Amber Archive Mar 2016: by author

A kS
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 (Tue Mar 22 2016 - 23:09:11 PDT)
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 (Tue Mar 22 2016 - 05:22:53 PDT)
- [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 (Mon Mar 21 2016 - 23:25:09 PDT)
alexander.zlobin
- [AMBER] GAFF of Amber 'ff..' force field to prepare ligands? (Tue Mar 22 2016 - 03:50:29 PDT)
- [AMBER] Problem with 'hydrogen' having multiple bonds using SHAKEH (Sat Mar 12 2016 - 06:47:28 PST)
amirhossein taghavi
- [AMBER] desc in leap (Thu Mar 24 2016 - 09:05:26 PDT)
Andy Watkins
- Re: [AMBER] Production phase for MMPBSA (Wed Mar 09 2016 - 02:10:24 PST)
- Re: [AMBER] Production phase for MMPBSA (Wed Mar 09 2016 - 01:06:31 PST)
Anna Cebrian Prats
- [AMBER] Chamber tool, error using the prmtop and inpcrd files (Tue Mar 08 2016 - 02:36:47 PST)
Annie Ancy
- [AMBER] Fwd: MMPBSA CalceError mmpbsa_py_energy failed with prmtop com.prmtop! (Wed Mar 23 2016 - 03:49:00 PDT)
anu chandra
- Re: [AMBER] Amber parameters for deprotonated threonine (Thu Mar 24 2016 - 14:59:55 PDT)
- [AMBER] Amber parameters for deprotonated threonine (Thu Mar 24 2016 - 09:03:54 PDT)
- Re: [AMBER] Error with make test.parallel in AmberTools 15 installation (Thu Mar 17 2016 - 06:03:51 PDT)
- [AMBER] Error with make test.parallel in AmberTools 15 installation (Wed Mar 16 2016 - 09:28:10 PDT)
- [AMBER] A query about using random seed generator in simulations (Tue Mar 15 2016 - 05:14:45 PDT)
- Re: [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 09:41:43 PST)
- [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 04:37:18 PST)
Arati Paudyal
- [AMBER] MMPBSA error (Sat Mar 12 2016 - 11:07:18 PST)
- Re: [AMBER] RMSD too high after simulation (Fri Mar 11 2016 - 18:07:23 PST)
- [AMBER] RMSD too high after simulation (Fri Mar 11 2016 - 17:41:36 PST)
- [AMBER] Igb and salt concentration for GBSA (Fri Mar 11 2016 - 15:09:02 PST)
- Re: [AMBER] Production phase for MMPBSA (Wed Mar 09 2016 - 05:53:56 PST)
- [AMBER] Production phase for MMPBSA (Tue Mar 08 2016 - 11:06:10 PST)
- [AMBER] LINMEN (Tue Mar 01 2016 - 14:48:58 PST)
Arjun Narayanan
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Mon Mar 07 2016 - 08:03:34 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Mon Mar 07 2016 - 05:19:59 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Mon Mar 07 2016 - 04:58:28 PST)
- [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Fri Mar 04 2016 - 08:26:36 PST)
Arnoult, Eric [JRDUS]
- Re: [AMBER] set up for a binding event MD (Fri Mar 25 2016 - 13:47:06 PDT)
- Re: [AMBER] set up for a binding event MD (Fri Mar 25 2016 - 07:24:57 PDT)
- [AMBER] set up for a binding event MD (Fri Mar 18 2016 - 11:02:17 PDT)
Aronica, Pietro
- [AMBER] Sign of outputs of MMPBSA.py (Thu Mar 03 2016 - 08:02:58 PST)
Ayesha Kanwal
- [AMBER] Need python code for the calculation of binding energy (Wed Mar 30 2016 - 03:21:55 PDT)
- Re: [AMBER] Need Amber entropy calculated values (Sat Mar 12 2016 - 14:29:11 PST)
- Re: [AMBER] Need Amber entropy calculated values (Tue Mar 01 2016 - 00:51:38 PST)
Balaji Selvam
- [AMBER] parmed -setBond command (Mon Mar 14 2016 - 11:19:39 PDT)
Bill Ross
- Re: [AMBER] Command to display simulation completion time (Thu Mar 31 2016 - 00:41:19 PDT)
- Re: [AMBER] Command to display simulation completion time (Thu Mar 31 2016 - 00:35:34 PDT)
- Re: [AMBER] membrane protein complex preparation (Wed Mar 30 2016 - 04:23:19 PDT)
- Re: [AMBER] membrane protein complex preparation (Wed Mar 30 2016 - 00:46:09 PDT)
- Re: [AMBER] membrane protein problem (Sat Mar 26 2016 - 13:45:37 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 12:03:42 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 12:01:02 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Thu Mar 24 2016 - 22:41:07 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Thu Mar 24 2016 - 22:39:25 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 18:35:51 PDT)
- [AMBER] AT_15 install/osx notes, xleap deselect not working (Thu Mar 24 2016 - 18:27:08 PDT)
- Re: [AMBER] desc in leap (Thu Mar 24 2016 - 17:53:35 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 12:24:30 PDT)
- Re: [AMBER] On alphabetizing impropers (Wed Mar 23 2016 - 23:01:10 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion (Wed Mar 23 2016 - 21:40:00 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sun Mar 20 2016 - 22:10:36 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 13:11:40 PDT)
- Re: [AMBER] restart file error (Fri Mar 18 2016 - 12:47:01 PDT)
- Re: [AMBER] Creating new atom (Wed Mar 09 2016 - 21:46:51 PST)
- Re: [AMBER] ambpdb could not read restart atoms/time. (Wed Mar 09 2016 - 19:25:02 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 00:13:42 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 22:39:57 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 20:55:03 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion (Thu Mar 03 2016 - 01:22:43 PST)
- Re: [AMBER] Error while creating neutralized topology and coordinates file (Tue Mar 01 2016 - 03:38:47 PST)
Bin Wang
- Re: [AMBER] ambpdb could not read restart atoms/time. (Wed Mar 09 2016 - 19:41:31 PST)
- Re: [AMBER] ambpdb could not read restart atoms/time. (Wed Mar 09 2016 - 19:40:09 PST)
- [AMBER] ambpdb could not read restart atoms/time. (Wed Mar 09 2016 - 19:07:31 PST)
Bin ZOU
- Re: [AMBER] MPI_ABORT in pH-REMD (Mon Mar 21 2016 - 02:36:25 PDT)
- [AMBER] The basis for selecting step sizes (Thu Mar 17 2016 - 22:51:41 PDT)
Brent Krueger
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 09:22:47 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 06:53:18 PDT)
Bruno Falcone
- Re: [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range (Wed Mar 16 2016 - 07:27:22 PDT)
- [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range (Tue Mar 15 2016 - 14:55:20 PDT)
Carlos Romero
- [AMBER] amber14 installation (Mon Mar 28 2016 - 22:52:38 PDT)
- Re: [AMBER] calculate free energy binding in presence of ions witn mmpbsa (Sat Mar 26 2016 - 14:51:22 PDT)
- [AMBER] calculate free energy binding in presence of ions witn mmpbsa (Tue Mar 01 2016 - 22:48:03 PST)
- [AMBER] mmpbsa.py question (Tue Mar 01 2016 - 11:03:44 PST)
Carlos Simmerling
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Thu Mar 31 2016 - 02:51:51 PDT)
