Amber Archive Jul 2015: by author

Ahmed Ayoub
- [AMBER] ESURF term in MMGBSA (Thu Jul 09 2015 - 19:46:54 PDT)
- [AMBER] Magnesium in MMGBSA (Thu Jul 09 2015 - 19:27:53 PDT)
Alan
- Re: [AMBER] Explicit Solvent Constant pH MD (Thu Jul 09 2015 - 13:47:05 PDT)
Albert
- Re: [AMBER] how to center on ligand? (Wed Jul 29 2015 - 23:08:16 PDT)
- Re: [AMBER] how to center on ligand? (Wed Jul 29 2015 - 08:50:38 PDT)
- [AMBER] how to center on ligand? (Wed Jul 29 2015 - 07:25:35 PDT)
- [AMBER] strange pbsa results (Mon Jul 27 2015 - 02:54:45 PDT)
- Re: [AMBER] QM/GBSA calculation failed (Wed Jul 22 2015 - 07:24:57 PDT)
- [AMBER] QM/GBSA calculation failed (Wed Jul 22 2015 - 00:25:17 PDT)
- Re: [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices (Tue Jul 21 2015 - 02:11:12 PDT)
- Re: [AMBER] frames in mmpbsa.py (Sun Jul 19 2015 - 23:10:16 PDT)
- [AMBER] countless warnning (Fri Jul 17 2015 - 08:17:10 PDT)
- [AMBER] no FINAL_RESULTS_MMPBSA.dat generated (Fri Jul 17 2015 - 05:46:23 PDT)
- [AMBER] frames in mmpbsa.py (Fri Jul 17 2015 - 03:12:45 PDT)
- Re: [AMBER] test failed but still work (Thu Jul 16 2015 - 06:46:40 PDT)
- Re: [AMBER] test failed but still work (Wed Jul 15 2015 - 23:36:31 PDT)
- Re: [AMBER] test failed but still work (Wed Jul 15 2015 - 10:53:17 PDT)
- Re: [AMBER] test failed but still work (Wed Jul 15 2015 - 10:43:22 PDT)
- [AMBER] test failed but still work (Wed Jul 15 2015 - 05:31:47 PDT)
- Re: [AMBER] MPI compiling failed (Wed Jul 15 2015 - 05:10:55 PDT)
- [AMBER] MPI compiling failed (Wed Jul 15 2015 - 02:32:11 PDT)
- [AMBER] strange output from vacuum minimization (Wed Jul 15 2015 - 01:30:48 PDT)
Amber Maharaj
- Re: [AMBER] Relaxing a heme molecule (Wed Jul 15 2015 - 12:26:49 PDT)
- [AMBER] Relaxing a heme molecule (Mon Jul 13 2015 - 13:02:17 PDT)
Amber mail
- Re: [AMBER] Speed of heating MD (Sun Jul 26 2015 - 04:20:33 PDT)
- [AMBER] Speed of heating MD (Sat Jul 25 2015 - 02:32:33 PDT)
- Re: [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 12:41:17 PDT)
- Re: [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 06:43:52 PDT)
- Re: [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 05:33:12 PDT)
- [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 05:28:02 PDT)
- [AMBER] setting up a MD simulation using AMBER (Wed Jul 15 2015 - 06:11:10 PDT)
antonio.coluccia.uniroma1.it
- [AMBER] PCA and motions visualization (Tue Jul 21 2015 - 02:59:54 PDT)
anu chandra
- [AMBER] Query about adding hydrogens (Sat Jul 11 2015 - 13:08:54 PDT)
ANWESHA SARKAR
- Re: [AMBER] Ambertools15 installation without Amber (Thu Jul 02 2015 - 03:25:37 PDT)
- Re: [AMBER] Ambertools15 installation without Amber (Thu Jul 02 2015 - 02:45:47 PDT)
- [AMBER] Ambertools15 installation without Amber (Thu Jul 02 2015 - 02:16:42 PDT)
Arjun Sharma
- [AMBER] Testing the titratable group definition CpHMD (Tue Jul 21 2015 - 08:22:55 PDT)
- [AMBER] Reference energies for Explicit solvent CpHMD (Mon Jul 06 2015 - 10:33:36 PDT)
Arnoult, Eric [JRDUS]
- [AMBER] Lipid linked to a peptide (Tue Jul 07 2015 - 09:57:48 PDT)
Aronica, Pietro
- Re: [AMBER] Periodic Box Size and Charge Determination (Wed Jul 22 2015 - 08:02:23 PDT)
- Re: [AMBER] Periodic Box Size and Charge Determination (Wed Jul 22 2015 - 05:43:46 PDT)
- [AMBER] Periodic Box Size and Charge Determination (Wed Jul 22 2015 - 04:31:11 PDT)
Asmita Gupta
- [AMBER] installation without ambertools (Mon Jul 20 2015 - 01:17:03 PDT)
- Re: [AMBER] running sgld in explicit solvent (Thu Jul 16 2015 - 07:28:23 PDT)
- [AMBER] running sgld in explicit solvent (Thu Jul 16 2015 - 04:01:48 PDT)
- [AMBER] pmemd.cuda implementation of sgld (Sat Jul 11 2015 - 00:50:31 PDT)
- Re: [AMBER] folding RNA using SGLD (Thu Jul 02 2015 - 05:49:02 PDT)
Ayesha Fatima
- Re: [AMBER] qm-mmgbsa error (Tue Jul 21 2015 - 22:59:19 PDT)
- Re: [AMBER] qm-mmgbsa error (Tue Jul 21 2015 - 18:19:52 PDT)
- Re: [AMBER] Immediate Postdoctoral Position Opening In Dr. Khaled Barakat’s Lab, Faculty Of Pharmacy, University Of Alberta (Tue Jul 21 2015 - 00:26:02 PDT)
- [AMBER] qm-mmgbsa error (Mon Jul 20 2015 - 21:55:17 PDT)
Beuerle, Matthias
- [AMBER] Problem cpptraj Bridging H-Bond analysis (Mon Jul 20 2015 - 06:52:22 PDT)
bharat lakhani
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Wed Jul 29 2015 - 19:47:32 PDT)
- Re: [AMBER] CpptrajPairDist (Tue Jul 21 2015 - 19:50:08 PDT)
Bill Miller III
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero (Tue Jul 14 2015 - 18:11:34 PDT)
- [AMBER] pmemd.cuda.MPI error - integer divide by zero (Fri Jul 10 2015 - 14:36:38 PDT)
Bill Ross
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. (Mon Jul 20 2015 - 13:11:46 PDT)
