Amber Archive Jul 2011: by author

Adrian Roitberg
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 12:21:17 PDT)
- Re: [AMBER] selective qmshake? (Tue Jul 26 2011 - 09:03:43 PDT)
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 03:01:05 PDT)
- Re: [AMBER] TR: Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 10:47:21 PDT)
- Re: [AMBER] number of solvent molecule around solute (Wed Jul 13 2011 - 03:21:41 PDT)
- Re: [AMBER] MMPBSA.py is crashing (Tue Jul 12 2011 - 23:53:41 PDT)
- Re: [AMBER] Please solve my problem (Tue Jul 12 2011 - 04:18:30 PDT)
- Re: [AMBER] regarding amber anal calculation (Tue Jul 12 2011 - 00:37:32 PDT)
- Re: [AMBER] Amber help (Thu Jul 07 2011 - 08:01:11 PDT)
- Re: [AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration (Wed Jul 06 2011 - 09:03:26 PDT)
- Re: [AMBER] About visualizing amber trajectory (periodic box) in VMD (Tue Jul 05 2011 - 11:12:40 PDT)
- Re: [AMBER] sander11 (Mon Jul 04 2011 - 03:56:23 PDT)
Aimin
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command (Thu Jul 21 2011 - 10:19:23 PDT)
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command (Thu Jul 21 2011 - 09:58:46 PDT)
- [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command (Thu Jul 21 2011 - 09:28:01 PDT)
Ali Faruqi
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 03:53:19 PDT)
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 01:43:28 PDT)
- Re: [AMBER] Sander Compilation Problem (Sun Jul 03 2011 - 21:22:27 PDT)
- Re: [AMBER] NETCDF Installation Error (Sat Jul 02 2011 - 01:59:06 PDT)
amir abbasi
- Re: [AMBER] create walls (Thu Jul 28 2011 - 01:15:13 PDT)
- Re: [AMBER] create walls (Wed Jul 27 2011 - 06:36:56 PDT)
- [AMBER] Element definition (Tue Jul 26 2011 - 04:45:35 PDT)
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 04:40:54 PDT)
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 01:42:57 PDT)
- Re: [AMBER] create walls (Mon Jul 25 2011 - 04:07:51 PDT)
- [AMBER] create walls (Sat Jul 23 2011 - 05:27:49 PDT)
Andre Serobian
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Thu Jul 28 2011 - 01:45:11 PDT)
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Fri Jul 22 2011 - 15:13:20 PDT)
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Thu Jul 21 2011 - 21:26:26 PDT)
- [AMBER] ERROR - No pdb file generated using NAB (Fri Jul 08 2011 - 21:08:18 PDT)
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Fri Jul 08 2011 - 18:38:01 PDT)
- [AMBER] Creating hoogsteen basepaired DNA using NAB (Fri Jul 08 2011 - 00:18:37 PDT)
Andreas Goetz
- Re: [AMBER] Make_Gnu_Win_error (Wed Jul 27 2011 - 08:04:08 PDT)
- Re: [AMBER] Make_Gnu_Win_error (Sun Jul 24 2011 - 11:15:05 PDT)
- [AMBER] Registration open - AMBER Workshop in Shanghai, China, August 22-26, 2011 (Mon Jul 04 2011 - 01:00:46 PDT)
Andrew Petersen
- [AMBER] AMBER10 pimd failure on =>16 cores (Wed Jul 27 2011 - 14:22:02 PDT)
aneesh cna
- Re: [AMBER] problem with xleap (Fri Jul 22 2011 - 05:30:41 PDT)
- [AMBER] problem with xleap (Thu Jul 21 2011 - 23:55:52 PDT)
Anjan Dwaraknath
- Re: [AMBER] (NAB issue) wc_helix : Problem in creating RNA structures (Wed Jul 27 2011 - 03:56:58 PDT)
- [AMBER] (NAB issue) wc_helix : Problem in creating RNA structures (Wed Jul 27 2011 - 03:03:52 PDT)
atila petrosian
- [AMBER] distance and angle cutoff for hydrogen bond (Sat Jul 30 2011 - 05:04:08 PDT)
Aust, Susanne
- [AMBER] MM-GBSA with QM data (Mon Jul 04 2011 - 02:04:17 PDT)
Azat Mukhametov
- [AMBER] Script to run mm_pbsa.pl for ENTROPY calculation in parallel on workstation (Wed Jul 27 2011 - 03:20:42 PDT)
Baker D.J.
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Wed Jul 06 2011 - 08:45:56 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Tue Jul 05 2011 - 08:42:00 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Tue Jul 05 2011 - 08:26:15 PDT)
- [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Tue Jul 05 2011 - 07:57:07 PDT)
Beale, John
- [AMBER] H-bond vs. time (Fri Jul 22 2011 - 03:06:46 PDT)
Ben Roberts
- Re: [AMBER] problem with type of pdb output. (Tue Jul 12 2011 - 11:51:50 PDT)
- Re: [AMBER] zinc parameters (Tue Jul 12 2011 - 10:11:01 PDT)
- Re: [AMBER] sander job crashed (Mon Jul 11 2011 - 08:24:21 PDT)
- Re: [AMBER] sander job crashed (Fri Jul 08 2011 - 04:59:23 PDT)
- Re: [AMBER] sander job crashed (Thu Jul 07 2011 - 17:02:30 PDT)
Bill Miller III
- Re: [AMBER] MMPBSA.py - cluster analysis (Fri Jul 29 2011 - 08:09:29 PDT)
- Re: [AMBER] MMPBSA.py - cluster analysis (Fri Jul 29 2011 - 06:56:17 PDT)
- Re: [AMBER] Script to run mm_pbsa.pl for ENTROPY calculation in parallel on workstation (Wed Jul 27 2011 - 03:26:50 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Sat Jul 23 2011 - 05:57:50 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Wed Jul 20 2011 - 11:50:09 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 17:51:30 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 14:54:02 PDT)
- Re: [AMBER] MMGBSA.py error (Tue Jul 19 2011 - 14:48:16 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 10:31:10 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 03:28:33 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 17:09:32 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 14:30:39 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 12:07:20 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 10:27:14 PDT)
- Re: [AMBER] problem with running MMPBSA.py on a single frame (Sun Jul 17 2011 - 09:49:39 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 09:47:16 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Tue Jul 05 2011 - 15:14:21 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Tue Jul 05 2011 - 09:57:29 PDT)
Bill Ross
- Re: [AMBER] possible problem with periodic cell (Thu Jul 28 2011 - 14:34:08 PDT)
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 10:52:55 PDT)
- Re: [AMBER] problem with addIons in tleap (Sat Jul 23 2011 - 13:45:40 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 13:51:10 PDT)
- Re: [AMBER] ions params for SPC/F water (Fri Jul 22 2011 - 13:13:46 PDT)
- Re: [AMBER] Urea box: artifacts or just a special distribution? (Wed Jul 20 2011 - 16:12:42 PDT)
- Re: [AMBER] Urea box: artifacts or just a special distribution? (Wed Jul 20 2011 - 12:27:47 PDT)
- Re: [AMBER] Edit prmtop file (Wed Jul 13 2011 - 10:31:18 PDT)
- Re: [AMBER] Minimization Question (Mon Jul 11 2011 - 19:25:12 PDT)
- Re: [AMBER] Minimization Question (Mon Jul 11 2011 - 19:15:35 PDT)
- Re: [AMBER] Problems with density in aqueous solution (Wed Jul 06 2011 - 12:22:23 PDT)
bkim.chem.ucsb.edu
- [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 09:58:41 PDT)
Bongkeun Kim
- Re: [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 13:59:53 PDT)
- Re: [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 12:49:23 PDT)
- Re: [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 12:18:04 PDT)
Brian Radak
- Re: [AMBER] Energy output when using ibelly (Thu Jul 28 2011 - 12:59:51 PDT)
- [AMBER] nmropt on dihedral angles, are half harmonic restraints possible? (Wed Jul 27 2011 - 11:39:41 PDT)
- Re: [AMBER] selective qmshake? (Tue Jul 26 2011 - 11:29:50 PDT)
- [AMBER] selective qmshake? (Tue Jul 26 2011 - 08:57:10 PDT)
- Re: [AMBER] CHARMM in AMBER (Thu Jul 21 2011 - 06:05:26 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 13:14:12 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 09:23:42 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 09:21:09 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 08:52:05 PDT)
- [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 07:09:42 PDT)
Bruno Rodrigues
- Re: [AMBER] possible problem with periodic cell (Thu Jul 28 2011 - 14:55:02 PDT)
- [AMBER] possible problem with periodic cell (Thu Jul 28 2011 - 14:01:32 PDT)
- Re: [AMBER] hbond analysis (Thu Jul 28 2011 - 09:45:10 PDT)
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 12:31:45 PDT)
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 12:15:45 PDT)
- Re: [AMBER] ions params for SPC/F water (Thu Jul 21 2011 - 06:49:24 PDT)
- [AMBER] ions params for SPC/F water (Wed Jul 20 2011 - 20:39:50 PDT)
