Amber Archive Dec 2013: by author

#YIP YEW MUN#
- [AMBER] Tleap Problem - Unable to bond atoms in amide linkages (Mon Dec 30 2013 - 00:43:15 PST)
- [AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory (Sun Dec 15 2013 - 21:22:37 PST)
Aditya sarkar
- [AMBER] MMPBSA of protein_DNA complex (Tue Dec 17 2013 - 02:18:21 PST)
Adrian Roitberg
- Re: [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 09:42:50 PST)
- Re: [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 09:42:42 PST)
- Re: [AMBER] Simulation time help (Thu Dec 12 2013 - 08:48:20 PST)
- Re: [AMBER] Simulation time help (Thu Dec 12 2013 - 08:30:49 PST)
- Re: [AMBER] capturing free energy landscape (Tue Dec 10 2013 - 13:26:58 PST)
agarai.physics.iisc.ernet.in
- Re: [AMBER] Regarding distance between residue masks (ptraj) (Sun Dec 22 2013 - 00:12:04 PST)
- [AMBER] Regarding distance between residue masks (ptraj) (Thu Dec 19 2013 - 04:47:13 PST)
Aldo Segura
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c (Mon Dec 09 2013 - 17:13:18 PST)
Andre C. Stiel
- [AMBER] math operations in cpptraj (Mon Dec 09 2013 - 08:26:14 PST)
- [AMBER] ptraj hbond output format (Fri Dec 06 2013 - 05:39:47 PST)
André C. Stiel
- [AMBER] cpptraj output and hbond (Wed Dec 11 2013 - 11:10:55 PST)
- [AMBER] cpptraj output and hbond (Wed Dec 11 2013 - 01:40:12 PST)
- Re: [AMBER] ptraj hbond output format (Sun Dec 08 2013 - 03:39:54 PST)
anu chandra
- Re: [AMBER] capturing free energy landscape (Mon Dec 30 2013 - 03:04:13 PST)
- Re: [AMBER] capturing free energy landscape (Thu Dec 26 2013 - 03:59:03 PST)
- Re: [AMBER] capturing free energy landscape (Fri Dec 20 2013 - 00:55:50 PST)
- [AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ (Thu Dec 19 2013 - 21:53:36 PST)
- Re: [AMBER] capturing free energy landscape (Wed Dec 11 2013 - 03:09:46 PST)
- [AMBER] capturing free energy landscape (Tue Dec 10 2013 - 02:23:46 PST)
anurag.dobhal
- [AMBER] error in installing ambertools 1.2 (Fri Dec 13 2013 - 10:31:31 PST)
- [AMBER] please tell me why this error is coming while doing the constant pH MD (Mon Dec 09 2013 - 10:37:47 PST)
- [AMBER] constant pH (Thu Dec 05 2013 - 04:36:08 PST)
- [AMBER] Constant pH (Thu Dec 05 2013 - 04:32:04 PST)
Arjun Sharma
- [AMBER] ANTECHAMBER PROBLEM (Fri Dec 20 2013 - 08:50:08 PST)
Aronica, Pietro
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 11:43:17 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 10:25:21 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 10:03:14 PST)
- [AMBER] parmed.py setBond (Tue Dec 03 2013 - 09:44:27 PST)
Asaminew Haile
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj (Fri Dec 20 2013 - 09:43:07 PST)
- [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj (Fri Dec 20 2013 - 08:52:56 PST)
Asfa Ali
- Re: [AMBER] Fwd: (Mon Dec 30 2013 - 13:44:13 PST)
- [AMBER] AMBER (Mon Dec 30 2013 - 13:43:52 PST)
- Re: [AMBER] Fwd: (Sat Dec 28 2013 - 01:40:31 PST)
- Re: [AMBER] Fwd: (Thu Dec 26 2013 - 05:37:55 PST)
- [AMBER] Amber (Wed Dec 25 2013 - 04:03:41 PST)
- [AMBER] Fwd: (Wed Dec 25 2013 - 04:01:04 PST)
Bennion, Brian
- [AMBER] issues with MMPBSA tutorial/MMPBSA.py (Fri Dec 13 2013 - 11:03:42 PST)
Biao Ma
- Re: [AMBER] Is restart file size different between minimization and heating MD? (Thu Dec 19 2013 - 08:36:22 PST)
- [AMBER] Is restart file size different between minimization and heating MD? (Tue Dec 17 2013 - 22:08:13 PST)
Bill Ross
- Re: [AMBER] xLeap (Fri Dec 27 2013 - 18:20:13 PST)
- Re: [AMBER] zinc parameters (Wed Dec 04 2013 - 23:46:13 PST)
- Re: [AMBER] zinc parameters (Tue Dec 03 2013 - 10:26:07 PST)
Brian Radak
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions (Tue Dec 24 2013 - 14:34:12 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions. (Thu Dec 19 2013 - 06:39:58 PST)
- Re: [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 (Mon Dec 16 2013 - 06:18:13 PST)
- Re: [AMBER] Need some advice on calculating diffusion constant (Mon Dec 16 2013 - 06:05:15 PST)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions (Wed Dec 11 2013 - 08:10:32 PST)
- Re: [AMBER] Amber QM/MM (Wed Dec 11 2013 - 06:55:31 PST)
- Re: [AMBER] Should vdW cutoff distance be system-dependent? (Fri Dec 06 2013 - 12:03:53 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 10:07:30 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 09:59:47 PST)