- Re: [AMBER] Amber MD simulation - viewing artifacts in VMD? (Tue Mar 29 2016 - 05:10:29 PDT)
- Re: [AMBER] Relation between binding affinity and free enegy (Mon Mar 28 2016 - 12:36:09 PDT)
- Re: [AMBER] set up for a binding event MD (Fri Mar 25 2016 - 07:30:05 PDT)
- Re: [AMBER] [Amber] Polarizable ff for vacuum (Thu Mar 24 2016 - 10:05:22 PDT)
- Re: [AMBER] [Amber] Polarizable ff for vacuum (Thu Mar 24 2016 - 09:16:19 PDT)
- Re: [AMBER] Amber parameters for deprotonated threonine (Thu Mar 24 2016 - 09:14:04 PDT)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Tue Mar 22 2016 - 04:30:13 PDT)
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 (Tue Mar 22 2016 - 04:29:03 PDT)
- Re: [AMBER] RMSD too high after simulation (Sat Mar 12 2016 - 03:09:02 PST)
- Re: [AMBER] RMSD too high after simulation (Fri Mar 11 2016 - 17:49:13 PST)
- Re: [AMBER] Igb and salt concentration for GBSA (Fri Mar 11 2016 - 17:37:41 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 05:47:07 PST)
- Re: [AMBER] problem with ionized residues (Thu Mar 10 2016 - 03:47:31 PST)
- Re: [AMBER] problem with ionized residues (Thu Mar 10 2016 - 03:16:15 PST)
- Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results (Wed Mar 09 2016 - 03:13:24 PST)
- Re: [AMBER] GB Parameterization (Thu Mar 03 2016 - 19:51:48 PST)
- Re: [AMBER] Dihedral angle values from .mdcrd file (Wed Mar 02 2016 - 04:10:18 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Tue Mar 01 2016 - 16:49:22 PST)
- Re: [AMBER] adding ion (Tue Mar 01 2016 - 05:26:46 PST)
chandan patel
- Re: [AMBER] problem running MD for diphosphoric acid anion (Thu Mar 03 2016 - 03:07:13 PST)
Charles Lin
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 12:29:04 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 12:19:58 PDT)
Charlotte RIEUX
- Re: [AMBER] Command to display simulation completion time (Thu Mar 31 2016 - 07:41:20 PDT)
chemjxn
- [AMBER] mmgbsa_error (Thu Mar 03 2016 - 00:09:42 PST)
chemjxn
- Re: [AMBER] mmgbsa_error (Fri Mar 04 2016 - 01:00:03 PST)
- [AMBER] mmgbsa_error (Thu Mar 03 2016 - 00:10:35 PST)
Chris Moth
- Re: [AMBER] membrane protein problem (Sat Mar 26 2016 - 15:14:51 PDT)
Christian Schafmeister
- Re: [AMBER] On alphabetizing impropers (Wed Mar 23 2016 - 23:10:18 PDT)
Christina Bergonzo
- Re: [AMBER] References (Fri Mar 11 2016 - 08:05:28 PST)
- Re: [AMBER] References (Fri Mar 11 2016 - 07:57:26 PST)
Cockroft, Nicholas T.
- Re: [AMBER] Normal Mode Job Allocation Failure (Wed Mar 23 2016 - 11:12:50 PDT)
- [AMBER] Normal Mode Job Allocation Failure (Mon Mar 21 2016 - 08:18:03 PDT)
conor parks
- Re: [AMBER] RMSD too high after simulation (Fri Mar 11 2016 - 17:50:32 PST)
Daniel Roe
- Re: [AMBER] problem in plotting total energy graphs by perl script (Wed Mar 30 2016 - 04:46:24 PDT)
- Re: [AMBER] trajin reads box info from a trajectory with no box info. (Mon Mar 28 2016 - 14:07:10 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Mon Mar 28 2016 - 06:37:52 PDT)
- Re: [AMBER] AT_15 install/osx notes, xleap deselect not working (Fri Mar 25 2016 - 09:35:05 PDT)
- Re: [AMBER] nonnative contacts (Fri Mar 25 2016 - 08:08:04 PDT)
- Re: [AMBER] Clustering (Fri Mar 25 2016 - 07:53:00 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Fri Mar 25 2016 - 07:48:40 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion (Thu Mar 24 2016 - 18:28:25 PDT)
- Re: [AMBER] desc in leap (Thu Mar 24 2016 - 09:29:06 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion (Thu Mar 24 2016 - 09:20:00 PDT)
- Re: [AMBER] Normal Mode Job Allocation Failure (Wed Mar 23 2016 - 08:54:59 PDT)
- Re: [AMBER] strange output with nativecontacts command (Tue Mar 22 2016 - 12:38:30 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Tue Mar 22 2016 - 09:01:00 PDT)
- Re: [AMBER] Calculating pair-wise interaction energy using MMPBSA for Gromacs files (Tue Mar 22 2016 - 07:30:31 PDT)
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 (Tue Mar 22 2016 - 07:25:15 PDT)
- Re: [AMBER] strange output with nativecontacts command (Mon Mar 21 2016 - 18:52:21 PDT)
- Re: [AMBER] strange output with nativecontacts command (Mon Mar 21 2016 - 17:53:30 PDT)
- Re: [AMBER] MPI_ABORT in pH-REMD (Mon Mar 21 2016 - 08:23:52 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Mon Mar 21 2016 - 07:38:16 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sun Mar 20 2016 - 09:00:33 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sun Mar 20 2016 - 08:29:54 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sat Mar 19 2016 - 07:20:47 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Fri Mar 18 2016 - 16:32:50 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Thu Mar 17 2016 - 17:13:43 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Thu Mar 17 2016 - 17:09:21 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Thu Mar 17 2016 - 06:37:19 PDT)
- Re: [AMBER] rmsd y axis value deviation. (Wed Mar 16 2016 - 12:12:32 PDT)
- Re: [AMBER] tests dont work after installation (Wed Mar 16 2016 - 10:56:25 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Wed Mar 16 2016 - 10:01:54 PDT)
- Re: [AMBER] Error with make test.parallel in AmberTools 15 installation (Wed Mar 16 2016 - 09:32:38 PDT)
- Re: [AMBER] shell script (Tue Mar 15 2016 - 19:35:53 PDT)
- Re: [AMBER] Attempting MC barostat change: Failed (Tue Mar 15 2016 - 07:42:37 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Tue Mar 15 2016 - 07:31:19 PDT)
- Re: [AMBER] Lifetime analysis of backbone hydrogen bonds (Mon Mar 14 2016 - 13:46:32 PDT)
- Re: [AMBER] Lifetime analysis of backbone hydrogen bonds (Mon Mar 14 2016 - 12:45:09 PDT)
- Re: [AMBER] parmed -setBond command (Mon Mar 14 2016 - 11:36:04 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Sun Mar 13 2016 - 13:40:39 PDT)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 13:53:15 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Thu Mar 10 2016 - 08:18:03 PST)
- Re: [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 08:16:21 PST)
- Re: [AMBER] energy calculation with cpptraj based on chamber topology file (Thu Mar 10 2016 - 08:07:48 PST)
- Re: [AMBER] velocity auto correlation function (Thu Mar 10 2016 - 07:43:03 PST)
- Re: [AMBER] energy calculation with cpptraj based on chamber topology file (Thu Mar 10 2016 - 07:34:00 PST)
- Re: [AMBER] ambpdb could not read restart atoms/time. (Thu Mar 10 2016 - 07:24:14 PST)