- Re: [AMBER] Inquiry about installing AMBER (Wed Jul 06 2011 - 04:41:40 PDT)
- Re: [AMBER] DNA simulation (Wed Jul 06 2011 - 04:40:19 PDT)
caobb0214
- [AMBER] nonbond parameter for copper(Ⅱ) ion (Fri Jul 15 2011 - 17:29:27 PDT)
Carlos P Sosa
- [AMBER] Problems installing AMBER 11 (Tue Jul 26 2011 - 19:04:40 PDT)
Carlos Simmerling
- Re: [AMBER] sander problem (Thu Jul 28 2011 - 11:26:08 PDT)
- Re: [AMBER] sander problem (Thu Jul 28 2011 - 11:00:20 PDT)
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command (Thu Jul 21 2011 - 09:34:56 PDT)
- Re: [AMBER] Query about switch function using AMBER ff99SB forcefield and NAMD simulation code (Tue Jul 19 2011 - 08:16:05 PDT)
- Re: [AMBER] Periodicity in MD simulations (Tue Jul 19 2011 - 07:42:53 PDT)
- Re: [AMBER] ptraj closest water (Mon Jul 18 2011 - 09:24:11 PDT)
- Re: [AMBER] ptraj closest water (Mon Jul 18 2011 - 09:06:46 PDT)
- Re: [AMBER] Restrained MD (Thu Jul 14 2011 - 14:22:21 PDT)
- Re: [AMBER] Please solve my problem (Tue Jul 12 2011 - 04:20:22 PDT)
- Re: [AMBER] Analysis the changes of secondary structure in MD trajectory (Mon Jul 11 2011 - 07:09:40 PDT)
- Re: [AMBER] About extracting partial atoms from a Amber trajectory file (Sun Jul 10 2011 - 08:53:17 PDT)
- Re: [AMBER] Interaction - Constrain (Sat Jul 09 2011 - 04:21:50 PDT)
Carlos Sosa
- Re: [AMBER] Problems installing AMBER 11 (Wed Jul 27 2011 - 10:25:39 PDT)
Carmen Di Giovanni
- [AMBER] configure_error (Tue Jul 19 2011 - 10:44:37 PDT)
- [AMBER] Make_Gnu_Win_error (Fri Jul 22 2011 - 08:53:01 PDT)
- [AMBER] Amber_CygWin_installation (Wed Jul 20 2011 - 01:35:11 PDT)
case
- Re: [AMBER] Energy output when using ibelly (Fri Jul 29 2011 - 08:34:05 PDT)
- Re: [AMBER] Energy output when using ibelly (Fri Jul 29 2011 - 07:44:43 PDT)
- Re: [AMBER] (NAB issue) wc_helix : Problem in creating RNA structures (Fri Jul 29 2011 - 07:32:07 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 17:18:43 PDT)
- Re: [AMBER] nmropt on dihedral angles, are half harmonic restraints possible? (Thu Jul 28 2011 - 07:33:52 PDT)
- Re: [AMBER] force field issues using AT15 (Wed Jul 27 2011 - 07:07:51 PDT)
- Re: [AMBER] SYBYL to GAFF atom types (Wed Jul 27 2011 - 06:57:56 PDT)
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 06:39:51 PDT)
- Re: [AMBER] confusions about some thermodynamic properties (Mon Jul 18 2011 - 19:40:49 PDT)
- Re: [AMBER] Related to the correlation function (Mon Jul 18 2011 - 08:07:52 PDT)
- Re: [AMBER] Error with na_anal.c (Mon Jul 18 2011 - 06:18:17 PDT)
- Re: [AMBER] Error with na_anal.c (Mon Jul 18 2011 - 05:35:22 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Mon Jul 18 2011 - 04:50:10 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Mon Jul 18 2011 - 04:46:53 PDT)
- Re: [AMBER] Problem related to the RMSD and Atomic fluctuation (Sun Jul 17 2011 - 18:51:40 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Sun Jul 17 2011 - 18:40:39 PDT)
- Re: [AMBER] Problem related to the Corelation Function (Sat Jul 16 2011 - 11:48:33 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 15:06:14 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 14:58:30 PDT)
- Re: [AMBER] atom mapping in leaprc.parmCHI_YIL.bsc (Sun Jul 10 2011 - 18:40:50 PDT)
- Re: [AMBER] sleap and ptraj output issue with terminal residues (Sun Jul 10 2011 - 18:39:10 PDT)
- Re: [AMBER] Problem related to the residue template of zwiterionic state (Sun Jul 10 2011 - 18:36:39 PDT)
- Re: [AMBER] ERROR - No pdb file generated using NAB (Sat Jul 09 2011 - 06:14:49 PDT)
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Fri Jul 08 2011 - 20:08:23 PDT)
- Re: [AMBER] Missing Na+ type in ff10 in maksing topolgy file (Fri Jul 08 2011 - 20:02:22 PDT)
- Re: [AMBER] extra_pts.f (Fri Jul 08 2011 - 15:07:22 PDT)
- Re: [AMBER] INSTALLATION ERROR ON RED HAT LINUX (Fri Jul 08 2011 - 13:35:32 PDT)
- Re: [AMBER] minimization error (Fri Jul 08 2011 - 13:27:00 PDT)
- Re: [AMBER] XLEaP parameters for nonstandard residues (Fri Jul 08 2011 - 13:26:54 PDT)
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Fri Jul 08 2011 - 05:41:39 PDT)
- Re: [AMBER] extra_pts.f (Fri Jul 08 2011 - 05:29:52 PDT)
- [AMBER] using sleap to load mol2 files (Mon Jul 04 2011 - 06:15:03 PDT)
- Re: [AMBER] amber (Mon Jul 04 2011 - 06:05:12 PDT)
- Re: [AMBER] dist restraint (Mon Jul 04 2011 - 05:53:40 PDT)
- Re: [AMBER] ff03 force field (Sun Jul 03 2011 - 09:59:17 PDT)
- Re: [AMBER] dist restraint (Sun Jul 03 2011 - 05:47:39 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 13:31:35 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 06:35:51 PDT)
- Re: [AMBER] dist restraint (Sat Jul 02 2011 - 06:00:18 PDT)
Chirag Vora
- Re: [AMBER] Error with na_anal.c (Mon Jul 18 2011 - 06:07:57 PDT)
- [AMBER] Error with na_anal.c (Mon Jul 18 2011 - 01:50:53 PDT)
Chris Chris
- [AMBER] continuing an mmpbsa run (Mon Jul 04 2011 - 06:29:20 PDT)
Craig West
- Re: [AMBER] CUDA 4.0 (Tue Jul 19 2011 - 22:24:22 PDT)
Daniel Aiello
- [AMBER] Zero values for gbsur (Tue Jul 19 2011 - 06:36:33 PDT)
- Re: [AMBER] APBS (Thu Jul 07 2011 - 11:24:16 PDT)
- Re: [AMBER] APBS (Thu Jul 07 2011 - 11:05:07 PDT)
- Re: [AMBER] Energy Decomp with mm_pbsa.pl (Thu Jul 07 2011 - 10:26:37 PDT)
- [AMBER] Energy Decomp with mm_pbsa.pl (Thu Jul 07 2011 - 09:58:11 PDT)
- [AMBER] APBS (Fri Jul 01 2011 - 07:06:23 PDT)
Daniel Kuroda
- [AMBER] Imaging everything inside an octahedral box (Sun Jul 17 2011 - 07:57:20 PDT)
Daniel Roe
- Re: [AMBER] Problem related to the RMSD (Wed Jul 27 2011 - 10:52:24 PDT)
- Re: [AMBER] Problem with removing Hydrogen in trajectory file using prtaj (Wed Jul 27 2011 - 06:07:41 PDT)
- Re: [AMBER] Problem with removing Hydrogen in trajectory file using prtaj (Wed Jul 27 2011 - 06:04:40 PDT)
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 13:26:03 PDT)
- Re: [AMBER] configure_error (Sat Jul 23 2011 - 10:50:04 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 04:19:28 PDT)
- Re: [AMBER] problem with xleap (Fri Jul 22 2011 - 04:10:21 PDT)
- Re: [AMBER] ptraj can not read NC file. and not succeed in apply patch. (Fri Jul 22 2011 - 04:05:44 PDT)
- Re: [AMBER] Amber_CygWin_installation (Wed Jul 20 2011 - 04:01:38 PDT)
- Re: [AMBER] Periodicity in MD simulations (Tue Jul 19 2011 - 08:15:37 PDT)
- Re: [AMBER] Error in ptraj trajin (Tue Jul 19 2011 - 08:08:03 PDT)
- Re: [AMBER] ptraj closest water (Mon Jul 18 2011 - 10:23:07 PDT)
- Re: [AMBER] Count number of frames in any trajectory file (Mon Jul 18 2011 - 10:10:11 PDT)
- Re: [AMBER] ptraj closest water (Mon Jul 18 2011 - 09:19:20 PDT)
- Re: [AMBER] Count number of frames in any trajectory file (Mon Jul 18 2011 - 08:32:05 PDT)
- Re: [AMBER] Imaging everything inside an octahedral box (Mon Jul 18 2011 - 06:52:14 PDT)
- Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond (Mon Jul 18 2011 - 06:25:54 PDT)
- Re: [AMBER] installation of ambertools-- help (Mon Jul 18 2011 - 06:13:47 PDT)
- Re: [AMBER] installation of ambertools-- help (Mon Jul 18 2011 - 05:31:43 PDT)
- Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond (Thu Jul 14 2011 - 04:27:13 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Tue Jul 12 2011 - 05:07:08 PDT)
- Re: [AMBER] AMBER (Mon Jul 11 2011 - 04:17:17 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 12:43:57 PDT)
- Re: [AMBER] ptraj analysis problems - protein leaving the box (Wed Jul 06 2011 - 10:06:18 PDT)
- Re: [AMBER] segmentation fault on tleap (Tue Jul 05 2011 - 09:20:02 PDT)
- Re: [AMBER] segmentation fault on tleap (Tue Jul 05 2011 - 08:43:48 PDT)
Daniel Scott
- [AMBER] ptraj analysis problems - protein leaving the box (Wed Jul 06 2011 - 09:14:43 PDT)
Daniel Sindhikara
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Tue Jul 26 2011 - 02:41:23 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Mon Jul 25 2011 - 01:26:29 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Mon Jul 25 2011 - 00:10:37 PDT)
- Re: [AMBER] REMD doubt : how to know the protein is not trapped in a conformation (Thu Jul 21 2011 - 06:25:12 PDT)
- Re: [AMBER] Regarding umbrella sampling (Wed Jul 20 2011 - 06:26:46 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Wed Jul 13 2011 - 19:44:45 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Wed Jul 13 2011 - 04:01:11 PDT)