Carlos Simmerling
- Re: [AMBER] Manually extending the size of the virtual box (Mon Dec 16 2013 - 11:18:42 PST)
case
- Re: [AMBER] sander's Segmentation fault (Sat Dec 28 2013 - 05:40:58 PST)
- Re: [AMBER] binding free energy and pose analysis (Sat Dec 28 2013 - 05:38:04 PST)
- Re: [AMBER] binding free energy and pose analysis (Fri Dec 27 2013 - 18:58:49 PST)
- Re: [AMBER] xLeap (Fri Dec 27 2013 - 06:23:07 PST)
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file (Fri Dec 27 2013 - 06:09:30 PST)
- Re: [AMBER] Manually extending the size of the virtual box (Thu Dec 26 2013 - 07:08:41 PST)
- Re: [AMBER] Polarizing solute in non-polarizing solvent (Thu Dec 26 2013 - 07:00:18 PST)
- Re: [AMBER] Simulating protein with Fe atom (Thu Dec 26 2013 - 06:55:59 PST)
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file (Thu Dec 26 2013 - 06:48:49 PST)
- Re: [AMBER] ErrorWithLeap (Mon Dec 23 2013 - 19:24:48 PST)
- Re: [AMBER] ErrorWithLeap (Mon Dec 23 2013 - 19:21:16 PST)
- Re: [AMBER] Improper terms in Amber (Mon Dec 16 2013 - 17:48:30 PST)
- Re: [AMBER] Proper Algorithm for GPU? (Sun Dec 15 2013 - 10:06:26 PST)
- Re: [AMBER] error in installing ambertools 1.2 (Sat Dec 14 2013 - 08:18:33 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber (Sat Dec 14 2013 - 08:09:50 PST)
- Re: [AMBER] Regarding generating parameters for protein with NAD+ (Wed Dec 11 2013 - 18:19:34 PST)
- Re: [AMBER] Atom Expression in NAB (Sun Dec 08 2013 - 08:29:57 PST)
- Re: [AMBER] Calculation of NMR relaxation rates (Tue Dec 03 2013 - 18:39:33 PST)
- Re: [AMBER] Restrained MD with COM restraint with PMEMD (Tue Dec 03 2013 - 18:33:17 PST)
- Re: [AMBER] How to compile amber12 in AIX UNIX? (Tue Dec 03 2013 - 18:22:31 PST)
- Re: [AMBER] planarity of Trp side chain and improper torsion term (Sun Dec 01 2013 - 14:23:28 PST)
Cuiyl
- [AMBER] MMGBSA Entropy Error: Trajectory _MMPBSA_complex.mdcrd.1 has 0 frames! (Tue Dec 17 2013 - 18:13:22 PST)
Daniel Roe
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD (Tue Dec 31 2013 - 08:47:46 PST)
- Re: [AMBER] request for help in water shell and closest command (Tue Dec 31 2013 - 08:27:29 PST)
- Re: [AMBER] capturing free energy landscape (Tue Dec 31 2013 - 08:04:46 PST)
- Re: [AMBER] AMBER (Tue Dec 31 2013 - 07:58:39 PST)
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD (Fri Dec 27 2013 - 06:01:12 PST)
- Re: [AMBER] cpptraj clustering (Thu Dec 26 2013 - 06:44:17 PST)
- Re: [AMBER] capturing free energy landscape (Thu Dec 26 2013 - 06:35:45 PST)
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj (Fri Dec 20 2013 - 09:39:51 PST)
- Re: [AMBER] RMSD-based clustering in CPPTRAJ/PTRAJ (Fri Dec 20 2013 - 07:39:18 PST)
- Re: [AMBER] Regarding distance between residue masks (ptraj) (Thu Dec 19 2013 - 07:37:58 PST)
- Re: [AMBER] CpptrajPairDist (Tue Dec 17 2013 - 13:52:15 PST)
- Re: [AMBER] CpptrajPairDist (Tue Dec 17 2013 - 13:44:32 PST)
- [AMBER] AmberTools update 22 for CPPTRAJ (Fri Dec 13 2013 - 09:04:37 PST)
- Re: [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 08:41:05 PST)
- Re: [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 20:07:42 PST)
- Re: [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 19:57:49 PST)
- Re: [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 15:10:24 PST)
- Re: [AMBER] Amber Tools v.13 (Wed Dec 11 2013 - 14:25:12 PST)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions (Wed Dec 11 2013 - 10:38:40 PST)
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c (Tue Dec 10 2013 - 10:18:42 PST)
- Re: [AMBER] math operations in cpptraj (Mon Dec 09 2013 - 08:43:09 PST)
- Re: [AMBER] Brookhaven pdb format (Sun Dec 08 2013 - 19:53:07 PST)
- Re: [AMBER] ptraj hbond output format (Fri Dec 06 2013 - 16:05:38 PST)
- Re: [AMBER] Keeping an hexamer whole. (Wed Dec 04 2013 - 20:27:42 PST)
- Re: [AMBER] Calculation of NMR relaxation rates (Wed Dec 04 2013 - 08:17:00 PST)
- Re: [AMBER] How to compile amber12 in AIX UNIX? (Tue Dec 03 2013 - 20:26:50 PST)
David A Case
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? (Tue Dec 31 2013 - 05:14:24 PST)
- Re: [AMBER] SQM seems to run out of memory? (Tue Dec 31 2013 - 05:10:40 PST)
- Re: [AMBER] angle restraint with atom groups (Mon Dec 30 2013 - 10:58:39 PST)