- Re: [AMBER] ambpdb could not read restart atoms/time. (Wed Mar 09 2016 - 20:32:02 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 11:54:38 PST)
- Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation (Wed Mar 09 2016 - 10:44:21 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 10:07:32 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 10:06:23 PST)
- Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results (Wed Mar 09 2016 - 07:55:37 PST)
- Re: [AMBER] How to using distance based strip action and generate the corresponding prmtop (Wed Mar 09 2016 - 07:51:30 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 07:41:14 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 20:43:04 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 14:38:22 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 13:43:39 PST)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Tue Mar 08 2016 - 07:02:38 PST)
- Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation. (Mon Mar 07 2016 - 13:23:07 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Mon Mar 07 2016 - 07:44:41 PST)
- Re: [AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 (Mon Mar 07 2016 - 07:41:53 PST)
- Re: [AMBER] Analysis of Radius of gyration (Fri Mar 04 2016 - 14:28:28 PST)
- Re: [AMBER] cpptraj molsurf: query on results (Fri Mar 04 2016 - 14:16:31 PST)
- Re: [AMBER] pseudo trajectories with 4 center of mass? (Thu Mar 03 2016 - 11:53:53 PST)
- Re: [AMBER] cpptraj molsurf: query on results (Thu Mar 03 2016 - 07:30:45 PST)
- Re: [AMBER] Dihedral angle values from .mdcrd file (Wed Mar 02 2016 - 09:49:16 PST)
David A Case
- Re: [AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0 (Thu Mar 31 2016 - 04:52:11 PDT)
- Re: [AMBER] Hydrophobic solution environment ??? (Wed Mar 30 2016 - 10:24:00 PDT)
- Re: [AMBER] Align namelist for direct dipolar coupling restraints (Wed Mar 30 2016 - 10:18:05 PDT)
- Re: [AMBER] Strange problem of running MD simulation with sander ? (Wed Mar 30 2016 - 08:40:47 PDT)
- Re: [AMBER] torsion angle rmsd by cpptraj ? (Tue Mar 29 2016 - 09:35:23 PDT)
- Re: [AMBER] cpptraj mask definition (Tue Mar 29 2016 - 04:25:40 PDT)
- Re: [AMBER] amber14 installation (Tue Mar 29 2016 - 04:24:15 PDT)
- Re: [AMBER] How does one derive parameters to modify GAFF? (Mon Mar 28 2016 - 18:13:13 PDT)
- Re: [AMBER] problem in nmode calculation by NAB (Mon Mar 28 2016 - 14:34:01 PDT)
- Re: [AMBER] mpirun .... hwloc (Fri Mar 25 2016 - 04:20:15 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 04:14:33 PDT)
- Re: [AMBER] [Amber] Polarizable ff for vacuum (Thu Mar 24 2016 - 09:46:42 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 09:00:04 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 04:23:29 PDT)
- Re: [AMBER] questions about mol2 and pdb file. (Thu Mar 24 2016 - 04:16:23 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Tue Mar 22 2016 - 09:57:05 PDT)
- Re: [AMBER] A query about using random seed generator in simulations (Tue Mar 15 2016 - 06:58:52 PDT)
- Re: [AMBER] Problem with 'hydrogen' having multiple bonds using SHAKEH (Sat Mar 12 2016 - 09:19:09 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 05:49:08 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 04:35:03 PST)
- Re: [AMBER] generate frcmod.user file for missing parameters (Fri Mar 11 2016 - 04:33:41 PST)
- Re: [AMBER] Lower energy frame from summary.EPTOT (Fri Mar 11 2016 - 04:32:03 PST)
- Re: [AMBER] Paradynamics simulations with Amber (Fri Mar 11 2016 - 04:26:22 PST)
- Re: [AMBER] Optimize in Gaussian with RESP (Fri Mar 11 2016 - 04:19:43 PST)
- Re: [AMBER] Installation error amber14 (Thu Mar 10 2016 - 04:17:28 PST)
- Re: [AMBER] ambpdb could not read restart atoms/time. (Thu Mar 10 2016 - 04:14:10 PST)
- Re: [AMBER] Optimize in Gaussian with RESP (Wed Mar 09 2016 - 04:43:49 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 16:34:15 PST)
- Re: [AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 (Mon Mar 07 2016 - 08:55:04 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Mon Mar 07 2016 - 08:51:55 PST)
- Re: [AMBER] nucleic acid residue representation in leap (Sat Mar 05 2016 - 06:45:04 PST)
- Re: [AMBER] GB Parameterization (Fri Mar 04 2016 - 09:35:53 PST)
- Re: [AMBER] Query regarding NMR refinement (Fri Mar 04 2016 - 06:00:50 PST)
- Re: [AMBER] mmgbsa_error (Fri Mar 04 2016 - 05:55:16 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Fri Mar 04 2016 - 05:49:50 PST)
- Re: [AMBER] GB Parameterization (Fri Mar 04 2016 - 05:42:11 PST)
- Re: [AMBER] problem running MD for diphosphoric acid anion (Thu Mar 03 2016 - 06:24:22 PST)
- Re: [AMBER] Error while creating neutralized topology and coordinates file (Wed Mar 02 2016 - 05:04:19 PST)
- Re: [AMBER] Doc of Amber to the html version (Wed Mar 02 2016 - 04:58:42 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Wed Mar 02 2016 - 04:54:58 PST)
- Re: [AMBER] LINMEN (Tue Mar 01 2016 - 17:53:40 PST)
- Re: [AMBER] Inquiry regarding amber installation (Tue Mar 01 2016 - 11:25:04 PST)
David Cerutti
- Re: [AMBER] Proper nfft* parameters for a very long solvent box? (Wed Mar 30 2016 - 13:25:21 PDT)
- Re: [AMBER] Proper nfft* parameters for a very long solvent box? (Wed Mar 30 2016 - 12:46:42 PDT)
- Re: [AMBER] How does one derive parameters to modify GAFF? (Mon Mar 28 2016 - 19:52:02 PDT)
- [AMBER] How does one derive parameters to modify GAFF? (Mon Mar 28 2016 - 14:34:11 PDT)
- Re: [AMBER] membrane protein problem (Sat Mar 26 2016 - 15:51:14 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 09:08:09 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 08:07:42 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 21:21:12 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 15:40:09 PDT)
- Re: [AMBER] On alphabetizing impropers (Thu Mar 24 2016 - 07:47:20 PDT)
- Re: [AMBER] On alphabetizing impropers (Wed Mar 23 2016 - 23:02:56 PDT)
- [AMBER] On alphabetizing impropers (Wed Mar 23 2016 - 22:42:52 PDT)
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit (Mon Mar 14 2016 - 15:07:10 PDT)
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit (Mon Mar 14 2016 - 09:42:53 PDT)
- Re: [AMBER] How did GAFF get force constants? (Sat Mar 12 2016 - 16:01:50 PST)
- Re: [AMBER] TIP3P (Sat Mar 12 2016 - 15:57:31 PST)