- [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Tue Jul 12 2011 - 04:35:05 PDT)
David A Case
- Re: [AMBER] Creating hoogsteen basepaired DNA using NAB (Fri Jul 22 2011 - 07:10:31 PDT)
- Re: [AMBER] protein-ligand-metal complex simulation (Fri Jul 22 2011 - 05:24:57 PDT)
- Re: [AMBER] H-bond vs. time (Fri Jul 22 2011 - 05:20:11 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 05:15:40 PDT)
- Re: [AMBER] AmberTools installation error (Thu Jul 21 2011 - 08:00:01 PDT)
- Re: [AMBER] ions params for SPC/F water (Thu Jul 21 2011 - 05:43:21 PDT)
- Re: [AMBER] Amber11 Tests fail (Wed Jul 20 2011 - 12:50:20 PDT)
- Re: [AMBER] Urea box: artifacts or just a special distribution? (Wed Jul 20 2011 - 09:41:58 PDT)
- Re: [AMBER] AmberTools installation error (Wed Jul 20 2011 - 07:57:28 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 07:19:25 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes (Tue Jul 19 2011 - 08:40:09 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Mon Jul 18 2011 - 11:00:58 PDT)
- Re: [AMBER] installation of ambertools-- help (Fri Jul 15 2011 - 05:30:48 PDT)
- Re: [AMBER] old prmtop and prmtop 7 (Thu Jul 14 2011 - 13:15:23 PDT)
- Re: [AMBER] pmemd trajectory for mm_pbsa/gbsa analysis on sander (Thu Jul 14 2011 - 08:05:46 PDT)
- Re: [AMBER] installation of ambertools-- help (Thu Jul 14 2011 - 05:42:16 PDT)
- Re: [AMBER-Developers] [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 11:10:44 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 05:15:18 PDT)
- Re: [AMBER] When and how is leap re-numbering residues? (Wed Jul 13 2011 - 05:11:55 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 13:00:47 PDT)
- Re: [AMBER] problem with type of pdb output. (Tue Jul 12 2011 - 12:46:49 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 11:43:34 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 09:32:03 PDT)
- Re: [AMBER] AmberTools compilation problem (Tue Jul 12 2011 - 09:29:41 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Tue Jul 12 2011 - 05:09:11 PDT)
- Re: [AMBER] xleap problem (Thu Jul 07 2011 - 10:01:43 PDT)
- Re: [AMBER] xleap problem (Thu Jul 07 2011 - 08:22:51 PDT)
- Re: [AMBER] xleap problem (Thu Jul 07 2011 - 07:24:06 PDT)
- Re: [AMBER] Sander Problem (Thu Jul 07 2011 - 04:46:32 PDT)
- Re: [AMBER] Amber11 using MPICH (parallel install problem) (Wed Jul 06 2011 - 12:36:13 PDT)
- Re: [AMBER] AmberTools installation - (Wed Jul 06 2011 - 06:11:51 PDT)
- Re: [AMBER] AmberTools installation - (Wed Jul 06 2011 - 05:37:34 PDT)
- Re: [AMBER] AmberTools1.5 &ff10 (Wed Jul 06 2011 - 05:27:38 PDT)
- Re: [AMBER] Problems with density in aqueous solution (Wed Jul 06 2011 - 04:47:13 PDT)
- Re: [AMBER] AMBER (Wed Jul 06 2011 - 04:40:42 PDT)
- Re: [AMBER] sleap cannot deal with lipids? (Wed Jul 06 2011 - 04:33:36 PDT)
- Re: [AMBER] install DFTB plus with Amber 11 (Tue Jul 05 2011 - 09:52:39 PDT)
- Re: [AMBER] segmentation fault on tleap (Tue Jul 05 2011 - 09:02:40 PDT)
- Re: [AMBER] Installation Problem (Tue Jul 05 2011 - 04:54:19 PDT)
- Re: [AMBER] NBONH is greater than number of hydrogen for protein. (Fri Jul 01 2011 - 05:01:50 PDT)
- Re: [AMBER] Non-Standard Residues Problems (Fri Jul 01 2011 - 04:59:18 PDT)
David Cantu
- Re: [AMBER] Oxygen Gaff Atom Type (Thu Jul 28 2011 - 10:29:10 PDT)
- [AMBER] Oxygen Gaff Atom Type (Wed Jul 27 2011 - 15:19:41 PDT)
- Re: [AMBER] CHARMM format to Amber format (Wed Jul 27 2011 - 08:11:11 PDT)
- Re: [AMBER] SYBYL to GAFF atom types (Wed Jul 27 2011 - 08:08:30 PDT)
- [AMBER] CHARMM format to Amber format (Tue Jul 26 2011 - 14:49:55 PDT)
- [AMBER] SYBYL to GAFF atom types (Tue Jul 26 2011 - 09:36:52 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes (Tue Jul 19 2011 - 09:42:59 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes (Tue Jul 19 2011 - 07:31:38 PDT)
- [AMBER] Ligands and cofactors in enzymes (Mon Jul 18 2011 - 21:54:50 PDT)
David Case
- Re: [AMBER] Energy output when using ibelly (Thu Jul 28 2011 - 15:15:29 PDT)
- Re: [AMBER] Oxygen Gaff Atom Type (Wed Jul 27 2011 - 16:24:32 PDT)
David Condon
- Re: [AMBER] chiral restraints in AMBER (Sun Jul 31 2011 - 04:40:48 PDT)
- [AMBER] chiral restraints in AMBER (Sat Jul 30 2011 - 16:55:05 PDT)
- Re: [AMBER] Error in ptraj trajin (Tue Jul 19 2011 - 11:00:30 PDT)
- Re: [AMBER] Error in ptraj trajin (Tue Jul 19 2011 - 10:28:09 PDT)
- [AMBER] Error in ptraj trajin (Tue Jul 19 2011 - 06:11:03 PDT)
Dean Cuebas
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, (Sat Jul 30 2011 - 15:58:53 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 13:04:04 PDT)
DEBOSTUTI GHOSHDASTIDAR
- Re: [AMBER] regarding hydrogen bonding (Thu Jul 14 2011 - 23:16:51 PDT)
Devlina Chakravarty
- [AMBER] Problem with removing Hydrogen in trajectory file using prtaj (Wed Jul 27 2011 - 05:23:17 PDT)
dhilip kumar ramalingam
- [AMBER] regarding hydrogen bonding (Thu Jul 14 2011 - 01:35:41 PDT)
- [AMBER] regarding amber anal calculation (Mon Jul 11 2011 - 22:07:05 PDT)
Dmitry Nilov
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 08:03:28 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes (Mon Jul 18 2011 - 23:06:13 PDT)
- Re: [AMBER] Restrained MD (Fri Jul 15 2011 - 01:45:46 PDT)
- Re: [AMBER] ligand & protein with dist restraint (Wed Jul 13 2011 - 02:54:12 PDT)
- Re: [AMBER] ligand & protein with dist restraint (Tue Jul 12 2011 - 23:45:06 PDT)
- Re: [AMBER] ligand & protein with dist restraint (Tue Jul 12 2011 - 04:30:35 PDT)
Dwight McGee
- Re: [AMBER] How to use nonlin option of APBS in MMPBSA.py? (Tue Jul 19 2011 - 10:31:32 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Fri Jul 15 2011 - 09:47:07 PDT)
- Re: [AMBER] MMPBSA.py is crashing (Tue Jul 12 2011 - 18:35:38 PDT)
- Re: [AMBER] MMPBSA.py is crashing (Tue Jul 12 2011 - 13:43:54 PDT)
- Re: [AMBER] AmberTools (Mon Jul 11 2011 - 14:44:57 PDT)
- Re: [AMBER] Ala double mutation scans (Mon Jul 11 2011 - 10:36:58 PDT)
- Re: [AMBER] Energy Decomp with mm_pbsa.pl (Thu Jul 07 2011 - 10:25:20 PDT)
- Re: [AMBER] Ala double mutation scans (Wed Jul 06 2011 - 08:01:18 PDT)
e p
- Re: [AMBER] ligand & protein with dist restraint (Wed Jul 13 2011 - 02:05:34 PDT)
- Re: [AMBER] Please solve my problem (Tue Jul 12 2011 - 22:46:19 PDT)
- Re: [AMBER] Please solve my problem (Tue Jul 12 2011 - 22:45:18 PDT)
- Re: [AMBER] ligand & protein with dist restraint (Tue Jul 12 2011 - 22:35:08 PDT)
- [AMBER] Please solve my problem (Tue Jul 12 2011 - 04:11:52 PDT)
- [AMBER] ligand & protein with dist restraint (Mon Jul 11 2011 - 07:08:10 PDT)
- Re: [AMBER] dist restraint (Fri Jul 08 2011 - 22:18:21 PDT)
- Re: [AMBER] dist restraint (Sun Jul 03 2011 - 22:53:39 PDT)
- [AMBER] dist restraint (Sun Jul 03 2011 - 03:29:57 PDT)
- Re: [AMBER] dist restraint (Sat Jul 02 2011 - 22:22:11 PDT)
- [AMBER] dist restraint (Fri Jul 01 2011 - 22:05:30 PDT)
- Re: [AMBER] dist restraint (Fri Jul 01 2011 - 22:03:00 PDT)
- Re: [AMBER] dist restraint (Fri Jul 01 2011 - 20:10:04 PDT)
Eliac Brown
- [AMBER] Minimization Question (Mon Jul 11 2011 - 18:18:41 PDT)
- [AMBER] Heavy atom definition (Mon Jul 11 2011 - 03:52:56 PDT)
- [AMBER] Interaction - Constrain (Sat Jul 09 2011 - 04:19:33 PDT)
Elisa Frezza
- Re: [AMBER] idecomp and res card (Thu Jul 28 2011 - 01:21:22 PDT)
- Re: [AMBER] idecomp and res card (Wed Jul 27 2011 - 12:36:31 PDT)
- [AMBER] idecomp and res card (Wed Jul 27 2011 - 06:28:13 PDT)
- Re: [AMBER] xleap problem (Fri Jul 08 2011 - 05:51:26 PDT)
- Re: [AMBER] xleap problem (Thu Jul 07 2011 - 08:26:20 PDT)
- Re: [AMBER] xleap problem (Thu Jul 07 2011 - 08:13:06 PDT)
- Re: [AMBER] xleap problem (Thu Jul 07 2011 - 07:40:43 PDT)
- [AMBER] xleap problem (Thu Jul 07 2011 - 06:37:35 PDT)
Emmanuel Baribefe Naziga
- Re: [AMBER] vdW issues during TI (Tue Jul 26 2011 - 17:14:01 PDT)
- [AMBER] vdW issues during TI (Tue Jul 26 2011 - 11:11:57 PDT)
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command (Thu Jul 21 2011 - 09:37:01 PDT)
Erin Kelly