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. (Sat Jul 18 2015 - 00:13:46 PDT)
- Re: [AMBER] Query about adding hydrogens (Sat Jul 11 2015 - 15:20:41 PDT)
Brent Krueger
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Thu Jul 09 2015 - 05:40:45 PDT)
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. (Thu Jul 09 2015 - 03:45:21 PDT)
- Re: [AMBER] Output format in sander (Tue Jun 30 2015 - 21:38:53 PDT)
Brian Radak
- Re: [AMBER] problems on amoeba force filed implemented in amber (Wed Jul 15 2015 - 09:53:17 PDT)
- Re: [AMBER] Cpptraj able to identify coordinates written by VMD? (Thu Jul 02 2015 - 11:58:19 PDT)
- Re: [AMBER] QM/MM Equilibration Troubles (Wed Jul 01 2015 - 11:31:27 PDT)
Brittany Boykin
- [AMBER] QM/MM Equilibration Troubles (Wed Jul 01 2015 - 11:00:11 PDT)
Carlos Simmerling
- Re: [AMBER] Targeted Molecular dynamics in Amber (Wed Jul 29 2015 - 07:12:57 PDT)
- Re: [AMBER] Prep file for chiral position (Mon Jul 27 2015 - 10:54:29 PDT)
- Re: [AMBER] Prep file for chiral position (Mon Jul 27 2015 - 10:07:44 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 11:24:33 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 10:49:38 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 09:43:23 PDT)
- [AMBER] articles published for ff14SB and GBneck2 (Thu Jul 09 2015 - 07:03:56 PDT)
Casalini Tommaso
- Re: [AMBER] About charge derivation for enantiomeric molecules (Sat Jul 11 2015 - 05:48:49 PDT)
case
- Re: [AMBER] test failed but still work (Wed Jul 15 2015 - 14:51:22 PDT)
- Re: [AMBER] Relaxing a heme molecule (Mon Jul 13 2015 - 17:35:19 PDT)
- Re: [AMBER] About charge derivation for enantiomeric molecules (Sat Jul 11 2015 - 05:41:25 PDT)
CHAMI F.
- [AMBER] ETOT drift and nscm in NVE for calculation of diffusion (Tue Jul 14 2015 - 11:13:52 PDT)
Clavel
- [AMBER] Namdenergy problems with non-standard amino acids (Thu Jul 09 2015 - 02:34:53 PDT)
D.J. Pattinson
- [AMBER] MMPBSA.py API quasi-harmonic error (Wed Jul 15 2015 - 01:36:03 PDT)
Damiano Spadoni
- [AMBER] Cluster restraints (Tue Jul 28 2015 - 09:24:39 PDT)
Daniel Mermelstein
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Thu Jul 16 2015 - 16:42:12 PDT)
Daniel Roe
- Re: [AMBER] cpptraj Help rmsd between two homologous proteins and their Trajectory (Thu Jul 30 2015 - 08:19:43 PDT)
- Re: [AMBER] how to center on ligand? (Thu Jul 30 2015 - 04:16:52 PDT)
- Re: [AMBER] how to center on ligand? (Wed Jul 29 2015 - 07:49:00 PDT)
- Re: [AMBER] detecting and removing corrupted frames (Mon Jul 27 2015 - 06:24:35 PDT)
- Re: [AMBER] CpptrajPairDist (Thu Jul 23 2015 - 08:56:55 PDT)
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory (Thu Jul 23 2015 - 08:48:54 PDT)
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory (Wed Jul 22 2015 - 13:53:18 PDT)
- Re: [AMBER] PCA and motions visualization (Tue Jul 21 2015 - 16:04:55 PDT)
- Re: [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 15:24:30 PDT)
- Re: [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 14:52:50 PDT)
- Re: [AMBER] hbond cpptraj (Tue Jul 21 2015 - 13:34:15 PDT)
- Re: [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values (Mon Jul 20 2015 - 16:40:53 PDT)
- Re: [AMBER] Problem cpptraj Bridging H-Bond analysis (Mon Jul 20 2015 - 10:32:23 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj (Tue Jul 14 2015 - 07:40:45 PDT)
- Re: [AMBER] Problem in Using the Average Command in Cpptraj (Mon Jul 13 2015 - 09:04:43 PDT)
- Re: [AMBER] atom mapping (Sun Jul 12 2015 - 08:30:33 PDT)
- Re: [AMBER] pmemd.cuda implementation of sgld (Sat Jul 11 2015 - 06:41:53 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj (Thu Jul 09 2015 - 08:15:59 PDT)
- Re: [AMBER] cpptraj: rmsd problem (Tue Jul 07 2015 - 07:20:17 PDT)
- Re: [AMBER] cpptraj: bounds command -> grid (Tue Jul 07 2015 - 03:24:27 PDT)
- Re: [AMBER] kclust help (Thu Jul 02 2015 - 10:08:11 PDT)
- Re: [AMBER] water networks and bridge option of the hbond command in cpptraj (Thu Jul 02 2015 - 09:49:45 PDT)
- Re: [AMBER] Cpptraj failure (Thu Jul 02 2015 - 09:45:37 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj (Thu Jul 02 2015 - 09:36:20 PDT)
David A Case
- Re: [AMBER] Cluster restraints (Tue Jul 28 2015 - 17:49:47 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 11:14:17 PDT)
- Re: [AMBER] Amber for phophorylated residue (Thu Jul 23 2015 - 07:45:29 PDT)
- Re: [AMBER] Periodic Box Size and Charge Determination (Wed Jul 22 2015 - 09:51:29 PDT)
- Re: [AMBER] Unchanged coordinates in leap (Tue Jul 21 2015 - 06:05:50 PDT)
- Re: [AMBER] Gaff Parameters Si (Tue Jul 21 2015 - 05:58:29 PDT)