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages (Mon Dec 30 2013 - 04:41:41 PST)
- Re: [AMBER] ANTECHAMBER PROBLEM (Fri Dec 20 2013 - 10:41:17 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions (Fri Dec 20 2013 - 06:37:41 PST)
- Re: [AMBER] Error while visualizing radius of gyration graph (Wed Dec 18 2013 - 04:58:21 PST)
- Re: [AMBER] Is restart file size different between minimization and heating MD? (Wed Dec 18 2013 - 04:57:01 PST)
- Re: [AMBER] Manually extending the size of the virtual box (Mon Dec 16 2013 - 04:30:00 PST)
- Re: [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 10:08:40 PST)
- Re: [AMBER] how to remove the rotational center-of-mass motion ? (Fri Dec 13 2013 - 04:44:41 PST)
- Re: [AMBER] not getting correct density for N,N-dimethylformamide (Mon Dec 09 2013 - 13:16:33 PST)
- Re: [AMBER] Should vdW cutoff distance be system-dependent? (Fri Dec 06 2013 - 11:22:27 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber (Fri Dec 06 2013 - 05:27:10 PST)
- Re: [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 (Fri Dec 06 2013 - 05:14:14 PST)
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 05:02:58 PST)
- Re: [AMBER] constant pH (Thu Dec 05 2013 - 05:01:03 PST)
- Re: [AMBER] internal geometry restraint (Mon Dec 02 2013 - 12:06:53 PST)
- Re: [AMBER] saveamberparameters problem (Mon Dec 02 2013 - 11:59:56 PST)
- Re: [AMBER] internal geometry restraint (Mon Dec 02 2013 - 05:04:10 PST)
David Chen
- [AMBER] I got a error (Fri Dec 13 2013 - 02:42:35 PST)
- [AMBER] I got a error (Thu Dec 12 2013 - 04:22:58 PST)
Dickson, Callum J
- Re: [AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation. (Tue Dec 17 2013 - 09:37:23 PST)
dongying0512
- Re: [AMBER] Problem when calculating MMPBSA (Jason Swails) (Sun Dec 29 2013 - 17:21:37 PST)
- [AMBER] Problem when calculating MMPBSA (Thu Dec 26 2013 - 22:53:49 PST)
- [AMBER] Problem when calculating MMPBSA (Thu Dec 26 2013 - 22:50:34 PST)
Eugene Yedvabny
- Re: [AMBER] Manually extending the size of the virtual box (Mon Dec 16 2013 - 17:58:33 PST)
- Re: [AMBER] Manually extending the size of the virtual box (Mon Dec 16 2013 - 11:03:54 PST)
- [AMBER] Manually extending the size of the virtual box (Mon Dec 16 2013 - 01:19:44 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber (Sat Dec 14 2013 - 16:01:27 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber (Fri Dec 13 2013 - 14:08:40 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber (Mon Dec 09 2013 - 14:27:38 PST)
- [AMBER] Converting Amoeba .xyz for use with Amber (Mon Dec 09 2013 - 14:24:31 PST)
- [AMBER] Converting Amoeba .xyz for use with Amber (Thu Dec 05 2013 - 20:05:09 PST)
Fengxue Li
- [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 (Mon Dec 16 2013 - 06:06:30 PST)
- [AMBER] Amber QM/MM (Wed Dec 11 2013 - 05:54:27 PST)
- [AMBER] MMPBSA errors :failed with prmtop (Tue Dec 10 2013 - 01:49:53 PST)
- [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe (Mon Dec 09 2013 - 05:25:09 PST)
filip fratev
- [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure (Sat Dec 21 2013 - 11:08:39 PST)
- [AMBER] FINAL_RESULTS_MMPBSA error (Thu Dec 19 2013 - 23:23:41 PST)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions (Wed Dec 11 2013 - 10:18:20 PST)
- [AMBER] Plotting heat maps in AMBER aMD simualtions (Wed Dec 11 2013 - 07:56:58 PST)
FyD
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Mon Dec 16 2013 - 01:49:30 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Fri Dec 13 2013 - 07:30:51 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Fri Dec 13 2013 - 01:24:35 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Wed Dec 11 2013 - 22:36:42 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Wed Dec 11 2013 - 21:21:51 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Mon Dec 09 2013 - 23:52:41 PST)
- [AMBER] Fwd: Re: Using the RED Server Dev. to parameterize a model transition state (Mon Dec 09 2013 - 12:00:15 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Mon Dec 09 2013 - 11:56:21 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Sat Dec 07 2013 - 13:30:00 PST)
- Re: [AMBER] not getting correct density for N,N-dimethylformamide (Sat Dec 07 2013 - 13:12:23 PST)
Guanglei Cui
