - 20:54:23 PDT)
[AMBER] Amber - Leap- SolvateBox help
(Wed May 13 2009 - 22:04:16 PDT)
Siavoush Dastmalchi
[AMBER] RE: ERROR in ptrajInitializeState(): Attempting ....
(Sat May 30 2009 - 10:11:55 PDT)
[AMBER] ERROR in ptrajInitializeState(): Attempting ....
(Sat May 30 2009 - 09:06:51 PDT)
[AMBER] parallel amber on cluster
(Sun May 17 2009 - 23:04:58 PDT)
Siddharth Rastogi
Re: [AMBER] multiple chain specification in Sander
(Thu May 07 2009 - 13:29:28 PDT)
[AMBER] multiple chain specification in Sander
(Wed May 06 2009 - 20:17:57 PDT)
Simon Becker
Re: [AMBER] Protein Docking
(Tue May 12 2009 - 08:23:02 PDT)
Simona Irrera
[AMBER] molecular crystal simulation
(Tue May 12 2009 - 04:04:26 PDT)
steinbrt.rci.rutgers.edu
Re: [AMBER] Strange high temperature in softcore TI
(Sun May 24 2009 - 21:13:38 PDT)
Re: [AMBER] Strange high temperature in softcore TI
(Sun May 24 2009 - 19:26:28 PDT)
Re: [AMBER] AMBER 10 output
(Tue May 19 2009 - 06:53:03 PDT)
Re: [AMBER] no equilibrium
(Mon May 18 2009 - 20:00:40 PDT)
Re: [AMBER] MM-PBSA tutorial
(Thu May 14 2009 - 10:26:50 PDT)
Re: [AMBER] Question about Thermal Integration with Softcore
(Wed May 13 2009 - 08:11:16 PDT)
Re: [AMBER] Protein Docking
(Mon May 11 2009 - 13:33:15 PDT)
Re: [AMBER] RE: Listing gaff parameters in frcmod
(Fri May 08 2009 - 07:23:45 PDT)
Re: [AMBER] ntf, ntc with softcore potentials and TI in amber10
(Tue May 05 2009 - 20:39:02 PDT)
Sunita Patel
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Thu May 07 2009 - 11:35:59 PDT)
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Tue May 05 2009 - 10:26:09 PDT)
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Tue May 05 2009 - 09:33:40 PDT)
Re: [AMBER] equilibration stops for dimer simulation with REMD
(Sun May 03 2009 - 18:30:05 PDT)
[AMBER] equilibration stops for dimer simulation with REMD
(Sat May 02 2009 - 13:11:48 PDT)
sychen
[AMBER] Can bond clevage & formation conducted by qm/mm via sander?
(Tue May 05 2009 - 06:12:32 PDT)
Syed Tarique Moin
RE: [AMBER] QM/MM
(Wed May 06 2009 - 00:12:17 PDT)
RE: [AMBER] QM/MM
(Wed May 06 2009 - 00:11:54 PDT)
RE: [AMBER] QM/MM
(Mon May 04 2009 - 15:13:22 PDT)
[AMBER] QM/MM
(Mon May 04 2009 - 08:32:29 PDT)
Taufik Al-Sarraj
[AMBER] Re: Help with xleap
(Tue May 26 2009 - 16:58:00 PDT)
Thomas Cheatham
Re: [AMBER] Why NaCl or KCl solution?
(Wed May 27 2009 - 17:50:56 PDT)
Re: [AMBER] hbond_ptraj
(Wed May 27 2009 - 17:39:15 PDT)
Re: [AMBER] problem with MM-PBSA
(Wed May 27 2009 - 17:35:30 PDT)
Re: [AMBER] nanoseconds of simulation with nscm=0
(Sun May 24 2009 - 13:37:23 PDT)
Re: [AMBER] nanoseconds of simulation with nscm=0
(Sun May 24 2009 - 11:27:33 PDT)
Thomas Cheatham III
RE: [Subject Filtered] [AMBER] hbond-error in amber9 8%
(Fri May 01 2009 - 11:07:40 PDT)
Thomas Spraggins
Re: [AMBER] Installation directory
(Thu May 21 2009 - 12:18:13 PDT)
[AMBER] Installation directory
(Thu May 21 2009 - 11:02:59 PDT)
Titus, Jamie (bairdje)
RE: [AMBER] QQD psuedoatom restraints
(Fri May 29 2009 - 12:01:34 PDT)
[AMBER] QQD psuedoatom restraints
(Fri May 29 2009 - 07:02:31 PDT)
todd.semichem.com
Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
(Sun May 10 2009 - 14:56:24 PDT)
Re: [AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
(Sat May 09 2009 - 11:36:17 PDT)
[AMBER] AMBER 94 Charges for terminal LYN, GLH, ASH and CYM residues and some other unusual cases.