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. (Tue Jul 21 2015 - 05:53:08 PDT)
- Re: [AMBER] incorrect determination of atomic number for atom Cl in tleap (Mon Jul 20 2015 - 07:31:16 PDT)
- Re: [AMBER] Distance restraint in AMBER 14 and GPU (Mon Jul 20 2015 - 07:28:28 PDT)
- Re: [AMBER] help in box size determination (Mon Jul 20 2015 - 07:24:54 PDT)
- Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead (Thu Jul 16 2015 - 09:30:18 PDT)
- Re: [AMBER] running sgld in explicit solvent (Thu Jul 16 2015 - 05:48:15 PDT)
- Re: [AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed (Thu Jul 16 2015 - 05:42:02 PDT)
- Re: [AMBER] test failed but still work (Thu Jul 16 2015 - 05:37:46 PDT)
- Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished (Thu Jul 16 2015 - 05:36:58 PDT)
- Re: [AMBER] Error in writing .lib file (Thu Jul 16 2015 - 05:30:21 PDT)
- Re: [AMBER] setting up a MD simulation using AMBER (Wed Jul 15 2015 - 08:41:18 PDT)
- Re: [AMBER] test failed but still work (Wed Jul 15 2015 - 08:35:55 PDT)
- Re: [AMBER] MPI compiling failed (Wed Jul 15 2015 - 04:50:00 PDT)
- Re: [AMBER] strange output from vacuum minimization (Wed Jul 15 2015 - 04:42:07 PDT)
- Re: [AMBER] Changing NMR restraint weights (Tue Jul 14 2015 - 08:48:29 PDT)
- Re: [AMBER] help in making xyz file (Tue Jul 14 2015 - 05:31:40 PDT)
- Re: [AMBER] Changing NMR restraint weights (Mon Jul 13 2015 - 06:52:04 PDT)
- Re: [AMBER] Unexpected prochirality change from si to re during MD simulation (Mon Jul 13 2015 - 05:13:31 PDT)
- Re: [AMBER] NOESY volumes restraints (Mon Jul 13 2015 - 04:50:01 PDT)
- Re: [AMBER] Order of the atom in prep ourput of antechamber (Sat Jul 11 2015 - 05:23:44 PDT)
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero (Fri Jul 10 2015 - 17:03:12 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Wed Jul 08 2015 - 17:26:49 PDT)
- Re: [AMBER] amber topology file for cytochrome c covalently bond to Heme (Tue Jul 07 2015 - 10:27:42 PDT)
- Re: [AMBER] Lipid linked to a peptide (Tue Jul 07 2015 - 10:23:46 PDT)
- Re: [AMBER] NOESY volumes restraints (Mon Jul 06 2015 - 07:42:02 PDT)
- Re: [AMBER] How to set interatomic distance restraint? (Sun Jul 05 2015 - 06:06:09 PDT)
- Re: [AMBER] How to set interatomic distance restraint? (Fri Jul 03 2015 - 05:26:56 PDT)
- Re: [AMBER] help in make .prepin file (Fri Jul 03 2015 - 05:22:16 PDT)
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations (Thu Jul 02 2015 - 06:19:27 PDT)
- Re: [AMBER] Compile Failure (Thu Jul 02 2015 - 06:13:00 PDT)
- Re: [AMBER] Compile Failure (Wed Jul 01 2015 - 05:41:39 PDT)
- Re: [AMBER] Output format in sander (Wed Jul 01 2015 - 05:38:05 PDT)
David Abia
- Re: [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices (Tue Jul 21 2015 - 03:15:34 PDT)
Eiros Zamora, Juan
- Re: [AMBER] About python usage in AmberTools (Tue Jul 07 2015 - 12:50:45 PDT)
Eleftherios A P Lambros
- [AMBER] MCPB.py mismatch error (Mon Jul 27 2015 - 12:36:35 PDT)
- [AMBER] MCPB.py Value / Syntax error (Mon Jul 20 2015 - 18:13:25 PDT)
- [AMBER] MCPB.py ValueError (Thu Jul 16 2015 - 18:48:03 PDT)
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 (Thu Jul 09 2015 - 15:12:58 PDT)
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 (Thu Jul 09 2015 - 14:16:36 PDT)
- [AMBER] NumPy Import Error for MCPB.py on Amber15 (Tue Jul 07 2015 - 16:23:54 PDT)
Elvis Martis
- Re: [AMBER] Error in writing .lib file (Fri Jul 17 2015 - 01:04:15 PDT)
- [AMBER] Error in writing .lib file (Wed Jul 15 2015 - 20:13:18 PDT)
Eugene Sviridov
- Re: [AMBER] NOESY volumes restraints (Fri Jul 10 2015 - 03:39:02 PDT)
- [AMBER] NOESY volumes restraints (Mon Jul 06 2015 - 04:08:30 PDT)
Evans, Shalton
- Re: [AMBER] FATAL: Atom () does not have a type???? (Fri Jul 10 2015 - 14:32:49 PDT)
- [AMBER] FATAL: Atom () does not have a type???? (Fri Jul 10 2015 - 13:36:05 PDT)
fjliu
- Re: [AMBER] problems on amoeba force filed implemented in amber (Tue Jul 14 2015 - 19:43:32 PDT)
- Re: [AMBER] problems on amoeba force filed implemented in amber (Tue Jul 14 2015 - 02:35:30 PDT)
- [AMBER] problems on amoeba force filed implemented in amber (Fri Jul 10 2015 - 01:53:01 PDT)
Francesca Cardamone
- [AMBER] parameters dATP (Thu Jul 09 2015 - 06:07:07 PDT)
FyD
- Re: [AMBER] assigning atom type and charge (Thu Jul 09 2015 - 01:51:58 PDT)
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. (Thu Jul 09 2015 - 01:44:28 PDT)
Gard Nelson
- [AMBER] atom mapping (Fri Jul 10 2015 - 11:38:40 PDT)
George Green
- Re: [AMBER] Rms fitting to a reference structure with a differnt number atoms to top file (Wed Jul 01 2015 - 02:35:04 PDT)
Georgios Gerogiokas
- [AMBER] mdfrc units (Fri Jul 31 2015 - 06:41:04 PDT)