- Re: [AMBER] How did GAFF get force constants? (Tue Mar 08 2016 - 22:13:02 PST)
- Re: [AMBER] more extra points needed (Mon Feb 29 2016 - 21:09:38 PST)
Dickson, Callum J
- Re: [AMBER] membrane protein complex preparation (Tue Mar 29 2016 - 10:12:00 PDT)
- Re: [AMBER] salt concentration KCl (Tue Mar 29 2016 - 06:25:07 PDT)
- Re: [AMBER] membrane protein complex preparation (Mon Mar 28 2016 - 09:42:03 PDT)
- Re: [AMBER] membrane protein complex preparation (Mon Mar 28 2016 - 08:01:42 PDT)
- Re: [AMBER] membrane protein complex preparation (Mon Mar 28 2016 - 06:52:38 PDT)
Dr. M. K. Yadav
- [AMBER] Installation error amber14 (Thu Mar 10 2016 - 00:28:20 PST)
Dr. Robert Molt
- Re: [AMBER] GROMACS File Conversion Subtlety (Fri Mar 18 2016 - 22:15:11 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Thu Mar 17 2016 - 17:18:28 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Thu Mar 17 2016 - 17:00:39 PDT)
Edwin Aponte
- Re: [AMBER] [Amber] Polarizable ff for vacuum (Thu Mar 24 2016 - 09:41:52 PDT)
- [AMBER] [Amber] Polarizable ff for vacuum (Thu Mar 24 2016 - 07:48:21 PDT)
Elisa Pieri
- Re: [AMBER] MPI_ABORT in pH-REMD (Mon Mar 21 2016 - 08:13:05 PDT)
- Re: [AMBER] MPI_ABORT in pH-REMD (Mon Mar 21 2016 - 02:46:21 PDT)
- Re: [AMBER] MPI_ABORT in pH-REMD (Mon Mar 21 2016 - 02:08:42 PDT)
- [AMBER] MPI_ABORT in pH-REMD (Fri Mar 18 2016 - 06:05:02 PDT)
- Re: [AMBER] R: R: Fwd: cpinutil.py problem (Fri Mar 11 2016 - 04:03:10 PST)
Enrique Frio
- Re: [AMBER] Amber MD simulation - viewing artifacts in VMD? (Tue Mar 29 2016 - 05:34:32 PDT)
- [AMBER] Amber MD simulation - viewing artifacts in VMD? (Tue Mar 29 2016 - 05:05:05 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Sun Mar 20 2016 - 20:53:10 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Fri Mar 18 2016 - 14:45:30 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Fri Mar 18 2016 - 05:55:49 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Fri Mar 18 2016 - 05:48:08 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Thu Mar 17 2016 - 18:25:18 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Thu Mar 17 2016 - 15:55:15 PDT)
- [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Thu Mar 17 2016 - 04:02:29 PDT)
Fabian Glaser
- [AMBER] Periodicity box (Wed Mar 30 2016 - 09:21:02 PDT)
- Re: [AMBER] membrane protein complex preparation (Wed Mar 30 2016 - 02:59:11 PDT)
Fabian gmail
- Re: [AMBER] aMD simulation of membrane protein ? (Thu Mar 31 2016 - 08:00:27 PDT)
- Re: [AMBER] membrane protein complex preparation (Tue Mar 29 2016 - 08:28:06 PDT)
- Re: [AMBER] salt concentration KCl (Tue Mar 29 2016 - 07:23:23 PDT)
- [AMBER] salt concentration KCl (Tue Mar 29 2016 - 03:33:35 PDT)
- Re: [AMBER] membrane protein complex preparation (Tue Mar 29 2016 - 03:26:14 PDT)
- Re: [AMBER] membrane protein complex preparation (Mon Mar 28 2016 - 08:14:56 PDT)
- Re: [AMBER] membrane protein complex preparation (Mon Mar 28 2016 - 07:42:19 PDT)
- [AMBER] membrane protein complex preparation (Mon Mar 28 2016 - 04:15:16 PDT)
- [AMBER] charge membrane (Mon Mar 28 2016 - 02:18:59 PDT)
Francesco Gentile
- Re: [AMBER] RMSD of 0 for coordinated ion (Fri Mar 25 2016 - 12:23:17 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion (Thu Mar 24 2016 - 16:19:19 PDT)
- [AMBER] RMSD of 0 for coordinated ion (Wed Mar 23 2016 - 21:25:36 PDT)
Francisco Corzana López
- Re: [AMBER] Align namelist for direct dipolar coupling restraints (Thu Mar 31 2016 - 10:13:38 PDT)
- [AMBER] Align namelist for direct dipolar coupling restraints (Wed Mar 30 2016 - 08:59:39 PDT)
- Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints (Wed Mar 23 2016 - 13:43:54 PDT)
- Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints (Wed Mar 23 2016 - 09:34:41 PDT)
- [AMBER] Problems running MD simulations with pseudocontact shifts as restraints (Wed Mar 23 2016 - 01:44:12 PDT)
FyD
- Re: [AMBER] questions about mol2 and pdb file. (Thu Mar 24 2016 - 02:04:29 PDT)
- Re: [AMBER] nitro tyrosine (Fri Mar 18 2016 - 05:03:12 PDT)
- Re: [AMBER] topology file for a graphene oxide with repetitive pattern (Fri Mar 18 2016 - 03:22:00 PDT)
- Re: [AMBER] red server error: ddikick.x: Fatal error detected (Fri Mar 18 2016 - 03:18:07 PDT)
- Re: [AMBER] generate frcmod.user file for missing parameters (Fri Mar 11 2016 - 04:48:00 PST)
- Re: [AMBER] Optimize in Gaussian with RESP (Fri Mar 11 2016 - 04:42:24 PST)
- Re: [AMBER] Optimize in Gaussian with RESP (Fri Mar 11 2016 - 04:27:19 PST)
- [AMBER] Doc of Amber to the html version (Tue Mar 01 2016 - 01:25:09 PST)
George Green
- [AMBER] geforce 970 versus 780 (Wed Mar 09 2016 - 11:14:04 PST)
George Tzotzos
- [AMBER] General question (Tue Mar 29 2016 - 09:35:22 PDT)
- Re: [AMBER] mmpbsa discrepancies (Wed Mar 23 2016 - 05:44:02 PDT)
- [AMBER] mmpbsa discrepancies (Mon Mar 21 2016 - 10:05:36 PDT)
- [AMBER] cpptraj surf (Fri Mar 04 2016 - 13:35:45 PST)
- Re: [AMBER] cpptraj molsurf: query on results (Thu Mar 03 2016 - 12:16:22 PST)
- [AMBER] cpptraj molsurf: query on results (Wed Mar 02 2016 - 13:58:19 PST)
Gerald Monard
- Re: [AMBER] geforce 970 versus 780 (Mon Mar 28 2016 - 14:12:19 PDT)
Guqin Shi
- [AMBER] [AmberTools15] “Cluster” with cpptraj: looking for SSR/SST ratio (Mon Mar 28 2016 - 14:35:15 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 13:48:56 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 12:27:36 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 12:24:54 PDT)
- [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 12:12:11 PDT)
Gustavo Seabra
- Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints (Wed Mar 23 2016 - 13:15:55 PDT)
- Re: [AMBER] Problems running MD simulations with pseudocontact shifts as restraints (Wed Mar 23 2016 - 06:34:00 PDT)
- Re: [AMBER] Convergence problem with the SCC-DFTB example. (Tue Mar 15 2016 - 12:09:05 PDT)
Hadeer ELHabashy
- Re: [AMBER] References (Fri Mar 11 2016 - 08:04:02 PST)
- [AMBER] References (Fri Mar 11 2016 - 07:55:29 PST)
Hai Nguyen
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 15:02:13 PDT)
- Re: [AMBER] RMSD of 0 for coordinated ion (Wed Mar 23 2016 - 21:30:28 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 02:48:35 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 01:55:51 PDT)