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Thu Jul 14 2011 - 07:07:46 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 15:08:07 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 13:10:42 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 12:59:03 PDT)
- Re: [AMBER] TR: Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 10:51:06 PDT)
- Re: [AMBER] TR: Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 10:43:44 PDT)
- Re: [AMBER] TR: Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 08:56:34 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 07:53:48 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 07:28:45 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 13:26:04 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 13:22:50 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 12:40:39 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 09:37:15 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 09:19:24 PDT)
- [AMBER] Antechamber trouble with COA-acyl chain (Tue Jul 12 2011 - 07:59:28 PDT)
Fabrício Bracht
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Sat Jul 30 2011 - 19:26:25 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Fri Jul 29 2011 - 10:42:33 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Wed Jul 27 2011 - 12:05:22 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Wed Jul 27 2011 - 08:52:31 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Tue Jul 26 2011 - 16:04:27 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Tue Jul 26 2011 - 06:07:28 PDT)
- [AMBER] Failure kReduceSoluteCOM with GPU (Mon Jul 25 2011 - 20:44:10 PDT)
- Re: [AMBER] Error compiling amber cuda (Mon Jul 25 2011 - 16:18:13 PDT)
- Re: [AMBER] Error compiling amber cuda (Mon Jul 25 2011 - 10:10:32 PDT)
- Re: [AMBER] Error compiling amber cuda (Mon Jul 25 2011 - 08:54:41 PDT)
- Re: [AMBER] Error compiling amber cuda (Sat Jul 23 2011 - 13:22:35 PDT)
- Re: [AMBER] Error compiling amber cuda (Sat Jul 23 2011 - 07:29:37 PDT)
- Re: [AMBER] Error compiling amber cuda (Fri Jul 22 2011 - 17:15:57 PDT)
- Re: [AMBER] Error compiling amber cuda (Fri Jul 22 2011 - 14:51:16 PDT)
- [AMBER] Error compiling amber cuda (Fri Jul 22 2011 - 14:30:31 PDT)
- [AMBER] Multiple CPU and single GPU doubt (Sat Jul 02 2011 - 15:36:26 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 15:26:52 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 09:34:11 PDT)
- [AMBER] MPI cuda compilation error (Fri Jul 01 2011 - 17:03:50 PDT)
Fernando Martín García
- [AMBER] Fwd: Cuda compilation problem (Tue Jul 19 2011 - 02:12:43 PDT)
- [AMBER] Cuda compilation problem (Mon Jul 18 2011 - 02:14:35 PDT)
filip fratev
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 02:46:29 PDT)
Francesco Pietra
- Re: [AMBER] /bin/sh /bin/dash (Sat Jul 02 2011 - 23:11:21 PDT)
- [AMBER] /bin/sh /bin/dash (Sat Jul 02 2011 - 10:08:30 PDT)
g t
- [AMBER] breaking down amber parameter file to create fragments of original molecule using tleap (Mon Jul 25 2011 - 19:49:44 PDT)
George Tzotzos
- Re: [AMBER] MMPBSA.py - cluster analysis (Fri Jul 29 2011 - 08:35:11 PDT)
- Re: [AMBER] MMPBSA.py - cluster analysis (Fri Jul 29 2011 - 07:58:47 PDT)
- [AMBER] MMPBSA.py - cluster analysis (Fri Jul 29 2011 - 06:21:25 PDT)
- Re: [AMBER] ptraj closest water (Mon Jul 18 2011 - 09:49:28 PDT)
- Re: [AMBER] ptraj closest water (Mon Jul 18 2011 - 09:16:32 PDT)
- [AMBER] ptraj closest water (Mon Jul 18 2011 - 09:00:59 PDT)
- [AMBER] Diffusion (Fri Jul 15 2011 - 05:18:17 PDT)
Giorgos Lamprinidis
- Re: [AMBER] segmentation fault on tleap (Wed Jul 06 2011 - 00:58:48 PDT)
- Re: [AMBER] segmentation fault on tleap (Tue Jul 05 2011 - 08:48:03 PDT)
- [AMBER] segmentation fault on tleap (Tue Jul 05 2011 - 08:32:14 PDT)
Gordon Freeman
- [AMBER] question about possible failures during Amber10 and AmberTools1.2 (Fri Jul 29 2011 - 06:58:02 PDT)
Gould, Ian R
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Tue Jul 05 2011 - 08:32:03 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Tue Jul 05 2011 - 08:21:41 PDT)
Guenegou, Guillaume [ORDFR]
- [AMBER] Aromatic bonds disappear during sdf creation with sleap (Wed Jul 27 2011 - 05:28:37 PDT)
Gustavo Seabra
- Re: [AMBER] Ligands and cofactors in enzymes (Tue Jul 19 2011 - 09:19:24 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes (Tue Jul 19 2011 - 08:37:02 PDT)
- Re: [AMBER] Ligands and cofactors in enzymes (Tue Jul 19 2011 - 03:58:31 PDT)
- Re: [AMBER] /dat/slko DFTB files (Sun Jul 17 2011 - 20:48:20 PDT)
- Re: [AMBER] zinc parameters (Tue Jul 12 2011 - 22:19:53 PDT)
- Re: [AMBER] zinc parameters (Tue Jul 12 2011 - 11:42:32 PDT)
- Re: [AMBER] install DFTB plus with Amber 11 (Wed Jul 06 2011 - 14:31:15 PDT)
- Re: [AMBER] install DFTB plus with Amber 11 (Tue Jul 05 2011 - 11:22:37 PDT)
hai wei
- Re: [AMBER] ptraj can not read NC file. and not succeed in apply patch. (Sat Jul 23 2011 - 15:41:49 PDT)
- [AMBER] ptraj can not read NC file. and not succeed in apply patch. (Fri Jul 22 2011 - 01:22:46 PDT)
- Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? (Mon Jul 18 2011 - 15:51:52 PDT)
- Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? (Sun Jul 17 2011 - 17:32:55 PDT)
- Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? (Sun Jul 17 2011 - 15:00:38 PDT)
- [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? (Sun Jul 17 2011 - 00:27:21 PDT)
haris p
- [AMBER] Amber test failure (Tue Jul 19 2011 - 23:41:33 PDT)
- [AMBER] sander11 (Mon Jul 04 2011 - 03:54:03 PDT)
Hirdesh Kumar
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 05:37:51 PDT)
- Re: [AMBER] problem with xleap (Fri Jul 22 2011 - 05:33:08 PDT)
- [AMBER] deletion of one water molecule from .rst and prmtop files (Thu Jul 07 2011 - 22:18:26 PDT)
- Re: [AMBER] Sander Problem (Thu Jul 07 2011 - 02:24:41 PDT)
- Re: [AMBER] regarding per residue wise free energy decomposition (Mon Jul 04 2011 - 22:26:05 PDT)
Ignacio J. General
- Re: [AMBER] Energy output when using ibelly (Fri Jul 29 2011 - 07:55:10 PDT)
- Re: [AMBER] Energy output when using ibelly (Fri Jul 29 2011 - 07:13:38 PDT)
- Re: [AMBER] Energy output when using ibelly (Thu Jul 28 2011 - 13:16:34 PDT)
- [AMBER] Energy output when using ibelly (Thu Jul 28 2011 - 12:48:46 PDT)
- [AMBER] belly energies (Tue Jul 26 2011 - 07:29:30 PDT)
- Re: [AMBER] Fwd: Periodicity in MD simulations (Wed Jul 20 2011 - 06:29:36 PDT)
- Re: [AMBER] Periodicity in MD simulations (Tue Jul 19 2011 - 08:09:17 PDT)
Ilyas Yildirim
- Re: [AMBER] chiral restraints in AMBER (Sat Jul 30 2011 - 20:39:21 PDT)
- Re: [AMBER] XLEaP parameters for nonstandard residues (Fri Jul 08 2011 - 10:49:56 PDT)
- Re: [AMBER] XLEaP parameters for nonstandard residues (Fri Jul 08 2011 - 07:29:58 PDT)
InSuk Joung
- Re: [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 12:58:20 PDT)
- Re: [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 12:40:28 PDT)
- Re: [AMBER] Changing the L-J parameter does not work? (Wed Jul 27 2011 - 11:24:25 PDT)
intra\\sa175950
- Re: [AMBER] TR: Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 09:03:23 PDT)
- [AMBER] TR: Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 08:34:36 PDT)
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Wed Jul 13 2011 - 08:30:20 PDT)
Irene Newhouse
- [AMBER] MMGBSA of Mg-containing ligand (Wed Jul 27 2011 - 14:57:02 PDT)
Jacopo Sgrignani
- [AMBER] renum water (Thu Jul 14 2011 - 01:50:06 PDT)
Jan-Philip Gehrcke
- Re: [AMBER] Count number of frames in any trajectory file (Mon Jul 18 2011 - 10:34:22 PDT)
- Re: [AMBER] Count number of frames in any trajectory file (Mon Jul 18 2011 - 08:53:40 PDT)
- [AMBER] Count number of frames in any trajectory file (Mon Jul 18 2011 - 07:45:37 PDT)
- Re: [AMBER] When and how is leap re-numbering residues? (Wed Jul 13 2011 - 06:08:15 PDT)
- [AMBER] When and how is leap re-numbering residues? (Tue Jul 12 2011 - 06:27:19 PDT)
jani vinod
- Re: [AMBER] Regarding umbrella sampling (Thu Jul 21 2011 - 02:26:28 PDT)
- [AMBER] Regarding umbrella sampling (Tue Jul 19 2011 - 21:00:41 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Mon Jul 18 2011 - 02:00:53 PDT)
- [AMBER] Regarding umbrella sampling (Mon Jul 18 2011 - 01:42:40 PDT)