- [AMBER] AMBER12 test discrepancy (Tue Dec 03 2013 - 07:55:44 PST)
Gustavo Seabra
- Re: [AMBER] Amber QM/MM (Wed Dec 11 2013 - 06:57:02 PST)
- Re: [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? (Wed Dec 11 2013 - 06:58:16 PST)
Hallel Freedman
- Re: [AMBER] zinc parameters (Thu Dec 05 2013 - 06:30:56 PST)
- Re: [AMBER] zinc parameters (Tue Dec 03 2013 - 10:30:47 PST)
- Re: [AMBER] zinc parameters (Tue Dec 03 2013 - 10:13:43 PST)
- [AMBER] zinc parameters (Mon Dec 02 2013 - 16:46:50 PST)
Hamed S. Hayatshahi
- [AMBER] changeLJSingleType problem in parmed.py (Thu Dec 12 2013 - 14:26:29 PST)
- Re: [AMBER] question (Thu Dec 05 2013 - 09:38:43 PST)
Harald Lanig
- [AMBER] MGMS-DS: Molecular Modelling Workshop 2014 in Erlangen, Germany (Fri Dec 13 2013 - 01:29:25 PST)
Hemant Gangwar
- [AMBER] Polarizing solute in non-polarizing solvent (Tue Dec 24 2013 - 12:02:19 PST)
Himanshu Joshi
- [AMBER] xLeap (Fri Dec 27 2013 - 04:08:07 PST)
houcemeddine
- Re: [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) (Tue Dec 24 2013 - 11:09:15 PST)
- [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) (Tue Dec 24 2013 - 07:55:12 PST)
Ibrahim Said
- [AMBER] AMDTutorial (Fri Dec 27 2013 - 10:08:38 PST)
- [AMBER] accelerated Molecular dynamics (Mon Dec 09 2013 - 00:17:33 PST)
Igor Marques
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? (Fri Dec 13 2013 - 12:17:57 PST)
JAIME RUBIO MARTINEZ
- Re: [AMBER] CpptrajPairDist (Sat Dec 28 2013 - 11:58:49 PST)
- Re: [AMBER] ErrorWithLeap (Tue Dec 24 2013 - 09:14:55 PST)
- [AMBER] ErrorWithLeap (Mon Dec 23 2013 - 16:17:20 PST)
- [AMBER] CpptrajPairDist (Tue Dec 17 2013 - 11:37:28 PST)
Jan-Philip Gehrcke
- Re: [AMBER] ptraj hbond output format (Sun Dec 08 2013 - 07:26:40 PST)
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 (Tue Dec 03 2013 - 04:54:29 PST)
Jason Swails
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? (Mon Dec 30 2013 - 12:32:21 PST)
- Re: [AMBER] binding free energy and pose analysis (Sun Dec 29 2013 - 09:10:31 PST)
- Re: [AMBER] Fwd: (Sat Dec 28 2013 - 10:17:37 PST)
- Re: [AMBER] Problem when calculating MMPBSA (Thu Dec 26 2013 - 23:03:35 PST)
- Re: [AMBER] Problems about invoking AMBER12 in calculating binding energy (Thu Dec 26 2013 - 18:36:45 PST)
- Re: [AMBER] Fwd: (Thu Dec 26 2013 - 18:33:01 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions (Thu Dec 26 2013 - 13:48:16 PST)
- Re: [AMBER] modified the amber parameter (Wed Dec 25 2013 - 12:10:24 PST)
- Re: [AMBER] Fwd: (Wed Dec 25 2013 - 11:42:52 PST)
- Re: [AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA (Wed Dec 25 2013 - 06:55:08 PST)
- Re: [AMBER] doubt in alanine scanning of phosphorylated residue (Tue Dec 24 2013 - 10:57:55 PST)
- Re: [AMBER] problems in nmode and -use-mdins option (MMPBSA.py) (Tue Dec 24 2013 - 10:31:07 PST)
- Re: [AMBER] ErrorWithLeap (Tue Dec 24 2013 - 10:18:39 PST)
- Re: [AMBER] ErrorWithLeap (Mon Dec 23 2013 - 19:29:43 PST)
- Re: [AMBER] MMPBSA for single re-minimised coordinate (Mon Dec 23 2013 - 05:50:47 PST)
- Re: [AMBER] doubt in alanine scanning of phosphorylated residue (Mon Dec 23 2013 - 05:44:55 PST)
- Re: [AMBER] capturing free energy landscape (Fri Dec 20 2013 - 04:03:37 PST)
- Re: [AMBER] Problems of invoking the Amber 12 (Fri Dec 20 2013 - 04:02:35 PST)
- Re: [AMBER] FINAL_RESULTS_MMPBSA error (Fri Dec 20 2013 - 03:58:03 PST)
- Re: [AMBER] Puzzles about calculating binding energy using MMGBSA (Thu Dec 19 2013 - 14:18:42 PST)
- Re: [AMBER] Bad atom type error during MMGBSA decomposition calsulations (Thu Dec 19 2013 - 07:47:36 PST)
- Re: [AMBER] Regarding distance between residue masks (ptraj) (Thu Dec 19 2013 - 07:45:53 PST)
- Re: [AMBER] Manually extending the size of the virtual box (Mon Dec 16 2013 - 12:12:54 PST)
- Re: [AMBER] MMPBSA.py strip_mask issue (Mon Dec 16 2013 - 05:29:37 PST)
- Re: [AMBER] Help: Producing a Prmtop file for a Truncated-Protein Trajectory (Mon Dec 16 2013 - 05:11:05 PST)
- Re: [AMBER] Puzzles about calculating binding energy using MMGBSA (Sat Dec 14 2013 - 06:44:07 PST)
- Re: [AMBER] I got a error (Fri Dec 13 2013 - 09:10:14 PST)
- Re: [AMBER] changeLJSingleType problem in parmed.py (Thu Dec 12 2013 - 14:45:30 PST)
- Re: [AMBER] Amber Tools v.13 (Wed Dec 11 2013 - 17:15:47 PST)