(Sat May 09 2009 - 09:27:52 PDT)
Tom Joseph
Re: [AMBER] Parameter file content
(Sat May 30 2009 - 19:23:48 PDT)
Re: [AMBER] protein molecular weight?
(Fri May 29 2009 - 16:40:58 PDT)
Re: [AMBER] Strange high temperature in softcore TI
(Sun May 24 2009 - 20:20:20 PDT)
[AMBER] Strange high temperature in softcore TI
(Sun May 24 2009 - 18:54:43 PDT)
Tomasio, Susana
[AMBER] AMOEBA and carbon nanotubes + include parameters
(Thu May 28 2009 - 03:23:00 PDT)
RE: [AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off- different labels
(Wed May 27 2009 - 05:13:58 PDT)
[AMBER] ACE residue - amoeba_amino.off and amoeba_aminont.off - different labels
(Wed May 27 2009 - 04:25:35 PDT)
[AMBER] get typeid of -1, sleap - AMBER with amoeba ff
(Tue May 26 2009 - 08:51:18 PDT)
[AMBER] ongoing issues using sander with AMOEBA
(Wed May 13 2009 - 03:00:00 PDT)
Vijay Manickam Achari
[AMBER] pmemd running very slow in amber10
(Wed May 13 2009 - 22:41:40 PDT)
vijayaraj.clri.res.in
[AMBER] MMPBSA extract coordinate
(Fri May 22 2009 - 11:00:57 PDT)
Vikas Sharma
Re: [AMBER] Loading PDB of complex
(Thu May 21 2009 - 22:56:36 PDT)
[AMBER] Loading PDB of complex
(Thu May 21 2009 - 06:13:36 PDT)
Re: 回复： [AMBER] MM PBSA output
(Wed May 20 2009 - 10:54:32 PDT)
[AMBER] MM PBSA output
(Wed May 20 2009 - 04:53:57 PDT)
Re: [AMBER] Error running MM _PBSA.pl script
(Wed May 20 2009 - 01:29:42 PDT)
Re: [AMBER] Error running MM _PBSA.pl script
(Tue May 19 2009 - 11:21:47 PDT)
Re: [AMBER] Error running MM _PBSA.pl script
(Tue May 19 2009 - 08:02:21 PDT)
Re: [AMBER] Error running MM _PBSA.pl script
(Mon May 18 2009 - 21:34:18 PDT)
Re: 回复： [AMBER] Error running MM _PBSA.pl script
(Mon May 18 2009 - 07:06:49 PDT)
[AMBER] Error running MM _PBSA.pl script
(Mon May 18 2009 - 05:00:13 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Mon May 11 2009 - 22:05:08 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Mon May 11 2009 - 01:08:28 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Sun May 10 2009 - 02:03:07 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Sat May 09 2009 - 00:20:09 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Sat May 09 2009 - 00:19:20 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Thu May 07 2009 - 23:50:40 PDT)
[AMBER] Error in binding energy (MM PBSA)
(Thu May 07 2009 - 23:44:33 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Thu May 07 2009 - 23:42:32 PDT)
Re: [AMBER] Error in binding energy (MM PBSA)
(Thu May 07 2009 - 06:29:22 PDT)
[AMBER] free enrgy error in MM PBSA
(Thu May 07 2009 - 03:11:44 PDT)
[AMBER] Error in binding energy (MM PBSA)
(Wed May 06 2009 - 22:47:33 PDT)
[AMBER] positive value of binding enrgy after MM PBSA
(Wed May 06 2009 - 08:07:03 PDT)
[AMBER] Error in MM PBSA
(Wed May 06 2009 - 01:35:57 PDT)
Vlad
[AMBER] The largest AMBER calculation(s)?