Gerald Monard
- Re: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI (Tue Jul 21 2015 - 06:46:20 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Wed Jul 08 2015 - 01:10:42 PDT)
- Re: [AMBER] Ambertools15 installation without Amber (Thu Jul 02 2015 - 04:49:46 PDT)
- Re: [AMBER] Ambertools15 installation without Amber (Thu Jul 02 2015 - 02:54:32 PDT)
- Re: [AMBER] Ambertools15 installation without Amber (Thu Jul 02 2015 - 02:30:12 PDT)
giulia palermo
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. (Thu Jul 09 2015 - 08:47:35 PDT)
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. (Wed Jul 08 2015 - 07:20:56 PDT)
- [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. (Wed Jul 08 2015 - 01:14:39 PDT)
Hai Nguyen
- Re: [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 14:41:15 PDT)
- Re: [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values (Mon Jul 20 2015 - 16:00:43 PDT)
- Re: [AMBER] NetCDF file (Wed Jul 15 2015 - 07:34:35 PDT)
- Re: [AMBER] compare two trajectories (Fri Jul 10 2015 - 12:41:27 PDT)
- Re: [AMBER] AMBER Digest, Vol 1274, Issue 1 (Thu Jul 09 2015 - 15:33:46 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 09:42:10 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 09:37:20 PDT)
- Re: [AMBER] NumPy Import Error for MCPB.py on Amber15 (Tue Jul 07 2015 - 17:10:57 PDT)
- Re: [AMBER] About python usage in AmberTools (Tue Jul 07 2015 - 14:54:30 PDT)
- Re: [AMBER] About python usage in AmberTools (Tue Jul 07 2015 - 11:33:42 PDT)
Hannes Loeffler
- Re: [AMBER] NetCDF file (Wed Jul 15 2015 - 07:47:22 PDT)
- Re: [AMBER] NetCDF file (Wed Jul 15 2015 - 07:33:46 PDT)
- Re: [AMBER] FEW tutorial (Fri Jul 10 2015 - 03:54:23 PDT)
- Re: [AMBER] Order of the atom in prep ourput of antechamber (Fri Jul 10 2015 - 02:01:52 PDT)
- [AMBER] another leap inconsistency (Thu Jul 02 2015 - 06:44:03 PDT)
- Re: [AMBER] leap changes residue order (Wed Jul 01 2015 - 09:12:05 PDT)
- Re: [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? (Wed Jul 01 2015 - 02:52:11 PDT)
hannes.loeffler.stfc.ac.uk
- Re: [AMBER] Lipid diffusion in cpptraj (Thu Jul 30 2015 - 23:42:35 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Sat Jul 18 2015 - 02:00:26 PDT)
- Re: [AMBER] help in resp charge (Sat Jul 18 2015 - 01:05:29 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Fri Jul 17 2015 - 13:35:02 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Fri Jul 17 2015 - 10:22:22 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Thu Jul 16 2015 - 23:30:40 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj (Mon Jul 13 2015 - 23:42:40 PDT)
- Re: [AMBER] another leap inconsistency (Fri Jul 03 2015 - 13:02:49 PDT)
Harmeet Kaur
- [AMBER] kclust help (Thu Jul 02 2015 - 05:00:37 PDT)
Harshala Haldankar
- Re: [AMBER] Problem in saving parameter/topology and coordinate file. (Mon Jul 20 2015 - 04:34:07 PDT)
- [AMBER] Problem in saving parameter/topology and coordinate file. (Fri Jul 17 2015 - 22:44:47 PDT)
- Re: [AMBER] Problem in loading the pdb file (Thu Jul 09 2015 - 21:39:03 PDT)
- [AMBER] Problem in loading the pdb file (Thu Jul 09 2015 - 03:58:07 PDT)
Ignacio Faustino
- Re: [AMBER] leap changes residue order (Thu Jul 02 2015 - 09:51:58 PDT)
- [AMBER] leap changes residue order (Wed Jul 01 2015 - 09:04:37 PDT)
jacob wick
- Re: [AMBER] Deleting multiple atoms in xleap (Fri Jul 17 2015 - 05:58:35 PDT)
- [AMBER] Deleting multiple atoms in xleap (Fri Jul 17 2015 - 05:32:54 PDT)
Jason Swails
- Re: [AMBER] mdfrc units (Fri Jul 31 2015 - 06:58:12 PDT)
- Re: [AMBER] Regarding ADP molecule force fields (Fri Jul 31 2015 - 05:19:26 PDT)
- Re: [AMBER] Explicit-solvent-pH-REMD (Fri Jul 31 2015 - 05:16:56 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion (Thu Jul 30 2015 - 13:53:14 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion (Wed Jul 29 2015 - 18:30:26 PDT)
- Re: [AMBER] how to center on ligand? (Wed Jul 29 2015 - 09:05:50 PDT)
- Re: [AMBER] how to center on ligand? (Wed Jul 29 2015 - 07:28:30 PDT)
- Re: [AMBER] MM-GBSA at different temperature (Wed Jul 29 2015 - 07:05:19 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion (Wed Jul 29 2015 - 06:49:44 PDT)
- Re: [AMBER] Restart of MMPBSA (Tue Jul 28 2015 - 11:11:39 PDT)
- Re: [AMBER] which solvent model to use with solvateCap (Mon Jul 27 2015 - 07:35:25 PDT)
- Re: [AMBER] which solvent model to use with solvateCap (Mon Jul 27 2015 - 07:19:10 PDT)
- Re: [AMBER] How to combine distance and torsion restraint? (Mon Jul 27 2015 - 06:54:32 PDT)
- Re: [AMBER] strange pbsa results (Mon Jul 27 2015 - 06:32:55 PDT)
- Re: [AMBER] Speed of heating MD (Sat Jul 25 2015 - 17:51:44 PDT)