- Re: [AMBER] runing sander (Wed Dec 11 2013 - 09:53:27 PST)
- Re: [AMBER] Plotting heat maps in AMBER aMD simualtions (Wed Dec 11 2013 - 09:52:19 PST)
- Re: [AMBER] sander command (Wed Dec 11 2013 - 04:22:10 PST)
- Re: [AMBER] capturing free energy landscape (Tue Dec 10 2013 - 12:45:46 PST)
- Re: [AMBER] AMBER GPU performance issue (Tue Dec 10 2013 - 12:42:53 PST)
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c (Mon Dec 09 2013 - 17:40:59 PST)
- Re: [AMBER] Amber Tools v.13 (Mon Dec 09 2013 - 14:00:44 PST)
- Re: [AMBER] please tell me why this error is coming while doing the constant pH MD (Mon Dec 09 2013 - 11:30:09 PST)
- Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe (Mon Dec 09 2013 - 07:53:55 PST)
- Re: [AMBER] accelerated Molecular dynamics (Mon Dec 09 2013 - 04:12:03 PST)
- Re: [AMBER] Atom Expression in NAB (Mon Dec 09 2013 - 04:08:20 PST)
- Re: [AMBER] Anisotropic & semi-anisotropic (Sat Dec 07 2013 - 07:32:09 PST)
- Re: [AMBER] Converting Amoeba .xyz for use with Amber (Fri Dec 06 2013 - 14:11:08 PST)
- Re: [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 (Fri Dec 06 2013 - 14:04:58 PST)
- Re: [AMBER] compile parallel mpi (Fri Dec 06 2013 - 08:50:40 PST)
- Re: [AMBER] question (Thu Dec 05 2013 - 09:35:57 PST)
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 07:41:26 PST)
- Re: [AMBER] Topology files of homodimer-ligand complex (Thu Dec 05 2013 - 07:20:20 PST)
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 05:54:39 PST)
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 05:04:22 PST)
- Re: [AMBER] Keeping an hexamer whole. (Wed Dec 04 2013 - 17:56:13 PST)
- Re: [AMBER] nasiri (Wed Dec 04 2013 - 07:15:04 PST)
- Re: [AMBER] Restrained MD with COM restraint with PMEMD (Wed Dec 04 2013 - 04:51:15 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 14:51:20 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 11:22:48 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 11:04:36 PST)
- Re: [AMBER] parmed.py setBond (Tue Dec 03 2013 - 10:45:49 PST)
- Re: [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? (Mon Dec 02 2013 - 10:49:42 PST)
Jio M
- Re: [AMBER] xLeap (Fri Dec 27 2013 - 17:45:57 PST)
- Re: [AMBER] internal geometry restraint (Mon Dec 02 2013 - 09:50:42 PST)
- Re: [AMBER] internal geometry restraint (Sun Dec 01 2013 - 16:41:12 PST)
John Smith
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 07:22:39 PST)
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 07:03:30 PST)
- Re: [AMBER] RMSF (Thu Dec 05 2013 - 05:32:12 PST)
- [AMBER] RMSF (Thu Dec 05 2013 - 04:41:14 PST)
Jonathan Saboury
- [AMBER] SQM seems to run out of memory? (Mon Dec 30 2013 - 11:20:37 PST)
Jonathan Sheehan
- Re: [AMBER] amber parameter for S2P (phosphoserine) (Tue Dec 24 2013 - 11:20:35 PST)
- Re: [AMBER] Error while visualizing radius of gyration graph (Wed Dec 18 2013 - 07:15:35 PST)
Jorge Iulek
- Re: [AMBER] planarity of Trp side chain and improper torsion term (Sun Dec 01 2013 - 03:30:21 PST)
Jose Borreguero
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? (Tue Dec 31 2013 - 11:26:06 PST)
- Re: [AMBER] how to minimize with full electrostatics and no boundary conditions? (Mon Dec 30 2013 - 12:59:33 PST)
- [AMBER] how to minimize with full electrostatics and no boundary conditions? (Mon Dec 30 2013 - 11:36:15 PST)
Julio Dominguez
- Re: [AMBER] Keeping an hexamer whole. (Thu Dec 05 2013 - 21:06:33 PST)
- [AMBER] Keeping an hexamer whole. (Wed Dec 04 2013 - 16:38:16 PST)
Kamali Sripathi
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Sun Dec 15 2013 - 15:43:19 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Fri Dec 13 2013 - 06:56:26 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Wed Dec 11 2013 - 12:56:35 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Tue Dec 10 2013 - 05:12:58 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Mon Dec 09 2013 - 15:26:00 PST)
- Re: [AMBER] Using the RED Server Dev. to parameterize a model transition state (Mon Dec 09 2013 - 08:30:10 PST)
- [AMBER] Using the RED Server Dev. to parameterize a model transition state (Fri Dec 06 2013 - 13:19:46 PST)
Kshatresh Dutta Dubey
- Re: [AMBER] constant pH (Thu Dec 05 2013 - 04:53:03 PST)
Mahendra B Thapa
- [AMBER] Calculation of NMR relaxation rates (Mon Dec 02 2013 - 16:43:10 PST)
Mele N.