- Re: [AMBER] FW: problem in plotting total energy graph by using perl script (Sat Mar 19 2016 - 01:23:34 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Sun Mar 13 2016 - 11:53:39 PDT)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 11:11:52 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 08:00:29 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 22:21:25 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 19:32:47 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 13:13:08 PST)
- Re: [AMBER] How did GAFF get force constants? (Tue Mar 08 2016 - 21:48:25 PST)
- Re: [AMBER] nucleic acid residue representation in leap (Fri Mar 04 2016 - 23:13:08 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 21:08:00 PST)
Hannes Loeffler
- Re: [AMBER] Command to display simulation completion time (Thu Mar 31 2016 - 08:06:09 PDT)
- Re: [AMBER] questions about mol2 and pdb file. (Thu Mar 24 2016 - 07:12:57 PDT)
- Re: [AMBER] rmsd y axis value deviation. (Wed Mar 16 2016 - 04:59:52 PDT)
- Re: [AMBER] red server error: ddikick.x: Fatal error detected (Wed Mar 16 2016 - 03:56:56 PDT)
- Re: [AMBER] topology file for a graphene oxide with repetitive pattern (Wed Mar 16 2016 - 03:27:13 PDT)
- Re: [AMBER] rmsd y axis value deviation. (Wed Mar 16 2016 - 03:08:39 PDT)
- Re: [AMBER] AMBER:neutralisation of non integral charges (Mon Mar 14 2016 - 06:37:42 PDT)
- Re: [AMBER] Production phase for MMPBSA (Wed Mar 09 2016 - 09:08:21 PST)
- Re: [AMBER] Production phase for MMPBSA (Wed Mar 09 2016 - 08:30:21 PST)
- Re: [AMBER] Production phase for MMPBSA (Wed Mar 09 2016 - 01:49:41 PST)
- Re: [AMBER] How to deal with fractional electron unit charges on small molecules?? (Mon Mar 07 2016 - 02:52:23 PST)
hannes.loeffler.stfc.ac.uk
- Re: [AMBER] questions about mol2 and pdb file. (Thu Mar 24 2016 - 00:26:48 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sat Mar 19 2016 - 00:42:00 PDT)
- Re: [AMBER] The basis for selecting step sizes (Fri Mar 18 2016 - 00:19:56 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Thu Mar 17 2016 - 01:41:37 PDT)
Hira Jabeen
- [AMBER] MMPBSA error (Tue Mar 01 2016 - 21:56:42 PST)
Hirdesh Kumar
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Wed Mar 16 2016 - 09:58:29 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Tue Mar 15 2016 - 05:54:46 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Sun Mar 13 2016 - 10:57:46 PDT)
- [AMBER] pseudo trajectories for 4 centers of mass? (Tue Mar 08 2016 - 06:34:48 PST)
- [AMBER] pseudo trajectories with 4 center of mass? (Thu Mar 03 2016 - 11:49:23 PST)
Hong Sun
- [AMBER] questions about mol2 and pdb file. (Wed Mar 23 2016 - 20:57:22 PDT)
Iqbal, Muhammad Sajid
- [AMBER] Analysis of Radius of gyration (Fri Mar 04 2016 - 14:19:26 PST)
Ivanov, Maxim
- Re: [AMBER] more extra points needed (Tue Mar 01 2016 - 18:31:49 PST)
Jason Swails
- Re: [AMBER] Need python code for the calculation of binding energy (Wed Mar 30 2016 - 05:36:10 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Tue Mar 29 2016 - 02:57:25 PDT)
- Re: [AMBER] membrane protein problem (Sat Mar 26 2016 - 13:08:16 PDT)
- Re: [AMBER] membrane protein problem (Sat Mar 26 2016 - 12:18:05 PDT)
- Re: [AMBER] AT_15 install/osx notes, xleap deselect not working (Fri Mar 25 2016 - 09:22:26 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 09:04:46 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 05:47:20 PDT)
- Re: [AMBER] On alphabetizing impropers (Fri Mar 25 2016 - 05:43:01 PDT)
- Re: [AMBER] Fwd: MMPBSA CalceError mmpbsa_py_energy failed with prmtop com.prmtop! (Wed Mar 23 2016 - 06:09:38 PDT)
- Re: [AMBER] set up for a binding event MD (Tue Mar 22 2016 - 18:48:08 PDT)
- Re: [AMBER] mmpbsa discrepancies (Tue Mar 22 2016 - 18:45:18 PDT)
- Re: [AMBER] Tutorial 18 - CpHMD with pmemd (Tue Mar 22 2016 - 09:36:01 PDT)
- Re: [AMBER] Tutorial 18 - CpHMD with pmemd (Tue Mar 22 2016 - 09:03:25 PDT)
- Re: [AMBER] MPI_ABORT in pH-REMD (Mon Mar 21 2016 - 07:59:21 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) (Sun Mar 20 2016 - 10:14:40 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sun Mar 20 2016 - 10:12:40 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sun Mar 20 2016 - 08:03:03 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sat Mar 19 2016 - 11:33:30 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Fri Mar 18 2016 - 15:07:10 PDT)
- Re: [AMBER] restart file error (Fri Mar 18 2016 - 14:19:30 PDT)
- Re: [AMBER] MPI_ABORT in pH-REMD (Fri Mar 18 2016 - 11:46:33 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Fri Mar 18 2016 - 10:15:55 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Fri Mar 18 2016 - 10:09:55 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Thu Mar 17 2016 - 16:05:47 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Thu Mar 17 2016 - 03:02:26 PDT)
- Re: [AMBER] Lower energy frame from summary.EPTOT (Fri Mar 11 2016 - 17:53:29 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 17:51:49 PST)
- Re: [AMBER] Igb and salt concentration for GBSA (Fri Mar 11 2016 - 17:50:39 PST)
- Re: [AMBER] Igb and salt concentration for GBSA (Fri Mar 11 2016 - 16:51:59 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 16:50:09 PST)
- Re: [AMBER] R: R: Fwd: cpinutil.py problem (Fri Mar 11 2016 - 09:00:29 PST)
- Re: [AMBER] energy calculation with cpptraj based on chamber topology file (Thu Mar 10 2016 - 09:35:17 PST)
- Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results (Wed Mar 09 2016 - 04:41:00 PST)
- Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results (Tue Mar 08 2016 - 18:44:13 PST)
- Re: [AMBER] Production phase for MMPBSA (Tue Mar 08 2016 - 18:39:39 PST)
- Re: [AMBER] Chamber tool, error using the prmtop and inpcrd files (Tue Mar 08 2016 - 05:09:08 PST)
- Re: [AMBER] nucleic acid residue representation in leap (Fri Mar 04 2016 - 23:14:01 PST)
- Re: [AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system (Fri Mar 04 2016 - 19:00:40 PST)
- Re: [AMBER] mmgbsa_error (Fri Mar 04 2016 - 05:11:02 PST)
- Re: [AMBER] Sign of outputs of MMPBSA.py (Thu Mar 03 2016 - 17:34:31 PST)
- Re: [AMBER] mmgbsa_error (Thu Mar 03 2016 - 03:52:59 PST)
- Re: [AMBER] adding ion (Tue Mar 01 2016 - 05:07:47 PST)
- Re: [AMBER] Need Amber entropy calculated values (Tue Mar 01 2016 - 04:56:14 PST)
Jesmita Dhar
- [AMBER] need help for using Re_fit (Wed Mar 30 2016 - 04:45:37 PDT)
- [AMBER] red server error: ddikick.x: Fatal error detected (Wed Mar 16 2016 - 03:44:10 PDT)