- Re: [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 13:56:01 PDT)
- Re: [AMBER] impose restraint mask for specific residues (Fri Jul 24 2015 - 12:30:04 PDT)
- Re: [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 12:24:36 PDT)
- Re: [AMBER] MPI_ABORT error (Fri Jul 24 2015 - 06:28:11 PDT)
- Re: [AMBER] Explicit solvent pH-REMD (Wed Jul 22 2015 - 09:47:37 PDT)
- Re: [AMBER] QM/GBSA calculation failed (Wed Jul 22 2015 - 07:31:00 PDT)
- Re: [AMBER] Periodic Box Size and Charge Determination (Wed Jul 22 2015 - 06:06:10 PDT)
- Re: [AMBER] Periodic Box Size and Charge Determination (Wed Jul 22 2015 - 05:22:39 PDT)
- Re: [AMBER] QM/GBSA calculation failed (Wed Jul 22 2015 - 04:38:37 PDT)
- Re: [AMBER] qm-mmgbsa error (Tue Jul 21 2015 - 18:27:16 PDT)
- Re: [AMBER] ETOT drift and nscm in NVE for calculation of diffusion (Tue Jul 21 2015 - 15:36:12 PDT)
- Re: [AMBER] qm-mmgbsa error (Tue Jul 21 2015 - 09:23:20 PDT)
- Re: [AMBER] PCA and motions visualization (Tue Jul 21 2015 - 09:20:20 PDT)
- Re: [AMBER] Testing the titratable group definition CpHMD (Tue Jul 21 2015 - 09:13:58 PDT)
- Re: [AMBER] installation without ambertools (Mon Jul 20 2015 - 07:29:31 PDT)
- Re: [AMBER] frames in mmpbsa.py (Mon Jul 20 2015 - 07:27:51 PDT)
- Re: [AMBER] Deleting multiple atoms in xleap (Sat Jul 18 2015 - 07:29:36 PDT)
- Re: [AMBER] no FINAL_RESULTS_MMPBSA.dat generated (Fri Jul 17 2015 - 12:54:22 PDT)
- Re: [AMBER] frames in mmpbsa.py (Fri Jul 17 2015 - 12:51:23 PDT)
- Re: [AMBER] test failed but still work (Wed Jul 15 2015 - 10:32:44 PDT)
- Re: [AMBER] MPI compiling failed (Wed Jul 15 2015 - 10:29:29 PDT)
- Re: [AMBER] help in making xyz file (Tue Jul 14 2015 - 05:24:43 PDT)
- Re: [AMBER] problems on amoeba force filed implemented in amber (Tue Jul 14 2015 - 05:11:54 PDT)
- Re: [AMBER] Problem in Using the Average Command in Cpptraj (Mon Jul 13 2015 - 09:04:35 PDT)
- Re: [AMBER] Explicit Solvent Constant pH MD (Sat Jul 11 2015 - 05:50:55 PDT)
- Re: [AMBER] pmemd.cuda.MPI error - integer divide by zero (Sat Jul 11 2015 - 05:27:58 PDT)
- Re: [AMBER] molecules split apart during MD (Fri Jul 10 2015 - 07:37:29 PDT)
- Re: [AMBER] ESURF term in MMGBSA (Fri Jul 10 2015 - 04:58:20 PDT)
- Re: [AMBER] Magnesium in MMGBSA (Fri Jul 10 2015 - 04:55:48 PDT)
- Re: [AMBER] problems on amoeba force filed implemented in amber (Fri Jul 10 2015 - 04:54:04 PDT)
- Re: [AMBER] Problem in loading the pdb file (Fri Jul 10 2015 - 03:49:46 PDT)
- Re: [AMBER] Explicit Solvent Constant pH MD (Thu Jul 09 2015 - 09:49:38 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Thu Jul 09 2015 - 06:06:51 PDT)
- Re: [AMBER] Problem in loading the pdb file (Thu Jul 09 2015 - 05:23:54 PDT)
- Re: [AMBER] Namdenergy problems with non-standard amino acids (Thu Jul 09 2015 - 05:04:08 PDT)
- Re: [AMBER] problem in amber (Thu Jul 09 2015 - 04:52:00 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 12:07:06 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 07:20:13 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 06:59:11 PDT)
- Re: [AMBER] help in amber (Wed Jul 08 2015 - 06:13:46 PDT)
- Re: [AMBER] Paramentrization of a Uracil base with an O3' terminus deprotonated. (Wed Jul 08 2015 - 06:11:02 PDT)
- Re: [AMBER] About python usage in AmberTools (Tue Jul 07 2015 - 12:54:19 PDT)
- Re: [AMBER] About python usage in AmberTools (Tue Jul 07 2015 - 11:55:28 PDT)
- Re: [AMBER] Reference energies for Explicit solvent CpHMD (Mon Jul 06 2015 - 11:09:19 PDT)
- Re: [AMBER] How to set interatomic distance restraint? (Mon Jul 06 2015 - 09:00:00 PDT)
- Re: [AMBER] PME large NFFT (Mon Jul 06 2015 - 08:15:33 PDT)
- Re: [AMBER] assigning atom type and charge (Mon Jul 06 2015 - 05:50:32 PDT)
- Re: [AMBER] Question about AMBER energy decomposition (Sat Jul 04 2015 - 16:00:18 PDT)
- Re: [AMBER] Question about AMBER energy decomposition (Fri Jul 03 2015 - 14:30:00 PDT)
- Re: [AMBER] another leap inconsistency (Thu Jul 02 2015 - 07:53:31 PDT)
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations (Thu Jul 02 2015 - 05:34:25 PDT)
- Re: [AMBER] leap changes residue order (Wed Jul 01 2015 - 09:14:17 PDT)
- Re: [AMBER] Output format in sander (Wed Jul 01 2015 - 09:00:17 PDT)
- Re: [AMBER] Output format in sander (Wed Jul 01 2015 - 08:55:59 PDT)
- Re: [AMBER] Output format in sander (Wed Jul 01 2015 - 03:16:15 PDT)
Jim Wu
- Re: [AMBER] Compile Failure (Wed Jul 01 2015 - 09:38:56 PDT)
John Dood
- [AMBER] PME large NFFT (Mon Jul 06 2015 - 06:18:47 PDT)
- Re: [AMBER] Output format in sander (Thu Jul 02 2015 - 10:24:19 PDT)
Jon Uranga
- [AMBER] MCPB.py N terminal error (Tue Jul 21 2015 - 06:21:52 PDT)