Jason Swails
- Re: [AMBER] Energy output when using ibelly (Sat Jul 30 2011 - 14:17:58 PDT)
- Re: [AMBER] question about possible failures during Amber10 and AmberTools1.2 (Sat Jul 30 2011 - 13:45:20 PDT)
- Re: [AMBER] idecomp and res card (Wed Jul 27 2011 - 14:52:14 PDT)
- Re: [AMBER] idecomp and res card (Wed Jul 27 2011 - 12:33:09 PDT)
- Re: [AMBER] force field issues using AT15 (Wed Jul 27 2011 - 12:30:29 PDT)
- Re: [AMBER] Problems installing AMBER 11 (Wed Jul 27 2011 - 11:51:44 PDT)
- Re: [AMBER] Problems installing AMBER 11 (Tue Jul 26 2011 - 21:37:12 PDT)
- Re: [AMBER] selective qmshake? (Tue Jul 26 2011 - 16:57:29 PDT)
- Re: [AMBER] force field issues using AT15 (Tue Jul 26 2011 - 16:41:38 PDT)
- Re: [AMBER] CHARMM format to Amber format (Tue Jul 26 2011 - 16:26:46 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Tue Jul 26 2011 - 16:23:36 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Mon Jul 25 2011 - 18:32:17 PDT)
- Re: [AMBER] Error compiling amber cuda (Mon Jul 25 2011 - 18:26:57 PDT)
- Re: [AMBER] create walls (Mon Jul 25 2011 - 18:17:20 PDT)
- Re: [AMBER] Cannot find MMPBSA.MPI (Mon Jul 25 2011 - 18:15:51 PDT)
- Re: [AMBER] reproducing a simulation (Sat Jul 23 2011 - 09:34:13 PDT)
- Re: [AMBER] create walls (Sat Jul 23 2011 - 09:22:03 PDT)
- Re: [AMBER] Error compiling amber cuda (Fri Jul 22 2011 - 18:38:31 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Fri Jul 22 2011 - 18:30:41 PDT)
- Re: [AMBER] sander.MPI is running on 8 nodes, but the output says it is running on 1 nodes (Fri Jul 22 2011 - 13:48:58 PDT)
- Re: [AMBER] reproducing a simulation (Fri Jul 22 2011 - 07:33:37 PDT)
- Re: [AMBER] How to choose MMGBSA saltcon varaible value (Fri Jul 22 2011 - 07:24:06 PDT)
- Re: [AMBER] Problem of creating trpcage TC5b amino acid sequence using "sequence" command (Thu Jul 21 2011 - 10:09:28 PDT)
- Re: [AMBER] AmberTools installation error (Thu Jul 21 2011 - 08:03:33 PDT)
- Re: [AMBER] AmberTools installation error (Wed Jul 20 2011 - 20:33:39 PDT)
- Re: [AMBER] Amber11 Tests fail (Wed Jul 20 2011 - 13:52:09 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Wed Jul 20 2011 - 10:03:25 PDT)
- Re: [AMBER] CUDA 4.0 (Wed Jul 20 2011 - 09:58:31 PDT)
- Re: [AMBER] MMGBSA.py error (Tue Jul 19 2011 - 15:43:21 PDT)
- Re: [AMBER] error: GBSA with mm_pbsa.pl (Mon Jul 18 2011 - 07:44:58 PDT)
- Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? (Sun Jul 17 2011 - 15:04:43 PDT)
- Re: [AMBER] error: GBSA with mm_pbsa.pl (Sun Jul 17 2011 - 03:58:07 PDT)
- Re: [AMBER] Tleap problem with save prmtop and inpcrd file. can someone give me advice? (Sun Jul 17 2011 - 03:55:09 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Fri Jul 15 2011 - 15:20:41 PDT)
- Re: [AMBER] converting amber8 prmtop to amber11 (Wed Jul 13 2011 - 13:17:59 PDT)
- Re: [AMBER] AmberTools installation error (Sat Jul 09 2011 - 08:00:51 PDT)
- Re: [AMBER] Ala double mutation scans (Sat Jul 09 2011 - 07:58:12 PDT)
- Re: [AMBER] Sander Problem (Thu Jul 07 2011 - 07:28:44 PDT)
- Re: [AMBER] Amber11 using MPICH (parallel install problem) (Thu Jul 07 2011 - 07:27:10 PDT)
- Re: [AMBER] continuing an mmpbsa run (Mon Jul 04 2011 - 08:42:27 PDT)
- Re: [AMBER] MM-GBSA with QM data (Mon Jul 04 2011 - 08:40:01 PDT)
- Re: [AMBER] DNA simulation (Sun Jul 03 2011 - 23:30:55 PDT)
- Re: [AMBER] Sander Compilation Problem (Sun Jul 03 2011 - 12:14:47 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Sat Jul 02 2011 - 17:18:55 PDT)
- Re: [AMBER] Multiple CPU and single GPU doubt (Sat Jul 02 2011 - 17:14:48 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 12:51:17 PDT)
- Re: [AMBER] /bin/sh /bin/dash (Sat Jul 02 2011 - 12:26:25 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Fri Jul 01 2011 - 09:39:19 PDT)
Jennifer L. Muzyka
- Re: [AMBER] AmberTools installation error (Thu Jul 21 2011 - 07:34:44 PDT)
- Re: [AMBER] AmberTools installation error (Wed Jul 20 2011 - 11:28:54 PDT)
- Re: [AMBER] AmberTools installation error (Wed Jul 20 2011 - 07:25:11 PDT)
- Re: [AMBER] AmberTools installation - (Wed Jul 06 2011 - 06:02:42 PDT)
- [AMBER] AmberTools installation - (Wed Jul 06 2011 - 05:18:28 PDT)
- [AMBER] AmberTools installation error (Wed Jul 06 2011 - 05:08:58 PDT)
Jesper Sørensen
- Re: [AMBER] Ala double mutation scans (Tue Jul 12 2011 - 04:36:27 PDT)
- Re: [AMBER] Ala double mutation scans (Sun Jul 10 2011 - 06:02:27 PDT)
- Re: [AMBER] Ala double mutation scans (Fri Jul 08 2011 - 00:24:42 PDT)
- [AMBER] Ala double mutation scans (Wed Jul 06 2011 - 01:27:35 PDT)
John S
- Re: [AMBER] Error mmpbsa (Fri Jul 01 2011 - 22:15:14 PDT)
- Re: [AMBER] Error mmpbsa (Fri Jul 01 2011 - 07:21:01 PDT)
- Re: [AMBER] Error mmpbsa (Thu Jun 30 2011 - 21:17:48 PDT)
Julia Blum
- Re: [AMBER] XLEaP parameters for nonstandard residues (Tue Jul 12 2011 - 06:31:28 PDT)
- Re: [AMBER] XLEaP parameters for nonstandard residues (Fri Jul 08 2011 - 09:26:04 PDT)
- [AMBER] XLEaP parameters for nonstandard residues (Fri Jul 08 2011 - 07:05:51 PDT)
Jyh-Shyong
- Re: [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 17:57:06 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 19:15:03 PDT)
- [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 17:00:27 PDT)
Kevin Wiehe
- [AMBER] sleap and ptraj output issue with terminal residues (Fri Jul 08 2011 - 21:45:54 PDT)
KIRTANA S
- Re: [AMBER] Error in unit 9 inpcrd file (Mon Jul 18 2011 - 11:44:46 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Mon Jul 18 2011 - 10:21:42 PDT)
- Re: [AMBER] Error in unit 9 inpcrd file (Sun Jul 17 2011 - 19:36:23 PDT)
- [AMBER] Error in unit 9 inpcrd file (Sat Jul 16 2011 - 21:24:51 PDT)
- [AMBER] glib(c) error in mmpbsa (Thu Jul 07 2011 - 14:57:59 PDT)
- [AMBER] Error (Tue Jul 05 2011 - 21:06:21 PDT)
kurisaki
- Re: [AMBER] NBONH is greater than number of hydrogen for protein. (Thu Jun 30 2011 - 20:42:47 PDT)
- [AMBER] NBONH is greater than number of hydrogen for protein. (Thu Jun 30 2011 - 20:23:22 PDT)
- Re: [AMBER] Kinetic energy in mdout file is not identical to that calculated from mdvel file. (Thu Jun 30 2011 - 20:10:31 PDT)
- [AMBER] How Kinetic energy is can be converted to Temperature under the SHAKE constraint? (Thu Jun 30 2011 - 19:18:43 PDT)
Lachele Foley (Lists)
- Re: [AMBER] sleap cannot deal with lipids? (Wed Jul 06 2011 - 07:08:46 PDT)
- Re: [AMBER] sleap cannot deal with lipids? (Tue Jul 05 2011 - 10:10:43 PDT)
- Re: [AMBER] sleap cannot deal with lipids? (Tue Jul 05 2011 - 07:10:44 PDT)
- Re: [AMBER] reference for GLYCAM_06 force field (Tue Jul 05 2011 - 07:08:39 PDT)
lawrence awadetsi
- Re: [AMBER] sander problem (Thu Jul 28 2011 - 11:19:32 PDT)
- [AMBER] sander problem (Thu Jul 28 2011 - 10:48:38 PDT)
- [AMBER] problem with type of pdb output. (Tue Jul 12 2011 - 11:07:33 PDT)
M Kang
- [AMBER] sander.MPI is running on 8 nodes, but the output says it is running on 1 nodes (Fri Jul 22 2011 - 11:36:49 PDT)
M. L. Dodson
- Re: [AMBER] Antechamber trouble with COA-acyl chain (Thu Jul 14 2011 - 08:28:36 PDT)
M. Shahid
- Re: [AMBER] Amber11 using MPICH (parallel install problem) (Thu Jul 07 2011 - 07:15:25 PDT)
Madhurima Jana
- [AMBER] Query about switch function using AMBER ff99SB forcefield and NAMD simulation code (Tue Jul 19 2011 - 04:42:07 PDT)
manikanthan bhavaraju
- Re: [AMBER] error: GBSA with mm_pbsa.pl (Sun Jul 17 2011 - 22:01:42 PDT)
- [AMBER] error: GBSA with mm_pbsa.pl (Wed Jul 13 2011 - 20:35:25 PDT)
- [AMBER] converting amber8 prmtop to amber11 (Wed Jul 13 2011 - 12:38:45 PDT)
- Re: [AMBER] Sander problem (Tue Jul 12 2011 - 21:02:03 PDT)
- Re: [AMBER] MMPBSA.py is crashing (Tue Jul 12 2011 - 14:07:26 PDT)
- [AMBER] MMPBSA.py is crashing (Tue Jul 12 2011 - 13:19:24 PDT)
- Re: [AMBER] AmberTools (Tue Jul 12 2011 - 11:52:21 PDT)
- [AMBER] AmberTools (Mon Jul 11 2011 - 13:26:15 PDT)
- Re: [AMBER] amber (Mon Jul 04 2011 - 11:47:37 PDT)
Marc van der Kamp
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 09:09:58 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 08:16:31 PDT)
- Re: [AMBER] Edit prmtop file (Wed Jul 13 2011 - 03:06:19 PDT)
- Re: [AMBER] Edit prmtop file (Wed Jul 13 2011 - 01:48:59 PDT)