- [AMBER] topology file for a graphene oxide with repetitive pattern (Wed Mar 16 2016 - 03:07:29 PDT)
- Re: [AMBER] Optimize in Gaussian with RESP (Fri Mar 11 2016 - 04:40:27 PST)
- [AMBER] generate frcmod.user file for missing parameters (Fri Mar 11 2016 - 03:03:04 PST)
- [AMBER] Fwd: Optimize in Gaussian with RESP (Fri Mar 11 2016 - 00:33:38 PST)
- Re: [AMBER] Optimize in Gaussian with RESP (Thu Mar 10 2016 - 22:47:21 PST)
- [AMBER] Optimize in Gaussian with RESP (Wed Mar 09 2016 - 00:37:50 PST)
- [AMBER] Optimize in Gaussian with RESP (Wed Mar 09 2016 - 00:36:50 PST)
Jinfeng Huang
- [AMBER] Strange problem of running MD simulation with sander ? (Wed Mar 30 2016 - 08:07:28 PDT)
- Re: [AMBER] Convergence problem with the SCC-DFTB example. (Fri Mar 25 2016 - 07:55:26 PDT)
- [AMBER] Convergence problem with the SCC-DFTB example. (Tue Mar 15 2016 - 01:29:17 PDT)
Jiri Sponer
- Re: [AMBER] for protein- RNA complex simulation (Sat Mar 05 2016 - 00:39:56 PST)
jixiaofeng
- [AMBER] errors in plumed and amber14 patch (Thu Mar 17 2016 - 01:06:04 PDT)
jixiaofeng
- Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) (Sun Mar 20 2016 - 20:14:41 PDT)
- Re: [AMBER] errors in plumed and amber14 patch (Jason Swails) (Thu Mar 17 2016 - 19:12:38 PDT)
Jose Borreguero
- Re: [AMBER] trajin reads box info from a trajectory with no box info. (Mon Mar 28 2016 - 14:14:17 PDT)
- [AMBER] trajin reads box info from a trajectory with no box info. (Mon Mar 28 2016 - 13:21:41 PDT)
Josh Berryman
- Re: [AMBER] calculate free energy binding in presence of ions witn mmpbsa (Thu Mar 17 2016 - 00:25:33 PDT)
Jérémie KNOOPS [531802]
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit (Mon Mar 14 2016 - 14:34:57 PDT)
Karl Kirschner
- Re: [AMBER] GAFF of Amber 'ff..' force field to prepare ligands? (Tue Mar 22 2016 - 04:43:33 PDT)
Kasprzak, Wojciech (NIH/NCI) [C]
- Re: [AMBER] Proper nfft* parameters for a very long solvent box? (Wed Mar 30 2016 - 13:28:04 PDT)
- Re: [AMBER] Proper nfft* parameters for a very long solvent box? (Wed Mar 30 2016 - 13:08:03 PDT)
- [AMBER] Proper nfft* parameters for a very long solvent box? (Wed Mar 30 2016 - 11:14:59 PDT)
Kenneth Huang
- [AMBER] bad atom type with MMPBSA decomposition? (Mon Mar 14 2016 - 06:58:25 PDT)
Krantzman, Kristin D
- Re: [AMBER] nonnative contacts (Fri Mar 25 2016 - 08:53:55 PDT)
- Re: [AMBER] strange output with nativecontacts command (Thu Mar 24 2016 - 10:32:25 PDT)
- [AMBER] nonnative contacts (Thu Mar 24 2016 - 10:27:09 PDT)
- Re: [AMBER] strange output with nativecontacts command (Tue Mar 22 2016 - 11:58:55 PDT)
- Re: [AMBER] strange output with nativecontacts command (Mon Mar 21 2016 - 17:57:19 PDT)
- [AMBER] strange output with nativecontacts command (Mon Mar 21 2016 - 17:22:06 PDT)
- Re: [AMBER] Lifetime analysis of backbone hydrogen bonds (Mon Mar 14 2016 - 13:37:02 PDT)
- Re: [AMBER] Lifetime analysis of backbone hydrogen bonds (Mon Mar 14 2016 - 13:34:30 PDT)
- [AMBER] Lifetime analysis of backbone hydrogen bonds (Mon Mar 14 2016 - 12:28:55 PDT)
Kshatresh Dutta Dubey
- Re: [AMBER] ambpdb could not read restart atoms/time. (Wed Mar 09 2016 - 20:30:21 PST)
lipengfei_mail
- [AMBER] Paradynamics simulations with Amber (Thu Mar 10 2016 - 23:02:13 PST)
lipengfei_mail
- Re: [AMBER] Paradynamics simulations with Amber (Fri Mar 11 2016 - 22:36:51 PST)
Madhura De
- [AMBER] Query regarding NMR refinement (Fri Mar 04 2016 - 02:47:15 PST)
Marc van der Kamp
- Re: [AMBER] shell script (Wed Mar 16 2016 - 02:18:34 PDT)
Marcelo Andrade Chagas
- [AMBER] mpirun .... hwloc (Thu Mar 24 2016 - 11:29:03 PDT)
- Re: [AMBER] tests dont work after installation (Wed Mar 16 2016 - 11:19:10 PDT)
- Re: [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 10:52:54 PST)
- Re: [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 10:39:52 PST)
- Re: [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 10:38:38 PST)
- Re: [AMBER] Failed installation of latest MCPB version (Thu Mar 10 2016 - 04:42:09 PST)
- Re: [AMBER] Optimize in Gaussian with RESP (Wed Mar 09 2016 - 04:40:12 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Fri Mar 04 2016 - 02:13:55 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Fri Mar 04 2016 - 01:55:46 PST)
Marcos Serrou do Amaral
- Re: [AMBER] set up for a binding event MD (Tue Mar 22 2016 - 19:41:04 PDT)
- Re: [AMBER] Tutorial 18 - CpHMD with pmemd (Tue Mar 22 2016 - 08:37:15 PDT)
Marek Maly
- [AMBER] MMPBSApy - APBS bug (Sat Mar 26 2016 - 10:09:30 PDT)
Mark Abraham
- Re: [AMBER] GROMACS File Conversion Subtlety (Sun Mar 20 2016 - 08:26:00 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sat Mar 19 2016 - 12:32:57 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Sat Mar 19 2016 - 09:48:06 PDT)
- Re: [AMBER] GROMACS File Conversion Subtlety (Fri Mar 18 2016 - 21:04:24 PDT)
Mary Varughese
- Re: [AMBER] MMPBSA doubt (Tue Mar 22 2016 - 16:26:24 PDT)
- Re: [AMBER] MMPBSA doubt (Tue Mar 22 2016 - 02:43:11 PDT)
- Re: [AMBER] MMPBSA doubt (Mon Mar 21 2016 - 19:06:45 PDT)
- Re: [AMBER] MMPBSA doubt (Fri Mar 18 2016 - 21:48:15 PDT)
- [AMBER] MMPBSA doubt (Wed Mar 16 2016 - 02:20:21 PDT)
Michael Shokhen
- Re: [AMBER] aMD simulation of membrane protein ? (Thu Mar 31 2016 - 03:07:56 PDT)
- [AMBER] aMD simulation of membrane protein ? (Wed Mar 30 2016 - 03:18:51 PDT)
- [AMBER] torsion angle rmsd by cpptraj ? (Tue Mar 29 2016 - 05:00:49 PDT)
- Re: [AMBER] membrane protein problem (Sat Mar 26 2016 - 12:45:42 PDT)
- [AMBER] membrane protein problem (Sat Mar 26 2016 - 11:35:55 PDT)
- [AMBER] Attempting MC barostat change: Failed (Tue Mar 15 2016 - 05:51:21 PDT)
- Re: [AMBER] problem with ionized residues (Thu Mar 10 2016 - 03:33:25 PST)
- [AMBER] problem with ionized residues (Thu Mar 10 2016 - 02:30:20 PST)
Mijiddorj Batsaikhan
- Re: [AMBER] Hydrophobic solution environment ??? (Thu Mar 31 2016 - 06:53:08 PDT)
- [AMBER] Hydrophobic solution environment ??? (Wed Mar 30 2016 - 09:33:17 PDT)
Mohammed Khaled Tumbi
- Re: [AMBER] Error while creating neutralized topology and coordinates file (Tue Mar 01 2016 - 03:41:42 PST)
necmettin pirinccioglu
- Re: [AMBER] problem running MD for diphosphoric acid anion (Wed Mar 16 2016 - 00:36:52 PDT)
- Re: [AMBER] problem running MD for diphosphoric acid anion (Thu Mar 03 2016 - 00:49:28 PST)
neha chaudhary
- [AMBER] regarding mm-pbsa calculation (Fri Mar 04 2016 - 20:58:10 PST)