Juan Eiros Zamora
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory (Fri Jul 24 2015 - 03:21:30 PDT)
- Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory (Thu Jul 23 2015 - 00:59:57 PDT)
- [AMBER] [cpptraj] Nativecontacts failing with long trajectory (Wed Jul 22 2015 - 12:36:08 PDT)
- Re: [AMBER] question about advanced tutorial 3 (Fri Jul 10 2015 - 03:30:29 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 07:26:35 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 07:19:02 PDT)
- Re: [AMBER] About python usage in AmberTools (Wed Jul 08 2015 - 06:31:46 PDT)
- [AMBER] About python usage in AmberTools (Tue Jul 07 2015 - 11:05:23 PDT)
Karl Debiec
- [AMBER] Cpptraj able to identify coordinates written by VMD? (Thu Jul 02 2015 - 10:31:48 PDT)
Kenneth Huang
- [AMBER] FATAL: Atom () does not have a type???? (Fri Jul 10 2015 - 15:16:38 PDT)
- Re: [AMBER] FATAL: Atom () does not have a type???? (Fri Jul 10 2015 - 13:55:47 PDT)
- [AMBER] molecules split apart during MD (Fri Jul 10 2015 - 07:39:42 PDT)
kurisaki
- Re: [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI (Tue Jul 21 2015 - 05:33:55 PDT)
- [AMBER] "nstlim" is not reflected correctly in REMD with pmemd.MPI (Tue Jul 21 2015 - 04:16:30 PDT)
Lara rajam
- [AMBER] hbond cpptraj (Tue Jul 21 2015 - 08:26:31 PDT)
- [AMBER] molecules split apart during MD (Fri Jul 10 2015 - 07:20:43 PDT)
Latorraca, Naomi Rose
- [AMBER] impose restraint mask for specific residues (Fri Jul 24 2015 - 11:09:02 PDT)
- [AMBER] illegal memory access in amber GPU simulations (Fri Jul 17 2015 - 19:48:47 PDT)
Lee-Ping Wang
- Re: [AMBER] Question about AMBER energy decomposition (Sat Jul 04 2015 - 06:41:04 PDT)
- [AMBER] Question about AMBER energy decomposition (Fri Jul 03 2015 - 12:28:53 PDT)
Life Sciences Inc
- Re: [AMBER] Lipid diffusion in cpptraj (Thu Jul 30 2015 - 14:22:16 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj (Mon Jul 13 2015 - 14:50:54 PDT)
- Re: [AMBER] Lipid diffusion in cpptraj (Wed Jul 08 2015 - 15:45:45 PDT)
- [AMBER] Lipid diffusion in cpptraj (Wed Jul 01 2015 - 07:11:56 PDT)
Lin Song
- Re: [AMBER] Cpptraj failure (Mon Jul 13 2015 - 09:14:42 PDT)
Lionel Sacconnay
- [AMBER] Distance restraint in AMBER 14 and GPU (Mon Jul 20 2015 - 02:28:23 PDT)
M Olivia Kim
- [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Thu Jul 16 2015 - 15:13:06 PDT)
M. Reza Ganjalikhany
- Re: [AMBER] GPU EVGA GTX 980 SC ACX (Sat Jul 25 2015 - 08:50:27 PDT)
- [AMBER] GPU EVGA GTX 980 SC ACX (Sat Jul 25 2015 - 04:48:36 PDT)
Marcus Arieno
- Re: [AMBER] NetCDF file (Wed Jul 15 2015 - 07:34:51 PDT)
Marta Wisniewska
- [AMBER] NetCDF file (Wed Jul 15 2015 - 07:21:16 PDT)
MASAOKI FUJII
- [AMBER] AMBER error : Coordinate resetting (SHAKE) cannot be accomplish ed (Thu Jul 16 2015 - 00:37:37 PDT)
Meij, Henk
- Re: [AMBER] multiple cpus per single gpu job (Thu Jul 30 2015 - 10:04:48 PDT)
- [AMBER] multiple cpus per single gpu job (Thu Jul 30 2015 - 08:11:13 PDT)
Michael Shokhen
- [AMBER] Antechamber for boronic acid derivatives? (Thu Jul 30 2015 - 00:19:17 PDT)
- [AMBER] How to combine distance and torsion restraint? (Mon Jul 27 2015 - 06:16:30 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 12:00:51 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 11:21:13 PDT)
- Re: [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 10:34:38 PDT)
- [AMBER] MD simulation: cis isomer of peptide bond (Sun Jul 26 2015 - 09:07:07 PDT)
- [AMBER] Unexpected prochirality change from si to re during MD simulation (Thu Jul 09 2015 - 01:28:59 PDT)
- Re: [AMBER] How to set interatomic distance restraint? (Thu Jul 09 2015 - 01:18:40 PDT)
- Re: [AMBER] How to set interatomic distance restraint? (Mon Jul 06 2015 - 08:43:08 PDT)
- Re: [AMBER] How to set interatomic distance restraint? (Sun Jul 05 2015 - 05:04:46 PDT)
- [AMBER] How to set interatomic distance restraint? (Fri Jul 03 2015 - 00:19:37 PDT)
Miroslav Krepl
- Re: [AMBER] Fwd: NMR restraints with pmemd.cuda problem (Thu Jul 30 2015 - 02:43:04 PDT)
mish
- Re: [AMBER] Unchanged coordinates in leap (Wed Jul 22 2015 - 07:44:30 PDT)
- [AMBER] Unchanged coordinates in leap (Tue Jul 21 2015 - 02:13:07 PDT)
Mohamed Faizan Momin
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 08:46:11 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 08:26:42 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 07:47:34 PDT)
- [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 07:12:37 PDT)
MOHD HOMAIDUR RAHMAN
- [AMBER] Regarding melt curve (Thu Jul 02 2015 - 21:16:31 PDT)
Mohsen Zakeri
- Re: [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 15:26:08 PDT)