Marek Maly
- [AMBER] Discrepancy in Ca++ Vdw parameters considering two Amber data sources - please comment (Tue Jul 19 2011 - 07:33:58 PDT)
- Re: [AMBER] nonbond parameter for copper(Ⅱ) ion (Sat Jul 16 2011 - 16:56:24 PDT)
- [AMBER] Discrepancy in Ca++ Vdw parameters ? (Sat Jul 16 2011 - 15:22:44 PDT)
- Re: [AMBER] nonbond parameter for copper(Ⅱ) ion (Sat Jul 16 2011 - 14:47:54 PDT)
- Re: [AMBER] Steered MD using pmemd.cuda ? (Thu Jul 14 2011 - 10:19:21 PDT)
- [AMBER] Steered MD using pmemd.cuda ? (Thu Jul 14 2011 - 09:51:21 PDT)
Massimiliano Porrini
- [AMBER] H++ protonation (Mon Jul 18 2011 - 11:43:51 PDT)
- [AMBER] H++ protonation (Mon Jul 18 2011 - 09:34:23 PDT)
Matteo Tiberti
- Re: [AMBER] AmberTools compilation problem (Wed Jul 13 2011 - 01:40:02 PDT)
- [AMBER] AmberTools compilation problem (Tue Jul 12 2011 - 07:54:35 PDT)
- [AMBER] Ligand parametrization (Fri Jul 08 2011 - 03:30:42 PDT)
Matthew Tessier
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, (Fri Jul 29 2011 - 05:47:12 PDT)
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, (Thu Jul 28 2011 - 11:13:10 PDT)
Maura Catherine Mooney
- [AMBER] Ptraj and glibc error (Tue Jul 26 2011 - 17:34:37 PDT)
Mengjuei Hsieh
- Re: [AMBER] PB calculation error when using MMPBSA.py (Wed Jul 20 2011 - 12:57:28 PDT)
- Re: [AMBER] Amber11 Tests fail (Wed Jul 20 2011 - 12:54:53 PDT)
mish
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM, (Fri Jul 29 2011 - 01:06:48 PDT)
- [AMBER] alpha 2-3 Sialyllactose in GLYCAM (Thu Jul 28 2011 - 02:29:40 PDT)
- Re: [AMBER] Amber11 using MPICH (parallel install problem) (Thu Jul 07 2011 - 07:08:39 PDT)
- [AMBER] Amber11 using MPICH (parallel install problem) (Wed Jul 06 2011 - 11:21:35 PDT)
- [AMBER] amber11 openmpi installation problem (Tue Jul 05 2011 - 09:19:47 PDT)
Mo Chen
- [AMBER] About extracting partial atoms from a Amber trajectory file (Sun Jul 10 2011 - 08:47:59 PDT)
- Re: [AMBER] Inquiry about installing AMBER (Wed Jul 06 2011 - 07:52:41 PDT)
- [AMBER] About visualizing amber trajectory (periodic box) in VMD (Tue Jul 05 2011 - 11:08:11 PDT)
moitrayee.mbu.iisc.ernet.in
- [AMBER] ZAFF parameters: non integral charge (Fri Jul 22 2011 - 06:27:50 PDT)
- [AMBER] problem with unperturbed charge of the unit (Fri Jul 22 2011 - 06:01:25 PDT)
- [AMBER] using zaff parameters (Sun Jul 17 2011 - 11:11:48 PDT)
- [AMBER] problem with ZAFF (Sun Jul 17 2011 - 07:52:47 PDT)
MUSTAFA BUGHIO
- Re: [AMBER] sander job crashed (Mon Jul 11 2011 - 11:09:57 PDT)
- Re: [AMBER] sander job crashed (Fri Jul 08 2011 - 07:50:07 PDT)
- Re: [AMBER] sander job crashed (Fri Jul 08 2011 - 07:44:35 PDT)
- Re: [AMBER] sander job crashed (Fri Jul 08 2011 - 01:02:23 PDT)
- [AMBER] sander job crashed (Thu Jul 07 2011 - 04:37:53 PDT)
Na Le Dang
- Re: [AMBER] Urea box: artifacts or just a special distribution? (Thu Jul 21 2011 - 07:53:23 PDT)
- [AMBER] Urea box: artifacts or just a special distribution? (Wed Jul 20 2011 - 08:57:58 PDT)
najmul arfin
- [AMBER] DNA simulation (Sun Jul 03 2011 - 22:55:38 PDT)
Neha Gandhi
- [AMBER] adiabatic conformational map of carbohydrates (Wed Jul 20 2011 - 00:34:42 PDT)
Niel Henriksen
- Re: [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 17:18:43 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 17:16:49 PDT)
- Re: [AMBER] vdW issues during TI (Tue Jul 26 2011 - 15:00:58 PDT)
- [AMBER] atom mapping in leaprc.parmCHI_YIL.bsc (Thu Jul 07 2011 - 16:05:42 PDT)
Nyla Zaman
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 22:28:14 PDT)
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 02:19:56 PDT)
- [AMBER] problem installing amber 10 (Mon Jul 25 2011 - 22:33:35 PDT)
- Re: [AMBER] installation of ambertools-- help (Sun Jul 17 2011 - 22:19:38 PDT)
- Re: [AMBER] installation of ambertools-- help (Fri Jul 15 2011 - 02:57:22 PDT)
- [AMBER] installation of ambertools-- help (Thu Jul 14 2011 - 04:50:15 PDT)
Oliver Grant
- Re: [AMBER] alpha 2-3 Sialyllactose in GLYCAM (Thu Jul 28 2011 - 02:57:27 PDT)
Oliver Kuhn
- Re: [AMBER] Fwd: Periodicity in MD simulations (Thu Jul 21 2011 - 07:10:49 PDT)
- Re: [AMBER] Fwd: Periodicity in MD simulations (Thu Jul 21 2011 - 01:56:18 PDT)
- [AMBER] Fwd: Periodicity in MD simulations (Wed Jul 20 2011 - 00:51:22 PDT)
- [AMBER] Fwd: Periodicity in MD simulations (Wed Jul 20 2011 - 00:43:39 PDT)
- [AMBER] Fwd: Periodicity in MD simulations (Tue Jul 19 2011 - 23:00:06 PDT)
- Re: [AMBER] Periodicity in MD simulations (Tue Jul 19 2011 - 22:30:43 PDT)
- [AMBER] Fwd: cluster MD trajectory by attribute - solved (Tue Jul 19 2011 - 07:20:38 PDT)
- [AMBER] Periodicity in MD simulations (Mon Jul 18 2011 - 11:17:35 PDT)
- [AMBER] cluster MD trajectory by attribute (Mon Jul 18 2011 - 11:01:23 PDT)
- Re: [AMBER] zinc parameters (Tue Jul 12 2011 - 12:08:48 PDT)
- Re: [AMBER] zinc parameters (Tue Jul 12 2011 - 10:29:44 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument (Mon Jul 11 2011 - 10:24:45 PDT)
- [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument (Mon Jul 11 2011 - 08:32:56 PDT)
Ozen, Aysegul
- Re: [AMBER] Restrained MD (Fri Jul 15 2011 - 10:44:58 PDT)
- [AMBER] Restrained MD (Thu Jul 14 2011 - 09:10:19 PDT)
Patrick von Glehn
- [AMBER] CHAMBER: problems reading bond parameters in charmm parameter file (Wed Jul 27 2011 - 04:27:10 PDT)
Paul Mortenson
- Re: [AMBER] Edit prmtop file (Wed Jul 13 2011 - 02:14:16 PDT)
- [AMBER] Edit prmtop file (Wed Jul 13 2011 - 01:37:53 PDT)
Peter Varnai
- Re: [AMBER] force field issues using AT15 (Wed Jul 27 2011 - 05:26:58 PDT)
- [AMBER] force field issues using AT15 (Tue Jul 26 2011 - 14:11:19 PDT)
peter.stauffert.boehringer-ingelheim.com
- [AMBER] Amber11 Tests fail (Wed Jul 20 2011 - 11:41:39 PDT)
- Re: [AMBER] Amber test failure (Wed Jul 20 2011 - 00:06:40 PDT)
Pooja Khurana
- [AMBER] Intercalation site creation (Tue Jul 05 2011 - 03:48:59 PDT)
Prajwal Nandekar
- [AMBER] Regarding "Total unperturbed charge: -0.507900" on CYP1A1 (Wed Jul 13 2011 - 11:44:54 PDT)
Qian Wang
- [AMBER] old prmtop and prmtop 7 (Thu Jul 14 2011 - 12:27:53 PDT)
qiao xue
- Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond (Tue Jul 19 2011 - 19:01:48 PDT)
- Re: [AMBER] How to make the picture of secstruct and the analysis of Hbond (Fri Jul 15 2011 - 20:21:04 PDT)
- [AMBER] How to make the picture of secstruct and the analysis of Hbond (Wed Jul 13 2011 - 16:54:10 PDT)
- [AMBER] the picture of secstruct and the analysis of Hbond (Tue Jul 12 2011 - 18:57:54 PDT)
- [AMBER] Analysis the changes of secondary structure in MD trajectory (Mon Jul 11 2011 - 05:45:31 PDT)
Raja Pandian
- [AMBER] MMPBSA_ERROR MAXNEI too short (Wed Jul 06 2011 - 00:14:09 PDT)
Rajabrata Bhuyan
- Re: [AMBER] INSTALLATION ERROR ON RED HAT LINUX (Fri Jul 08 2011 - 09:15:10 PDT)
- [AMBER] INSTALLATION ERROR ON RED HAT LINUX (Thu Jun 30 2011 - 23:13:28 PDT)
Rajesh Raju
- [AMBER] MMPBSA.MPI running error problem (Mon Jul 25 2011 - 22:16:32 PDT)
- [AMBER] Cannot find MMPBSA.MPI (Mon Jul 25 2011 - 15:23:08 PDT)
- [AMBER] How to choose MMGBSA saltcon varaible value (Thu Jul 21 2011 - 16:37:49 PDT)
- Re: [AMBER] MMGBSA.py error (Tue Jul 19 2011 - 14:54:48 PDT)
- [AMBER] MMGBSA.py error (Tue Jul 19 2011 - 13:53:28 PDT)
- [AMBER] Missing Na+ type in ff10 in maksing topolgy file (Fri Jul 08 2011 - 17:15:25 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 15:46:56 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 14:00:07 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 13:59:35 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 13:16:48 PDT)
- [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 10:49:15 PDT)
- Re: [AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration (Wed Jul 06 2011 - 09:15:53 PDT)
- [AMBER] Different trajectories with large difference in RMSD with changing the parameters values of gamma_ln, taup, timesteps and extend of density equilibration (Wed Jul 06 2011 - 08:59:32 PDT)
- [AMBER] Large flcutions in the RMSD deviations upon changing the parameters values of gamma_ln, taup and timesteps ..How a small variation leads to such a larage change?? (Tue Jul 05 2011 - 16:27:58 PDT)
Rajeswari A.