- Re: [AMBER] AMD simulation (Wed Dec 18 2013 - 03:57:07 PST)
- [AMBER] AMD simulation (Wed Dec 18 2013 - 03:47:00 PST)
Meng
- [AMBER] Improper terms in Amber (Mon Dec 16 2013 - 13:26:11 PST)
Mengyuan Zhu
- Re: [AMBER] How to compile amber12 in AIX UNIX? (Thu Dec 05 2013 - 21:17:46 PST)
- Re: [AMBER] How to compile amber12 in AIX UNIX? (Tue Dec 03 2013 - 19:05:40 PST)
- Re: [AMBER] How to compile amber12 in AIX UNIX? (Tue Dec 03 2013 - 18:55:37 PST)
- [AMBER] How to compile amber12 in AIX UNIX? (Tue Dec 03 2013 - 11:19:32 PST)
Mike Limb
- Re: [AMBER] Restrained MD with COM restraint with PMEMD (Wed Dec 04 2013 - 03:41:03 PST)
- [AMBER] Restrained MD with COM restraint with PMEMD (Tue Dec 03 2013 - 14:16:59 PST)
Mohammed Khaled Tumbi
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages (Mon Dec 30 2013 - 00:54:23 PST)
Neha Gandhi
- [AMBER] cpptraj clustering (Thu Dec 26 2013 - 03:03:39 PST)
- [AMBER] AMBER GPU performance issue (Tue Dec 10 2013 - 03:04:37 PST)
Nicole Ippolito
- Re: [AMBER] Simulation time help (Thu Dec 12 2013 - 08:56:56 PST)
- Re: [AMBER] Simulation time help (Thu Dec 12 2013 - 08:44:45 PST)
- [AMBER] Simulation time help (Thu Dec 12 2013 - 08:28:31 PST)
Nitin Sharma
- Re: [AMBER] binding free energy and pose analysis (Sun Dec 29 2013 - 09:23:58 PST)
- Re: [AMBER] binding free energy and pose analysis (Sun Dec 29 2013 - 07:44:24 PST)
- Re: [AMBER] binding free energy and pose analysis (Sat Dec 28 2013 - 02:42:59 PST)
- [AMBER] binding free energy and pose analysis (Fri Dec 27 2013 - 09:52:50 PST)
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD (Fri Dec 27 2013 - 09:29:06 PST)
- [AMBER] RMSD vs RMSF vs nofit-RMSD (Thu Dec 26 2013 - 09:40:05 PST)
O Z
- Re: [AMBER] Temperature raises abnormally during accelerated MD (Wed Dec 04 2013 - 17:02:19 PST)
onetwo
- Re: [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file (Thu Dec 26 2013 - 22:42:40 PST)
- [AMBER] unable to recognize Chlorine atom even after defining in lib and frcmod file (Wed Dec 25 2013 - 21:57:20 PST)
- [AMBER] Simulating protein with Fe atom (Tue Dec 24 2013 - 20:45:50 PST)
Pranjal Mahanta
- [AMBER] atom-atom contact analysis in PTRAj (Wed Dec 11 2013 - 23:51:09 PST)
Prema Mallipeddi
- [AMBER] Regarding generating parameters for protein with NAD+ (Wed Dec 11 2013 - 14:49:55 PST)
psu4.uic.edu
- Re: [AMBER] MMPBSA.py strip_mask issue (Sun Dec 15 2013 - 20:52:43 PST)
- Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA (Mon Dec 02 2013 - 15:52:40 PST)
Ray Luo, Ph.D.