- Re: [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 15:08:49 PDT)
- Re: [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 15:06:14 PDT)
- [AMBER] Error in loading inpcrd file in sander (Tue Jul 21 2015 - 14:29:25 PDT)
- [AMBER] Producing Decoys with AmberTools (Sun Jul 12 2015 - 12:49:25 PDT)
- [AMBER] FEW tutorial (Fri Jul 10 2015 - 03:37:43 PDT)
- [AMBER] question about advanced tutorial 3 (Fri Jul 10 2015 - 03:12:03 PDT)
Morteza Chehel Amirani
- [AMBER] extract coordinates of a specific atom (Fri Jul 03 2015 - 16:43:20 PDT)
Muthukumaran R
- [AMBER] Accelerated md for protein dna complex with modified residue (Tue Jul 14 2015 - 11:05:59 PDT)
Naomi Rose Latorraca
- [AMBER] anisotropic vs. semi-isotropic membrane simulations (Wed Jul 01 2015 - 15:01:51 PDT)
Needham, Perri
- Re: [AMBER] NMR restraints with pmemd.cuda problem (Thu Jul 16 2015 - 12:34:18 PDT)
Nhai
- Re: [AMBER] extract coordinates of a specific atom (Fri Jul 03 2015 - 16:50:42 PDT)
nhai.wn
- Re: [AMBER] Regarding melt curve (Thu Jul 02 2015 - 21:26:12 PDT)
Nicholus Bhattacharjee
- Re: [AMBER] Prep file for chiral position (Mon Jul 27 2015 - 10:37:14 PDT)
- [AMBER] Prep file for chiral position (Mon Jul 27 2015 - 09:51:56 PDT)
- [AMBER] Order of the atom in prep ourput of antechamber (Fri Jul 10 2015 - 01:52:24 PDT)
Ofir Tal
- [AMBER] Chlorophyll A .mol2 file (Thu Jul 02 2015 - 06:45:12 PDT)
Oliver Grant
- Re: [AMBER] Changing NMR restraint weights (Tue Jul 14 2015 - 07:02:35 PDT)
- [AMBER] Changing NMR restraint weights (Fri Jul 10 2015 - 02:02:29 PDT)
Olivia Pierce
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Fri Jul 17 2015 - 16:36:34 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Fri Jul 17 2015 - 12:57:13 PDT)
- Re: [AMBER] Mutation of a protein residue in TI computation with pmemd.MPI (Fri Jul 17 2015 - 09:52:02 PDT)
Osman, Roman
- [AMBER] Restart of MMPBSA (Tue Jul 28 2015 - 11:09:29 PDT)
Pengfei Li
- Re: [AMBER] MCPB.py mismatch error (Fri Jul 31 2015 - 13:50:30 PDT)
- Re: [AMBER] MCPB.py mismatch error (Tue Jul 28 2015 - 20:26:56 PDT)
- Re: [AMBER] MCPB.py Value / Syntax error (Wed Jul 22 2015 - 14:18:24 PDT)
peter.schmidtke.discngine.servier.com
- Re: [AMBER] which solvent model to use with solvateCap (Mon Jul 27 2015 - 07:23:26 PDT)
- [AMBER] which solvent model to use with solvateCap (Mon Jul 27 2015 - 04:12:18 PDT)
- Re: [AMBER] Using TIP4PEW amber FF in NAMD (Fri Jul 24 2015 - 05:13:18 PDT)
- [AMBER] Using TIP4PEW amber FF in NAMD (Fri Jul 24 2015 - 01:27:34 PDT)
Rahul Ramesh
- Re: [AMBER] Explicit Solvent Constant pH MD (Fri Jul 10 2015 - 14:52:52 PDT)
- Re: [AMBER] Explicit Solvent Constant pH MD (Thu Jul 09 2015 - 09:42:17 PDT)
Ramin Ekhteiari
- [AMBER] charmmlipid2amber.py (Sat Jul 04 2015 - 11:35:49 PDT)
Ray Luo, Ph.D.
- Re: [AMBER] countless warnning (Fri Jul 17 2015 - 11:34:13 PDT)
Robert Molt
- Re: [AMBER] Problem in Using the Average Command in Cpptraj (Mon Jul 13 2015 - 09:12:38 PDT)
- [AMBER] Problem in Using the Average Command in Cpptraj (Mon Jul 13 2015 - 08:38:15 PDT)
Robin Jain
- [AMBER] help in box size determination (Sun Jul 19 2015 - 22:08:33 PDT)
- [AMBER] help in box size detremination (Sun Jul 19 2015 - 02:19:04 PDT)
- [AMBER] help in resp charge (Sat Jul 18 2015 - 00:16:50 PDT)
- [AMBER] help in making xyz file (Tue Jul 14 2015 - 02:14:01 PDT)
- [AMBER] problem in amber (Thu Jul 09 2015 - 00:32:05 PDT)
- [AMBER] help in amber (Wed Jul 08 2015 - 02:31:26 PDT)
- [AMBER] help in make .prepin file (Fri Jul 03 2015 - 00:06:00 PDT)
Rohith Mohan
- Re: [AMBER] Issues with running simulation after ParmEd conversion (Fri Jul 31 2015 - 13:49:14 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion (Thu Jul 30 2015 - 13:06:11 PDT)
- Re: [AMBER] Issues with running simulation after ParmEd conversion (Wed Jul 29 2015 - 14:06:47 PDT)
- [AMBER] Issues with running simulation after ParmEd conversion (Tue Jul 28 2015 - 16:30:26 PDT)
ROOPALI VERMA
- [AMBER] Targeted Molecular dynamics in Amber (Mon Jul 27 2015 - 03:00:43 PDT)
Ross Walker
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more (Fri Jul 31 2015 - 09:00:41 PDT)
- Re: [AMBER] multiple cpus per single gpu job (Thu Jul 30 2015 - 09:06:37 PDT)
- Re: [AMBER] NMR restraints with pmemd.cuda problem (Thu Jul 30 2015 - 07:54:56 PDT)
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more (Wed Jul 29 2015 - 07:31:45 PDT)
- Re: [AMBER] GPU EVGA GTX 980 SC ACX (Sat Jul 25 2015 - 14:47:32 PDT)
- Re: [AMBER] GPU EVGA GTX 980 SC ACX (Sat Jul 25 2015 - 07:59:16 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 09:05:01 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 07:51:31 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 07:41:12 PDT)