Nhai
- Re: [AMBER] interview with David Case (Tue Mar 22 2016 - 22:19:28 PDT)
- Re: [AMBER] problem running MD for diphosphoric acid anion (Wed Mar 16 2016 - 00:58:32 PDT)
- Re: [AMBER] Igb and salt concentration for GBSA (Fri Mar 11 2016 - 17:24:41 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 21:30:20 PST)
Niel Henriksen
- Re: [AMBER] Attempting MC barostat change: Failed (Tue Mar 15 2016 - 09:49:32 PDT)
Nikolai Skrynnikov
- [AMBER] interview with David Case (Tue Mar 22 2016 - 22:02:17 PDT)
Ofir Tal
- Re: [AMBER] aMD simulation of membrane protein ? (Thu Mar 31 2016 - 07:10:27 PDT)
Pengfei Li
- [AMBER] Is there a shift of QM energy in a QM/MM simulation? (Fri Mar 18 2016 - 05:26:47 PDT)
- Re: [AMBER] Paradynamics simulations with Amber (Sat Mar 12 2016 - 05:10:13 PST)
- [AMBER] IMPORTANT FOR 12-6-4 USERS (Sat Mar 05 2016 - 18:30:10 PST)
peter.schmidtke.discngine.servier.com
- Re: [AMBER] Gist calculation on clustered structures (Mon Mar 07 2016 - 23:31:40 PST)
- [AMBER] Gist calculation on clustered structures (Mon Feb 29 2016 - 23:23:01 PST)
- Re: [AMBER] Bounds command with GIst (Mon Feb 29 2016 - 23:18:28 PST)
Prayagraj Fandilolu
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Wed Mar 30 2016 - 20:13:23 PDT)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Mon Mar 21 2016 - 22:28:16 PDT)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Wed Mar 02 2016 - 01:48:07 PST)
- Re: [AMBER] SP3 Nitrogen planarity issue with ff14SB (Mon Feb 29 2016 - 21:37:14 PST)
psu4.uic.edu
- Re: [AMBER] Need Amber entropy calculated values (Sat Mar 12 2016 - 14:12:01 PST)
R.G. Mantell
- Re: [AMBER] Tutorial 18 - CpHMD with pmemd (Tue Mar 22 2016 - 10:31:34 PDT)
- [AMBER] Tutorial 18 - CpHMD with pmemd (Tue Mar 22 2016 - 05:09:45 PDT)
Ray Luo
- Re: [AMBER] MMPBSA doubt (Tue Mar 22 2016 - 11:08:51 PDT)
- Re: [AMBER] MMPBSA doubt (Mon Mar 21 2016 - 23:11:15 PDT)
- Re: [AMBER] MMPBSA doubt (Mon Mar 21 2016 - 17:39:19 PDT)
- Re: [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range (Fri Mar 18 2016 - 18:16:12 PDT)
- Re: [AMBER] MMPBSA doubt (Fri Mar 18 2016 - 18:13:36 PDT)
- Re: [AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range (Tue Mar 15 2016 - 15:16:48 PDT)
- Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) (Sun Mar 13 2016 - 20:52:30 PDT)
- Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) (Sat Mar 12 2016 - 20:21:58 PST)
- Re: [AMBER] MMPBSA error (Sat Mar 12 2016 - 20:00:12 PST)
- Re: [AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？ (Tue Mar 08 2016 - 20:43:23 PST)
- Re: [AMBER] regarding mm-pbsa calculation (Fri Mar 04 2016 - 21:32:14 PST)
Robert Molt
- [AMBER] GROMACS File Conversion Subtlety (Wed Mar 16 2016 - 23:03:10 PDT)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 18:47:35 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 17:33:03 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 12:28:42 PST)
- Re: [AMBER] References (Fri Mar 11 2016 - 08:07:31 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 05:32:30 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 20:48:23 PST)
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 17:45:00 PST)
- [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 12:55:13 PST)
- [AMBER] On Amber to Gromacs Parameter Conversion (Thu Mar 10 2016 - 12:55:19 PST)
Robin Betz
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit (Mon Mar 14 2016 - 15:38:56 PDT)
Ross Walker
- Re: [AMBER] Command to display simulation completion time (Thu Mar 31 2016 - 07:56:38 PDT)
- Re: [AMBER] Proper nfft* parameters for a very long solvent box? (Wed Mar 30 2016 - 13:14:36 PDT)
- Re: [AMBER] General question (Tue Mar 29 2016 - 09:54:52 PDT)
- Re: [AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not (Thu Mar 24 2016 - 12:22:56 PDT)
- Re: [AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected" (Thu Mar 17 2016 - 08:02:24 PDT)
- Re: [AMBER] I have a problem when installing GPU version of Pmemd(Amber14). (Tue Mar 01 2016 - 08:13:04 PST)
Ruixing Wang
- Re: [AMBER] How did GAFF get force constants? (Wed Mar 16 2016 - 02:24:18 PDT)
- [AMBER] How did GAFF get force constants? (Tue Mar 08 2016 - 20:01:13 PST)
Saman Yousuf ali
- Re: [AMBER] rmsd y axis value deviation. (Wed Mar 16 2016 - 12:04:40 PDT)
- Re: [AMBER] rmsd y axis value deviation. (Wed Mar 16 2016 - 03:29:58 PDT)
- [AMBER] rmsd y axis value deviation. (Wed Mar 16 2016 - 02:55:35 PDT)
- [AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1 (Sun Mar 06 2016 - 22:52:23 PST)
Sangita Kachhap
- Re: [AMBER] Relation between binding affinity and free enegy (Thu Mar 31 2016 - 21:49:55 PDT)
- [AMBER] Relation between binding affinity and free enegy (Mon Mar 28 2016 - 11:55:34 PDT)
Sanjib Paul
- [AMBER] problem in nmode calculation by NAB (Mon Mar 28 2016 - 07:19:37 PDT)
Sarah Witzke
- Re: [AMBER] On Amber to Gromacs Parameter Conversion (Fri Mar 11 2016 - 03:57:24 PST)
Sehrish Naz Aijaz
- Re: [AMBER] problem in plotting total energy graphs by perl script (Wed Mar 30 2016 - 21:38:44 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Wed Mar 30 2016 - 00:49:34 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Mon Mar 28 2016 - 21:03:01 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Mon Mar 28 2016 - 02:54:44 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Fri Mar 25 2016 - 04:18:01 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Thu Mar 24 2016 - 21:59:13 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Tue Mar 22 2016 - 08:50:41 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sun Mar 20 2016 - 21:58:01 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sun Mar 20 2016 - 21:56:46 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 03:29:52 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 03:16:30 PDT)
- Re: [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 02:26:32 PDT)
- [AMBER] problem in plotting total energy graphs by perl script (Sat Mar 19 2016 - 01:25:27 PDT)
- [AMBER] FW: problem in plotting total energy graph by using perl script (Sat Mar 19 2016 - 01:20:41 PDT)
SHAILESH KUMAR
- [AMBER] How to deal with fractional electron unit charges on small molecules?? (Mon Mar 07 2016 - 02:30:44 PST)
Shilpa Gupta
- Re: [AMBER] AMBER:neutralisation of non integral charges (Mon Mar 14 2016 - 06:22:42 PDT)
Sidhu, Khushwant (Dr.)