(Mon May 18 2009 - 19:58:27 PDT)
Wei Huang
RE: [AMBER] ambertools for NAMD
(Thu May 07 2009 - 07:51:06 PDT)
RE: [AMBER] MMPBSA- interaction energy for every frame
(Mon May 04 2009 - 07:58:26 PDT)
Wei Zhang
Re: [AMBER] please help me out
(Sun May 10 2009 - 06:21:06 PDT)
Re: [AMBER] unable to start xleap
(Fri May 01 2009 - 11:39:03 PDT)
Workalemhu Berhanu
[AMBER] solutes in a simulation box
(Sun May 31 2009 - 09:59:39 PDT)
[AMBER] create a simulation box
(Sat May 30 2009 - 20:06:24 PDT)
[AMBER] the atom number exceeds the MAXATOM, reallocate memory automatically
(Sat May 30 2009 - 04:20:03 PDT)
[AMBER] How to take into account the charge in GAFF parameterization
(Thu May 28 2009 - 16:22:07 PDT)
[AMBER] Tutorial 4 Parameter file was not saved
(Wed May 27 2009 - 09:00:30 PDT)
[AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber
(Tue May 26 2009 - 14:45:55 PDT)
[AMBER] Tutorial 4 Please check the total charge and your -nc flag
(Tue May 26 2009 - 12:47:07 PDT)
[AMBER] mdfil: Error unknown flag during sander minimization
(Tue May 26 2009 - 06:57:29 PDT)
Re: [AMBER] Unit 8 Error on OPEN: prmtop
(Sun May 24 2009 - 15:12:00 PDT)
[AMBER] Unit 8 Error on OPEN: prmtop
(Sun May 24 2009 - 10:27:38 PDT)
[AMBER] file contains 2 atoms not in residue templates
(Sat May 23 2009 - 17:17:09 PDT)
[AMBER] 2 atoms not in residue template
(Sat May 23 2009 - 17:11:12 PDT)
[AMBER] Tutorial A1
(Tue May 19 2009 - 16:05:15 PDT)
[AMBER] Alignment of small molecule on peptide fragment
(Sat May 16 2009 - 02:32:38 PDT)
[AMBER] Alignment of small molecule on peptide fragment
(Sat May 16 2009 - 02:31:08 PDT)
Re: [AMBER] MM-PBSA tutorial
(Thu May 14 2009 - 11:53:25 PDT)
[AMBER] MM-PBSA tutorial
(Thu May 14 2009 - 10:16:55 PDT)
xiaoqin huang
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 14:43:15 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 14:09:26 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 13:32:02 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 13:09:28 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:51:59 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:46:23 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:41:54 PDT)
RE: [AMBER] ask for parm99MOD
(Thu May 28 2009 - 12:31:14 PDT)
[AMBER] ask for parm99MOD
(Thu May 28 2009 - 11:16:35 PDT)
xueqin pang
[AMBER] Can we use GROMACS or NAMD for MD, and then use MM-PBSA to culculate binding energy
(Sun May 31 2009 - 05:47:57 PDT)
[AMBER] can I get partial charge for lipid membrane with Antechamber and RESP
(Sun May 31 2009 - 05:43:09 PDT)
[AMBER] partial charges of lipid membrane for GPCR system
(Tue May 26 2009 - 06:34:34 PDT)
[AMBER] lipid membrane(dppc) in amber
(Fri May 22 2009 - 02:01:26 PDT)
[AMBER] lipid membrane(dppc) in amber
(Fri May 22 2009 - 01:42:54 PDT)
Ye MEI
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber
(Sat May 02 2009 - 05:01:20 PDT)
[AMBER] how to assign radii parameters to certain atoms when fitting RESP charge using antechamber
(Sat May 02 2009 - 05:00:06 PDT)
Yunjie Zhao
Re: [AMBER] problem with cutoff
(Mon May 04 2009 - 05:58:00 PDT)
[AMBER] problem with cutoff
(Sun May 03 2009 - 20:53:00 PDT)
zgong.hust
[AMBER] errors when add ions
(Wed May 20 2009 - 19:51:48 PDT)
廖青华
[AMBER] decomposition and alanine scanning
(Fri May 22 2009 - 07:13:49 PDT)
回复： [AMBER] MM PBSA output
(Wed May 20 2009 - 05:15:04 PDT)
回复： 回复： [AMBER] Error running MM _PBSA.pl script
(Mon May 18 2009 - 07:41:14 PDT)
回复： [AMBER] Error running MM _PBSA.pl script
(Mon May 18 2009 - 05:08:47 PDT)
欧阳德方
[AMBER] contacts in ptraj
(Thu May 28 2009 - 04:55:28 PDT)
董昊
[AMBER] charge of Fe-heme
(Fri May 01 2009 - 12:08:12 PDT)
Last message date
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Mon Jun 01 2009 - 01:11:52 PDT
Archived on
: Wed Dec 25 2024 - 05:53:51 PST
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