- Re: [AMBER] Monitoring GPU voltage (Wed Jul 22 2015 - 17:57:43 PDT)
- [AMBER] GTX980Ti's now supported for AMBER and Exxact GTX780Tis available at discounted prices (Mon Jul 20 2015 - 17:16:54 PDT)
- Re: [AMBER] illegal memory access in amber GPU simulations (Fri Jul 17 2015 - 21:22:52 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Thu Jul 09 2015 - 04:27:58 PDT)
- Re: [AMBER] anisotropic vs. semi-isotropic membrane simulations (Wed Jul 01 2015 - 15:48:05 PDT)
Sanjib Paul
- [AMBER] assigning atom type and charge (Mon Jul 06 2015 - 04:41:08 PDT)
Scott Le Grand
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 08:39:28 PDT)
- Re: [AMBER] GTX Titan Xs slowing down after 200ns (Thu Jul 23 2015 - 08:12:15 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Thu Jul 09 2015 - 07:47:24 PDT)
Sharapa
- Re: [AMBER] Gaff Parameters Si (Thu Jul 30 2015 - 04:30:51 PDT)
- [AMBER] Solvents that are not in a list. (Thu Jul 30 2015 - 04:16:55 PDT)
- [AMBER] Gaff Parameters Si (Mon Jul 20 2015 - 16:08:47 PDT)
Shoresh Shafei
- [AMBER] amber topology file for cytochrome c covalently bond to Heme (Mon Jul 06 2015 - 10:07:58 PDT)
Shruti Koulgi
- [AMBER] MM-GBSA at different temperature (Tue Jul 28 2015 - 23:02:00 PDT)
Stevens, David
- [AMBER] CPPTRAJ - Filtering frames based on lowest of the two RMSD values (Mon Jul 20 2015 - 15:30:00 PDT)
Takeshi Baba
- Re: [AMBER] MCPB.py N terminal error (Tue Jul 21 2015 - 07:34:19 PDT)
- Re: [AMBER] MCPB.py ValueError (Thu Jul 16 2015 - 19:01:28 PDT)
- Re: [AMBER] NumPy Import Error for MCPB.py on Amber15 (Tue Jul 07 2015 - 16:39:25 PDT)
Thomas Cheatham
- Re: [AMBER] Cpptraj able to identify coordinates written by VMD? (Thu Jul 02 2015 - 12:47:48 PDT)
Thomas Evangelidis
- [AMBER] detecting and removing corrupted frames (Mon Jul 27 2015 - 03:32:23 PDT)
Thomas Fox
- Re: [AMBER] Order of the atom in prep ourput of antechamber (Fri Jul 10 2015 - 02:54:38 PDT)
- [AMBER] cpptraj: rmsd problem (Tue Jul 07 2015 - 02:15:34 PDT)
- [AMBER] cpptraj: bounds command -> grid (Tue Jul 07 2015 - 00:10:11 PDT)
Tommaso Casalini
- [AMBER] About charge derivation for enantiomeric molecules (Sat Jul 11 2015 - 02:30:39 PDT)
- [AMBER] About charge derivation for enantiomers (Fri Jul 10 2015 - 13:51:40 PDT)
Tru Huynh
- Re: [AMBER] Monitoring GPU voltage (Wed Jul 22 2015 - 13:01:49 PDT)
- Re: [AMBER] Monitoring GPU voltage (Wed Jul 22 2015 - 12:52:30 PDT)
Vahid Kshani
- [AMBER] Coordinate resetting (SHAKE) cannot be accomplished (Wed Jul 15 2015 - 22:27:59 PDT)
Vlad Cojocaru
- Re: [AMBER] Accelerated md for protein dna complex with modified residue (Wed Jul 15 2015 - 06:11:13 PDT)
- Re: [AMBER] articles published for ff14SB and GBneck2 (Fri Jul 10 2015 - 05:45:35 PDT)
- [AMBER] water networks and bridge option of the hbond command in cpptraj (Wed Jul 01 2015 - 10:44:49 PDT)
whb
- [AMBER] Explicit-solvent-pH-REMD (Fri Jul 31 2015 - 00:48:28 PDT)
- [AMBER] Explicit solvent pH-REMD (Wed Jul 22 2015 - 07:33:14 PDT)
wliu
- Re: [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? (Wed Jul 01 2015 - 21:19:47 PDT)
- [AMBER] Why the entropy contribution from quasi-harmonic and normal mode methods are so different? (Wed Jul 01 2015 - 02:13:54 PDT)
Xing
- [AMBER] compare two trajectories (Fri Jul 10 2015 - 12:35:10 PDT)
Ye Renlo
- [AMBER] incorrect determination of atomic number for atom Cl in tleap (Mon Jul 20 2015 - 06:32:15 PDT)
Yip Yew Mun
- Re: [AMBER] RESP Fit to Atomic Multipoles (Thu Jul 16 2015 - 08:30:53 PDT)
- [AMBER] RESP Fit to Atomic Multipoles (Thu Jul 16 2015 - 08:01:46 PDT)
ymei
- Re: [AMBER] RESP Fit to Atomic Multipoles (Thu Jul 16 2015 - 08:18:54 PDT)
Yogeeshwar Ajjugal
- [AMBER] Regarding ADP molecule force fields (Fri Jul 31 2015 - 02:41:24 PDT)
Ziba Bahadori
- Re: [AMBER] Amber for phophorylated residue (Thu Jul 23 2015 - 08:27:39 PDT)
- [AMBER] Amber for phophorylated residue (Thu Jul 23 2015 - 03:12:19 PDT)
Åke Sandgren
- Re: [AMBER] svdcmp in sander/ncsu-rmsd.F90 (AmberTools15) is sensitive to higher optimizations, suggest using lapack routine instead (Thu Jul 16 2015 - 10:05:29 PDT)
Éric Germaneau
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Wed Jul 08 2015 - 17:33:57 PDT)
- Re: [AMBER] issue using CUDA+MPI+OpenMP (Wed Jul 08 2015 - 17:02:08 PDT)
- [AMBER] issue using CUDA+MPI+OpenMP (Tue Jul 07 2015 - 23:12:45 PDT)
浅井賢
- Re: [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more (Thu Jul 30 2015 - 23:36:37 PDT)
- [AMBER] Utilization of 3 GPUs suddenly drop to 0% and won't work any more (Tue Jul 28 2015 - 23:35:38 PDT)

Amber Archive Jul 2015 by author