- Re: [AMBER] MMPBSA with inp=1 (Mon Dec 23 2013 - 11:31:30 PST)
- Re: [AMBER] MMPBSA with inp=1 (Thu Dec 19 2013 - 10:34:21 PST)
- Re: [AMBER] MMPBSA with inp=1 (Thu Dec 19 2013 - 09:40:05 PST)
- Re: [AMBER] MMPBSA errors :failed with prmtop (Mon Dec 16 2013 - 15:13:44 PST)
- Re: [AMBER] MMPBSA errors :failed with prmtop (Tue Dec 10 2013 - 10:04:22 PST)
- Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe (Mon Dec 09 2013 - 10:03:18 PST)
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 (Tue Dec 03 2013 - 10:38:47 PST)
- Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA (Mon Dec 02 2013 - 16:35:17 PST)
Rejwan
- [AMBER] C12 from OL (Tue Dec 31 2013 - 10:32:08 PST)
Robin Jain
- [AMBER] request for help in water shell and closest command (Sun Dec 29 2013 - 22:43:57 PST)
ros
- Re: [AMBER] cpptraj can not pass empty trajectory entry which is ok for ptraj (Fri Dec 20 2013 - 09:00:37 PST)
Ross Walker
- Re: [AMBER] cudaMemcpy GpuBuffer::Download failed unspecified launch failure (Sat Dec 21 2013 - 11:23:20 PST)
- Re: [AMBER] status of the Amber lipid framework? (Thu Dec 19 2013 - 12:01:21 PST)
- Re: [AMBER] amber QM/MM :vlimit exceeded for step 1; vmax = 71.9072 (Mon Dec 16 2013 - 09:26:23 PST)
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? (Fri Dec 13 2013 - 12:25:18 PST)
- Re: [AMBER] Amber QM/MM (Thu Dec 12 2013 - 07:38:32 PST)
- Re: [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? (Mon Dec 02 2013 - 10:42:49 PST)
Roza M
- Re: [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? (Wed Dec 11 2013 - 08:29:42 PST)
- [AMBER] Is there any way I can complete a production run which has been interrupted by a sudden power cut ? (Wed Dec 11 2013 - 05:44:14 PST)
Saeed Nasiri
- [AMBER] sander's Segmentation fault (Sat Dec 28 2013 - 03:36:13 PST)
- [AMBER] modified the amber parameter (Wed Dec 25 2013 - 08:12:13 PST)
- [AMBER] runing sander (Wed Dec 11 2013 - 07:38:50 PST)
- [AMBER] sander command (Tue Dec 10 2013 - 00:07:37 PST)
- [AMBER] nasiri (Wed Dec 04 2013 - 07:00:02 PST)
- [AMBER] saveamberparameters problem (Mon Dec 02 2013 - 08:25:22 PST)
Sajeewa Pemasinghe
- Re: [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c (Tue Dec 10 2013 - 10:14:24 PST)
- [AMBER] netcdf compilation error in Amber12 serial installation: Couldn't compile conftest.c (Mon Dec 09 2013 - 16:25:59 PST)
- [AMBER] Error in amber12 serial installation in file alltasks_setup.F90:352 (Thu Dec 05 2013 - 19:46:38 PST)
Sally Pias
- [AMBER] status of the Amber lipid framework? (Thu Dec 19 2013 - 11:54:59 PST)
Sangeetha B
- Re: [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 10:00:18 PST)
- Re: [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 09:28:52 PST)
- [AMBER] 3D projection of pairwise-RMSD (Fri Dec 13 2013 - 06:11:57 PST)
Silvestre
- Re: [AMBER] Amber Tools v.13 (Wed Dec 11 2013 - 12:57:45 PST)
- Re: [AMBER] Amber Tools v.13 (Mon Dec 09 2013 - 14:25:48 PST)
- [AMBER] Amber Tools v.13 (Mon Dec 09 2013 - 13:18:48 PST)
Sohag Biswas
- [AMBER] Finding difficulty during calculation of diffusion coefficient from MSD plot (Sat Dec 28 2013 - 21:40:33 PST)
- [AMBER] not getting correct density for N,N-dimethylformamide (Sat Dec 07 2013 - 08:39:58 PST)
Sourav Purohit
- Re: [AMBER] angle restraint with atom groups (Mon Dec 30 2013 - 13:30:54 PST)
- [AMBER] angle restraint with atom groups (Mon Dec 30 2013 - 10:49:08 PST)
suma jayakrishnan
- [AMBER] Fwd: doubt in alanine scanning of phosphorylated residue (Tue Dec 24 2013 - 18:45:17 PST)
- [AMBER] doubt in alanine scanning of phosphorylated residue (Mon Dec 23 2013 - 02:39:08 PST)
Sumra Wajid Abbasi 30-FBAS/MSBI/F09
- [AMBER] Error while visualizing radius of gyration graph (Tue Dec 17 2013 - 22:56:03 PST)
sunita gupta
- [AMBER] MMPBSA for single re-minimised coordinate (Mon Dec 23 2013 - 04:23:31 PST)
- Re: [AMBER] Atom Expression in NAB (Sun Dec 08 2013 - 21:21:09 PST)
- Re: [AMBER] Atom Expression in NAB (Sun Dec 08 2013 - 21:11:49 PST)
- [AMBER] Atom Expression in NAB (Sun Dec 08 2013 - 07:59:58 PST)
sunita.tifrh.res.in
- Re: [AMBER] amber parameter for S2P (phosphoserine) (Tue Dec 24 2013 - 00:32:15 PST)
- [AMBER] amber parameter for S2P (phosphoserine) (Mon Dec 23 2013 - 22:47:54 PST)
Tanmoy Paul
- [AMBER] SETTING QM ZONE (Mon Dec 02 2013 - 02:52:46 PST)
Thomas Evangelidis
- Re: [AMBER] capturing free energy landscape (Fri Dec 20 2013 - 05:35:31 PST)
- Re: [AMBER] capturing free energy landscape (Tue Dec 10 2013 - 12:59:46 PST)