- [AMBER] restart file error (Fri Mar 18 2016 - 03:59:37 PDT)
Sigurd Friis Truelsen
- Re: [AMBER] Problems when trying to improve angle parameters whith paramfit (Mon Mar 14 2016 - 08:28:52 PDT)
Song-Ho Chong
- Re: [AMBER] energy calculation with cpptraj based on chamber topology file (Thu Mar 10 2016 - 08:37:45 PST)
- Re: [AMBER] energy calculation with cpptraj based on chamber topology file (Thu Mar 10 2016 - 07:51:54 PST)
- [AMBER] energy calculation with cpptraj based on chamber topology file (Thu Mar 10 2016 - 04:30:08 PST)
- Re: [AMBER] reading Amber trajectory files with chamber topology file (Mon Feb 29 2016 - 08:24:04 PST)
- Re: [AMBER] reading Amber trajectory files with chamber topology file (Mon Feb 29 2016 - 08:01:36 PST)
- [AMBER] reading Amber trajectory files with chamber topology file (Mon Feb 29 2016 - 07:31:12 PST)
Sreemol G
- Re: [AMBER] Command to display simulation completion time (Thu Mar 31 2016 - 07:27:25 PDT)
- [AMBER] Command to display simulation completion time (Wed Mar 30 2016 - 23:58:48 PDT)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 22:07:45 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 05:26:32 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 04:47:18 PST)
- [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 03:57:51 PST)
- [AMBER] Creating new atom (Wed Mar 09 2016 - 20:25:09 PST)
- Re: [AMBER] nucleic acid residue representation in leap (Fri Mar 04 2016 - 23:26:03 PST)
- [AMBER] nucleic acid residue representation in leap (Fri Mar 04 2016 - 23:04:00 PST)
- [AMBER] for protein- RNA complex simulation (Fri Mar 04 2016 - 19:49:46 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Fri Mar 04 2016 - 01:14:49 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 21:40:26 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 21:24:45 PST)
- Re: [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 21:04:18 PST)
- [AMBER] Error while creating topology file after adding ions (Thu Mar 03 2016 - 20:40:03 PST)
- Re: [AMBER] Error while creating neutralized topology and coordinates file (Tue Mar 01 2016 - 22:54:08 PST)
- [AMBER] Error while creating neutralized topology and coordinates file (Tue Mar 01 2016 - 03:33:44 PST)
- [AMBER] Inquiry regarding amber installation (Mon Feb 29 2016 - 22:05:14 PST)
Stefan Ivanov
- Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) (Sun Mar 13 2016 - 22:11:33 PDT)
- Re: [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) (Sun Mar 13 2016 - 19:11:01 PDT)
- [AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist) (Fri Mar 11 2016 - 23:28:32 PST)
Steven Ramsey
- Re: [AMBER] Gist calculation on clustered structures (Tue Mar 01 2016 - 06:30:26 PST)
Suchetana Gupta
- [AMBER] Calculating pair-wise interaction energy using MMPBSA for Gromacs files (Mon Mar 21 2016 - 22:01:48 PDT)
Taylor Harville
- Re: [AMBER] GB Parameterization (Fri Mar 04 2016 - 08:28:14 PST)
- [AMBER] GB Parameterization (Thu Mar 03 2016 - 19:27:13 PST)
Thomas Cheatham
- Re: [AMBER] GROMACS File Conversion Subtlety (Fri Mar 18 2016 - 22:04:23 PDT)
- [AMBER] ISQBP 2016 meeting - registration opened! (Sun Mar 13 2016 - 22:15:46 PDT)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 22:21:27 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 22:19:05 PST)
- Re: [AMBER] How did GAFF get force constants? (Fri Mar 11 2016 - 19:52:11 PST)
- Re: [AMBER] for protein- RNA complex simulation (Fri Mar 04 2016 - 20:09:30 PST)
Thomas Exner
- [AMBER] Training and Innovation Course in Drug Design (Thu Mar 17 2016 - 08:02:56 PDT)
Timothy Christopher Schutt
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 13:13:54 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 11:24:03 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Wed Mar 09 2016 - 10:02:53 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 22:43:56 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 17:05:07 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 14:54:19 PST)
- Re: [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 14:30:00 PST)
- [AMBER] Diffusion/msd cpptraj bug? (Tue Mar 08 2016 - 13:11:54 PST)
Vasantha Kumar
- Re: [AMBER] Lower energy frame from summary.EPTOT (Fri Mar 11 2016 - 08:49:20 PST)
- [AMBER] Lower energy frame from summary.EPTOT (Fri Mar 11 2016 - 01:06:47 PST)
- Re: [AMBER] Dihedral angle values from .mdcrd file (Wed Mar 02 2016 - 11:18:11 PST)
- Re: [AMBER] Dihedral angle values from .mdcrd file (Wed Mar 02 2016 - 11:18:10 PST)
- [AMBER] Dihedral angle values from .mdcrd file (Wed Mar 02 2016 - 03:47:21 PST)
Vertika Gautam
- Re: [AMBER] velocity auto correlation function (Wed Mar 09 2016 - 21:25:02 PST)
Vlad Cojocaru
- [AMBER] 2016 ISQBP Meeting: early registration / abstract submission deadline approaching (Thu Mar 17 2016 - 01:50:08 PDT)
- Re: [AMBER] pseudo trajectories for 4 centers of mass? (Sun Mar 13 2016 - 11:11:09 PDT)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 22:59:10 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 05:33:07 PST)
- Re: [AMBER] protein-RNA complex simulation (Fri Mar 11 2016 - 05:04:33 PST)
- Re: [AMBER] nucleic acid residue representation in leap (Sat Mar 05 2016 - 01:28:30 PST)
waleed zalloum
- [AMBER] Clustering (Fri Mar 25 2016 - 02:06:13 PDT)
Weinzierl, Robert O J
- [AMBER] cpptraj mask definition (Tue Mar 29 2016 - 03:51:26 PDT)
Wesley Alves
- [AMBER] tests dont work after installation (Wed Mar 16 2016 - 10:48:02 PDT)
- Re: [AMBER] tests dont work for serial, parallel or cuda amber instalation (Wed Mar 09 2016 - 08:57:24 PST)
- [AMBER] tests dont work for serial, parallel or cuda amber instalation. (Mon Mar 07 2016 - 12:20:05 PST)
windy
- [AMBER] How to using distance based strip action and generate the corresponding prmtop (Wed Mar 09 2016 - 07:02:39 PST)
Wu Xu
- [AMBER] nitro tyrosine (Thu Mar 17 2016 - 19:06:00 PDT)
- Re: [AMBER] TIP3P (Sat Mar 12 2016 - 16:51:39 PST)
- [AMBER] TIP3P (Sat Mar 12 2016 - 14:11:44 PST)
yhzahsc
- [AMBER] 回复：Re: shell script (Wed Mar 16 2016 - 17:54:06 PDT)
- [AMBER] shell script (Tue Mar 15 2016 - 19:27:35 PDT)
- [AMBER] I have a problem when installing GPU version of Pmemd(Amber14). (Tue Mar 01 2016 - 00:44:07 PST)
zahra khatti
- [AMBER] adding ion (Mon Feb 29 2016 - 22:45:19 PST)
Zhang Marc
- Re: [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results (Wed Mar 09 2016 - 00:26:15 PST)
- [AMBER] How to interpret MMGBSA ligand binding free energy decomposition results (Tue Mar 08 2016 - 09:08:08 PST)
姜阳
- [AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？ (Tue Mar 08 2016 - 19:27:01 PST)

Amber Archive Mar 2016 by author