- Re: [AMBER] REMD doubt : how to know the protein is not trapped in a conformation (Thu Jul 21 2011 - 23:58:32 PDT)
- [AMBER] REMD doubt : how to know the protein is not trapped in a conformation (Thu Jul 21 2011 - 04:17:02 PDT)
Ramu Anandakrishnan
- Re: [AMBER] H++ protonation (Mon Jul 18 2011 - 16:30:29 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] Problem with MMPBSA.py (Fri Jul 29 2011 - 15:51:22 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Tue Jul 26 2011 - 15:36:42 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Tue Jul 26 2011 - 15:21:05 PDT)
- Re: [AMBER] MM_pbsa (Fri Jul 22 2011 - 16:59:40 PDT)
- Re: [AMBER] MMPBSA_ERROR MAXNEI too short (Wed Jul 06 2011 - 09:37:32 PDT)
- Re: [AMBER] Error mmpbsa (Fri Jul 01 2011 - 07:57:41 PDT)
Robert Konecny
- Re: [AMBER] APBS (Thu Jul 07 2011 - 11:17:22 PDT)
- Re: [AMBER] APBS (Thu Jul 07 2011 - 10:48:21 PDT)
Roman Osman
- Re: [AMBER] Problem with MMPBSA.py (Sat Jul 30 2011 - 11:04:31 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Fri Jul 29 2011 - 11:53:34 PDT)
- Re: [AMBER] MMPBSA.py - cluster analysis (Fri Jul 29 2011 - 08:41:34 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Tue Jul 26 2011 - 17:52:54 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Tue Jul 26 2011 - 15:23:58 PDT)
- [AMBER] Problem with MMPBSA.py (Tue Jul 26 2011 - 15:18:22 PDT)
ros
- Re: [AMBER] nonbond parameter for copper(Ⅱ) ion (Sat Jul 16 2011 - 15:35:56 PDT)
- Re: [AMBER] nonbond parameter for copper(Ⅱ) ion (Fri Jul 15 2011 - 18:58:06 PDT)
Ross Walker
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Sat Jul 30 2011 - 13:15:22 PDT)
- Re: [AMBER] AMBER/sander parallel performance problem (Thu Jul 28 2011 - 17:29:10 PDT)
- Re: [AMBER] Energy output when using ibelly (Thu Jul 28 2011 - 13:03:33 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Wed Jul 27 2011 - 14:57:12 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Wed Jul 27 2011 - 10:28:18 PDT)
- Re: [AMBER] CHARMM format to Amber format (Wed Jul 27 2011 - 10:22:35 PDT)
- Re: [AMBER] selective qmshake? (Tue Jul 26 2011 - 09:40:40 PDT)
- Re: [AMBER] Error compiling amber cuda (Mon Jul 25 2011 - 11:20:19 PDT)
- Re: [AMBER] Error compiling amber cuda (Mon Jul 25 2011 - 09:53:25 PDT)
- Re: [AMBER] Error compiling amber cuda (Sat Jul 23 2011 - 09:23:22 PDT)
- Re: [AMBER] Error compiling amber cuda (Fri Jul 22 2011 - 16:38:58 PDT)
- Re: [AMBER] Error compiling amber cuda (Fri Jul 22 2011 - 14:55:47 PDT)
- Re: [AMBER] Fwd: Periodicity in MD simulations (Thu Jul 21 2011 - 04:28:27 PDT)
- Re: [AMBER] CHARMM in AMBER (Wed Jul 20 2011 - 16:06:52 PDT)
- Re: [AMBER] Steered MD using pmemd.cuda ? (Thu Jul 14 2011 - 10:24:49 PDT)
- Re: [AMBER] cudaMemcpy GpuBuffer::Upload failed invalid argument (Mon Jul 11 2011 - 09:12:18 PDT)
- Re: [AMBER] Amber11 using MPICH (parallel install problem) (Wed Jul 06 2011 - 11:32:25 PDT)
- Re: [AMBER] scee=scnb=1 (Wed Jul 06 2011 - 11:02:12 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Wed Jul 06 2011 - 08:54:42 PDT)
- Re: [AMBER] Amber11 (Wed Jul 06 2011 - 08:28:31 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Tue Jul 05 2011 - 08:57:44 PDT)
- Re: [AMBER] Multiple CPU and single GPU doubt (Sun Jul 03 2011 - 04:59:50 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 11:31:34 PDT)
- Re: [AMBER] MPI cuda compilation error (Sat Jul 02 2011 - 03:01:07 PDT)
Roy Lee
- [AMBER] amber11 forcefield (Mon Jul 25 2011 - 02:13:34 PDT)
- [AMBER] Amber11 (Tue Jul 05 2011 - 20:02:54 PDT)
RUI_YAO
- [AMBER] Amber help (Thu Jul 07 2011 - 07:59:56 PDT)
Sangeetha B
- [AMBER] protein-ligand-metal complex simulation (Fri Jul 22 2011 - 03:18:40 PDT)
- [AMBER] protein-ligand-metal complex simulation (Wed Jul 20 2011 - 03:25:17 PDT)
- [AMBER] pmemd trajectory for mm_pbsa/gbsa analysis on sander (Thu Jul 14 2011 - 07:38:40 PDT)
Sangita Kachhap
- [AMBER] MM_PBSA analysis warning (Wed Jul 13 2011 - 04:30:09 PDT)
Santosh Mogurampelly
- [AMBER] Fatal error in MPI_Init: Other MPI error (Tue Jul 05 2011 - 11:30:19 PDT)
Scott Brozell
- Re: [AMBER] problem installing amber 10 (Tue Jul 26 2011 - 23:59:23 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Tue Jul 26 2011 - 23:55:01 PDT)
- Re: [AMBER] problem installing amber 10 (Mon Jul 25 2011 - 23:55:34 PDT)
- Re: [AMBER] MMPBSA.MPI running error problem (Mon Jul 25 2011 - 23:37:18 PDT)
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Mon Jul 25 2011 - 23:27:37 PDT)
Scott Le Grand
- Re: [AMBER] Failure kReduceSoluteCOM with GPU (Sat Jul 30 2011 - 09:51:32 PDT)
- Re: [AMBER] Running Amber 11 simulations using pmemd.cuda.MPI (Wed Jul 06 2011 - 10:34:36 PDT)
Sel Ercan
- [AMBER] zinc parameters (Tue Jul 12 2011 - 10:00:56 PDT)
Sergey Samsonov
- Re: [AMBER] Steered dynamics related questions (Thu Jul 28 2011 - 02:49:41 PDT)
- Re: [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 03:49:50 PDT)
- [AMBER] Steered dynamics related questions (Tue Jul 26 2011 - 02:32:22 PDT)
Seungyeul Yoo
- Re: [AMBER] Problem with MMPBSA.py (Sat Jul 23 2011 - 08:05:08 PDT)
- Re: [AMBER] Problem with MMPBSA.py (Fri Jul 22 2011 - 23:07:14 PDT)
- [AMBER] Problem with MMPBSA.py (Fri Jul 22 2011 - 15:15:18 PDT)
Sheau Chen Lee
- Re: [AMBER] AMBER9- error in LEaP while learning MMPBSA tutorial (Thu Jun 30 2011 - 20:41:51 PDT)
Shesh Nath
- [AMBER] AMBER (Sun Jul 10 2011 - 23:20:04 PDT)
- [AMBER] AMBER (Tue Jul 05 2011 - 23:36:20 PDT)
- [AMBER] amber (Mon Jul 04 2011 - 03:08:34 PDT)
Sindrila Dutta banik
- [AMBER] Proble related to with dipole-dipole correlation function (Sun Jul 31 2011 - 04:54:39 PDT)
- [AMBER] Volume of a Cavity (Fri Jul 29 2011 - 03:08:31 PDT)
- [AMBER] Energy or Temperature Fluctuation (Thu Jul 28 2011 - 03:44:56 PDT)
- [AMBER] Sorry (Thu Jul 28 2011 - 03:29:38 PDT)
- [AMBER] Problem related to the RMSD (Thu Jul 28 2011 - 03:25:30 PDT)
- [AMBER] Problem related to the RMSD (Wed Jul 27 2011 - 07:02:45 PDT)
- [AMBER] Related to the correlation function (Mon Jul 18 2011 - 07:55:25 PDT)
- [AMBER] Problem related to the Velocity correlation function (Mon Jul 18 2011 - 05:01:40 PDT)
- [AMBER] Problem related to the Velocity correlation function (Sun Jul 17 2011 - 21:31:45 PDT)
- [AMBER] Problem related to the velocity correlation function (Sat Jul 16 2011 - 22:48:16 PDT)
- [AMBER] Thanks (Sat Jul 16 2011 - 22:43:41 PDT)
- [AMBER] Problem related to the RMSD and Atomic fluctuation (Sat Jul 16 2011 - 21:02:06 PDT)
- [AMBER] Problem related to the Corelation Function (Sat Jul 16 2011 - 07:20:53 PDT)
- [AMBER] Problem related to the residue template of zwiterionic state (Sat Jul 09 2011 - 20:36:22 PDT)
- [AMBER] Problem related to the Potential Mean Force (Tue Jul 05 2011 - 23:37:32 PDT)
Somaye Badieyan