vadiraj kurdekar
- Re: [AMBER] RMSD vs RMSF vs nofit-RMSD (Fri Dec 27 2013 - 02:34:33 PST)
Vijay Manickam Achari
- [AMBER] The use of ansiotropic & semi-anisotropic pressure couplings in bilayer simulation. (Wed Dec 11 2013 - 20:20:00 PST)
- Re: [AMBER] Anisotropic & semi-anisotropic (Mon Dec 09 2013 - 19:35:11 PST)
- [AMBER] Anisotropic & semi-anisotropic (Sat Dec 07 2013 - 00:46:54 PST)
- [AMBER] anisotropic & semi-anisotropic pressure coupling. (Fri Dec 06 2013 - 01:24:29 PST)
- [AMBER] When to use semi-anisotropic pressure couplings (Thu Dec 05 2013 - 22:34:33 PST)
Vlad Cojocaru
- Re: [AMBER] MMPBSA with inp=1 (Thu Dec 19 2013 - 10:28:07 PST)
- [AMBER] MMPBSA with inp=1 (Thu Dec 19 2013 - 02:38:25 PST)
- Re: [AMBER] MMPBSA of protein_DNA complex (Tue Dec 17 2013 - 02:49:06 PST)
- [AMBER] MMPBSA: eneopt=1 versus eneopt=3 (Mon Dec 16 2013 - 08:06:51 PST)
wangyanforward.gmail.com
- [AMBER] RE： Bad atom type error during MMGBSA decompositioncalsulations (Thu Dec 19 2013 - 18:47:33 PST)
wmsmith.uci.edu
- Re: [AMBER] MMPBSA with inp=1 (Thu Dec 19 2013 - 11:49:41 PST)
- Re: [AMBER] MMPBSA with inp=1 (Thu Dec 19 2013 - 11:47:06 PST)
- Re: [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 16:45:28 PST)
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation (Tue Dec 10 2013 - 10:08:12 PST)
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation (Tue Dec 10 2013 - 08:11:45 PST)
- Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0 (Tue Dec 03 2013 - 12:21:15 PST)
X Sun
- [AMBER] Proper Algorithm for GPU? (Sat Dec 14 2013 - 15:31:10 PST)
- [AMBER] Compare the result between pmemd.cuda and pmemd.mpi? (Mon Dec 02 2013 - 10:11:42 PST)
Yanyan ZHU
- [AMBER] Problems about invoking AMBER12 in calculating binding energy (Thu Dec 26 2013 - 18:19:00 PST)
- [AMBER] Errors about the values of PBSUR when calculating binding energy using MMPBSA (Wed Dec 25 2013 - 01:35:57 PST)
- [AMBER] Problems of invoking the Amber 12 and calculating the energy of each residue using the MMPBSA (Sat Dec 21 2013 - 20:13:29 PST)
- [AMBER] Problems of invoking the Amber 12 (Thu Dec 19 2013 - 23:53:41 PST)
- [AMBER] Puzzles about calculating binding energy using MMGBSA (Sat Dec 14 2013 - 04:05:41 PST)
- [AMBER] Puzzles about calculating the binding energy of residues (Thu Dec 12 2013 - 06:10:40 PST)
Ye MEI
- Re: [AMBER] input file with leap or antechamber? (Wed Dec 25 2013 - 00:18:01 PST)
Yip Yew Mun
- Re: [AMBER] Tleap Problem - Unable to bond atoms in amide linkages (Mon Dec 30 2013 - 01:27:02 PST)
- [AMBER] Plotting a Dynamic Cross Correlation Map (Fri Dec 06 2013 - 00:28:25 PST)
yunshi11 .
- [AMBER] Should vdW cutoff distance be system-dependent? (Fri Dec 06 2013 - 09:38:28 PST)
Zahra Khatti
- [AMBER] input file with leap or antechamber? (Wed Dec 25 2013 - 00:02:19 PST)
- [AMBER] compile parallel mpi (Fri Dec 06 2013 - 06:55:03 PST)
- [AMBER] question (Thu Dec 05 2013 - 09:13:37 PST)
zhongqiao hu
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions (Thu Dec 26 2013 - 06:10:34 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions (Sat Dec 21 2013 - 05:48:42 PST)
- Re: [AMBER] How to decompose PMF into electrostatic and van der Waals contributions (Thu Dec 19 2013 - 18:35:41 PST)
- [AMBER] How to decompose PMF into electrostatic and van der Waals contributions. (Thu Dec 19 2013 - 01:44:00 PST)
- Re: [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? (Sun Dec 01 2013 - 06:52:35 PST)
- [AMBER] Does pmemd or pmemd.mpi support center of mass restraint? (Sat Nov 30 2013 - 08:01:36 PST)
张明焜
- [AMBER] how to remove the rotational center-of-mass motion ? (Thu Dec 12 2013 - 22:30:26 PST)
王衍
- [AMBER] Bad atom type error during MMGBSA decomposition calsulations (Thu Dec 19 2013 - 00:47:06 PST)
肖立
- Re: [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 21:36:37 PST)
- Re: [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 15:49:47 PST)
- [AMBER] Does anyone knows how to generate an ired vector (Wed Dec 11 2013 - 14:51:47 PST)
- Re: [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation (Tue Dec 10 2013 - 09:03:15 PST)
- [AMBER] Does anyone know which parameter controls the wavenumber related to the Helmholtz equation (Mon Dec 09 2013 - 20:47:04 PST)
闫玉娜
- Re: [AMBER] Brookhaven pdb format (Sun Dec 08 2013 - 21:04:44 PST)
- [AMBER] Brookhaven pdb format (Sun Dec 08 2013 - 19:22:40 PST)

Amber Archive Dec 2013 by author