- [AMBER] /dat/slko DFTB files (Sun Jul 17 2011 - 15:38:24 PDT)
souvik sur
- [AMBER] Sander problem (Tue Jul 12 2011 - 20:43:24 PDT)
- [AMBER] Sander Problem (Thu Jul 07 2011 - 02:08:52 PDT)
- [AMBER] Installation Problem (Tue Jul 05 2011 - 00:00:02 PDT)
steinbrt.rci.rutgers.edu
- Re: [AMBER] create walls (Thu Jul 28 2011 - 03:56:49 PDT)
- Re: [AMBER] create walls (Wed Jul 27 2011 - 07:51:51 PDT)
- Re: [AMBER] confusions about some thermodynamic properties (Tue Jul 19 2011 - 01:12:30 PDT)
- Re: [AMBER] confusions about some thermodynamic properties of TIP3P water (Mon Jul 18 2011 - 02:02:01 PDT)
- Re: [AMBER] Regarding "Total unperturbed charge: -0.507900" on CYP1A1 (Wed Jul 13 2011 - 13:26:07 PDT)
subrata paul
- [AMBER] hbond analysis (Thu Jul 28 2011 - 02:51:11 PDT)
- [AMBER] hbond vs time (Fri Jul 22 2011 - 03:02:42 PDT)
- [AMBER] number of solvent molecule around solute (Wed Jul 13 2011 - 02:56:59 PDT)
- [AMBER] scee=scnb=1 (Wed Jul 06 2011 - 10:57:26 PDT)
- [AMBER] reference for GLYCAM_06 force field (Mon Jul 04 2011 - 22:14:34 PDT)
sunita gupta
- [AMBER] MMPBSA yielding different values when processed with .prepin and .lib file (Thu Jul 28 2011 - 01:14:41 PDT)
Sushil Mishra
- Re: [AMBER] reference for GLYCAM_06 force field (Mon Jul 04 2011 - 22:49:47 PDT)
Takeshi Baba
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Tue Jul 26 2011 - 18:53:13 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Mon Jul 25 2011 - 01:04:52 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Wed Jul 13 2011 - 22:10:25 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Wed Jul 13 2011 - 04:28:03 PDT)
- Re: [AMBER] Undefined symbols when compiling AMBER11 on Mac OSX 10.6 (Tue Jul 12 2011 - 07:42:12 PDT)
- Re: [AMBER] AmberTools1.5 &ff10 (Wed Jul 06 2011 - 05:51:11 PDT)
- Re: [AMBER] using Mg with ff99SB (Thu Jun 30 2011 - 18:12:46 PDT)
tdo.chem.ucsb.edu
- [AMBER] Parm .dat format and frcmod (Sat Jul 30 2011 - 23:29:32 PDT)
Thomas Cheatham
- Re: [AMBER] Error in ptraj trajin (Tue Jul 19 2011 - 10:53:56 PDT)
Thomas Cheatham III
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 12:33:59 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 16:11:59 PDT)
- Re: [AMBER] Different trajectories with different RMSD with changing the parameters of gamma_ln, taup, timesteps and extend of density equilibration (Fri Jul 08 2011 - 14:49:34 PDT)
Thomas Gaillard
- Re: [AMBER] Parm .dat format and frcmod (Sun Jul 31 2011 - 04:42:46 PDT)
- Re: [AMBER] Ligand parametrization (Fri Jul 08 2011 - 04:18:46 PDT)
tommaso.casalini.mail.polimi.it
- [AMBER] Problems with density in aqueous solution (Wed Jul 06 2011 - 03:05:11 PDT)
Tomoshi Kameda
- Re: [AMBER] sleap cannot deal with lipids? (Wed Jul 06 2011 - 05:26:10 PDT)
- Re: [AMBER] sleap cannot deal with lipids? (Tue Jul 05 2011 - 20:27:09 PDT)
- Re: [AMBER] sleap cannot deal with lipids? (Tue Jul 05 2011 - 09:12:18 PDT)
- [AMBER] sleap cannot deal with lipids? (Mon Jul 04 2011 - 23:09:32 PDT)
tsurma.umich.edu
- Re: [AMBER] extra_pts.f (Sun Jul 10 2011 - 13:47:37 PDT)
- Re: [AMBER] extra_pts.f (Fri Jul 08 2011 - 06:30:02 PDT)
- [AMBER] extra_pts.f (Thu Jul 07 2011 - 14:08:47 PDT)
- Re: [AMBER] ff03 force field (Thu Jul 07 2011 - 14:08:07 PDT)
- Re: [AMBER] ff03 force field (Wed Jul 06 2011 - 20:59:56 PDT)
Victor Ma
- [AMBER] problem with running MMPBSA.py on a single frame (Thu Jul 14 2011 - 14:33:27 PDT)
- [AMBER] problem with running MMPBSA.py on a single frame (Thu Jul 14 2011 - 14:10:22 PDT)
Vitor Felix
- Re: [AMBER] selective qmshake? (Tue Jul 26 2011 - 09:20:11 PDT)
waqasuddin.khan.iccs.edu
- Re: [AMBER] installation of ambertools-- help (Fri Jul 15 2011 - 03:37:05 PDT)
Wei Chen
- Re: [AMBER] problem with addIons in tleap (Sat Jul 23 2011 - 14:12:56 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 13:55:58 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 11:33:51 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 11:28:41 PDT)
- Re: [AMBER] problem with addIons in tleap (Fri Jul 22 2011 - 11:25:04 PDT)
- [AMBER] problem with addIons in tleap (Thu Jul 21 2011 - 22:22:36 PDT)
Wei Huang
- [AMBER] How to use nonlin option of APBS in MMPBSA.py? (Tue Jul 19 2011 - 10:03:38 PDT)
Xiao Chen
- Re: [AMBER] reproducing a simulation (Sat Jul 23 2011 - 05:45:47 PDT)
- [AMBER] reproducing a simulation (Fri Jul 22 2011 - 04:34:35 PDT)
xiao fugui
- [AMBER] help (Mon Jul 11 2011 - 19:16:56 PDT)
Ye Fan
- Re: [AMBER] MMPBSA.MPI running issue (Tue Jul 19 2011 - 10:39:59 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Fri Jul 15 2011 - 12:27:08 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Fri Jul 15 2011 - 09:33:17 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Wed Jul 06 2011 - 07:51:28 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Tue Jul 05 2011 - 12:53:29 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Tue Jul 05 2011 - 09:50:18 PDT)
- Re: [AMBER] MMPBSA.MPI running issue (Fri Jul 01 2011 - 16:08:49 PDT)
- [AMBER] MMPBSA.MPI running issue (Fri Jul 01 2011 - 09:00:33 PDT)
Ye MEI
- Re: [AMBER] INSTALLATION ERROR ON RED HAT LINUX (Thu Jun 30 2011 - 23:45:00 PDT)
ysjho
- [AMBER] Error on installing AMBERTOOLS 1.5 (Thu Jul 21 2011 - 18:53:33 PDT)
Yubo Fan
- Re: [AMBER] install DFTB plus with Amber 11 (Wed Jul 06 2011 - 12:41:56 PDT)
- [AMBER] install DFTB plus with Amber 11 (Tue Jul 05 2011 - 09:39:44 PDT)
Zhi Wang
- Re: [AMBER] PB calculation error when using MMPBSA.py (Wed Jul 20 2011 - 12:46:13 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 15:02:30 PDT)
zhouhaibin2008.ok
- [AMBER] confusions about some thermodynamic properties (Mon Jul 18 2011 - 17:42:13 PDT)
- Re: [AMBER] confusions about some thermodynamic properties of TIP3P water (Mon Jul 18 2011 - 07:01:52 PDT)
- [AMBER] confusions about some thermodynamic properties of TIP3P water (Mon Jul 18 2011 - 01:30:47 PDT)
Zhu Tong
- [AMBER] minimization error (Fri Jul 08 2011 - 05:55:24 PDT)
zw258.cam.ac.uk
- Re: [AMBER] PB calculation error when using MMPBSA.py (Wed Jul 20 2011 - 01:01:45 PDT)
- Re: [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 05:47:25 PDT)
- [AMBER] PB calculation error when using MMPBSA.py (Tue Jul 19 2011 - 01:03:29 PDT)
刘金峰
- Re: [AMBER] MM_pbsa (Fri Jul 22 2011 - 17:29:25 PDT)
- [AMBER] MM_pbsa (Fri Jul 22 2011 - 01:40:21 PDT)
徐见容
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 16:33:59 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 14:12:26 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 10:48:34 PDT)
- Re: [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 10:19:49 PDT)
- [AMBER] MMPBSA calculation in complex with Membrane (Sun Jul 17 2011 - 09:43:29 PDT)

Amber Archive Jul 2011 by author