Amber Archive Feb 2019: by thread

[AMBER] MCPB.py and ambmask for IRON Prasanth G, Research Scholar (Fri Feb 01 2019 - 01:58:13 PST)
- Re: [AMBER] MCPB.py and ambmask for IRON Pengfei Li (Tue Feb 05 2019 - 08:27:20 PST)
- Re: [AMBER] MCPB.py and ambmask for IRON Prasanth G, Research Scholar (Tue Feb 05 2019 - 20:36:38 PST)
Re: [AMBER] PCA Analyze mode evec.pev Shirin Jamshidi (Fri Feb 01 2019 - 04:12:17 PST)
- Re: [AMBER] PCA Analyze mode evec.pev Daniel Roe (Fri Feb 01 2019 - 05:01:27 PST)
[AMBER] Adding an atom to a residue by parmed mish (Fri Feb 01 2019 - 07:46:40 PST)
- Re: [AMBER] Adding an atom to a residue by parmed mish (Sat Feb 02 2019 - 06:40:19 PST)
  - Re: [AMBER] Adding an atom to a residue by parmed Jason Swails (Mon Feb 18 2019 - 12:37:39 PST)
    - Re: [AMBER] Adding an atom to a residue by parmed mish (Tue Feb 19 2019 - 10:18:25 PST)
[AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Fri Feb 01 2019 - 08:55:57 PST)
- Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 Goetz, Andreas (Fri Feb 01 2019 - 11:07:42 PST)
  - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Sat Feb 02 2019 - 04:08:50 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 Goetz, Andreas (Sat Feb 02 2019 - 16:45:23 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 Ross Walker (Sun Feb 03 2019 - 07:34:11 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Sun Feb 03 2019 - 09:32:58 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 David Case (Sun Feb 03 2019 - 17:21:50 PST)
    - Re: [AMBER] QMMM differences between AMBER PM3 and Orca PM3 GiovanniMaria Piccini (Mon Feb 04 2019 - 02:46:21 PST)
[AMBER] mpi installation problem Prabir Khatua (Fri Feb 01 2019 - 11:02:42 PST)
- Re: [AMBER] mpi installation problem David Case (Sat Feb 02 2019 - 09:07:51 PST)
  - Re: [AMBER] mpi installation problem Prabir Khatua (Mon Feb 04 2019 - 09:06:12 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Mon Feb 04 2019 - 09:21:32 PST)
    - Re: [AMBER] mpi installation problem Daniel Roe (Mon Feb 04 2019 - 09:35:26 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Mon Feb 04 2019 - 14:17:18 PST)
    - Re: [AMBER] mpi installation problem David Case (Mon Feb 04 2019 - 17:38:03 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Tue Feb 05 2019 - 09:22:50 PST)
    - Re: [AMBER] mpi installation problem Prabir Khatua (Wed Feb 06 2019 - 11:40:38 PST)
Re: [AMBER] Problem regarding RMSD Daniel Roe (Fri Feb 01 2019 - 12:48:30 PST)
- Re: [AMBER] Problem regarding RMSD Saikat Pal (Fri Feb 01 2019 - 20:46:21 PST)
[AMBER] vdw radii of sodium ion in GAFF Qasim Pars (Fri Feb 01 2019 - 16:34:55 PST)
- Re: [AMBER] vdw radii of sodium ion in GAFF David Case (Sat Feb 02 2019 - 09:14:53 PST)
  - Re: [AMBER] vdw radii of sodium ion in GAFF Thomas Cheatham (Sat Feb 02 2019 - 10:31:25 PST)
[AMBER] merging molecules Stefano Guglielmo (Sat Feb 02 2019 - 09:10:11 PST)
- Re: [AMBER] merging molecules Daniel Roe (Mon Feb 04 2019 - 10:23:18 PST)
- Re: [AMBER] merging molecules Jason Swails (Mon Feb 18 2019 - 12:50:21 PST)
  - Re: [AMBER] merging molecules Wesley Michael Botello-Smith (Mon Feb 18 2019 - 13:10:46 PST)
[AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Prasanth G, Research Scholar (Mon Feb 04 2019 - 05:43:32 PST)
- Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Pengfei Li (Tue Feb 05 2019 - 08:31:40 PST)
- Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Prasanth G, Research Scholar (Wed Feb 06 2019 - 02:06:02 PST)
  - Re: [AMBER] MCPB.py & error: coordinates number in fchk file are not consistent with the atom number Pengfei Li (Fri Feb 08 2019 - 19:03:02 PST)
[AMBER] RMSD of single residue, fit to main structure Rosellen, Martin (Mon Feb 04 2019 - 06:33:18 PST)
- Re: [AMBER] RMSD of single residue, fit to main structure Daniel Roe (Mon Feb 04 2019 - 10:26:14 PST)
[AMBER] NaN in QM-MMPBSA results Sundar (Mon Feb 04 2019 - 11:13:57 PST)
[AMBER] Wham analysis on amber18 (pmemd.cuda) output file mish (Tue Feb 05 2019 - 03:05:32 PST)
- Re: [AMBER] Wham analysis on amber18 (pmemd.cuda) output file mish (Tue Feb 05 2019 - 03:07:17 PST)
[AMBER] Cpptraj hist command Pablo Palomino (Tue Feb 05 2019 - 03:23:22 PST)
- Re: [AMBER] Cpptraj hist command Daniel Roe (Tue Feb 05 2019 - 06:08:24 PST)
- Re: [AMBER] Cpptraj hist command Pablo Palomino (Mon Feb 11 2019 - 05:08:50 PST)
  - Re: [AMBER] Cpptraj hist command LuxStyle International (Mon Feb 11 2019 - 05:10:18 PST)
  - Re: [AMBER] Cpptraj hist command Daniel Roe (Wed Feb 13 2019 - 05:36:00 PST)
[AMBER] pairwise command in cpptraj Leena Aggarwal (Tue Feb 05 2019 - 04:27:22 PST)
- Re: [AMBER] pairwise command in cpptraj Daniel Roe (Tue Feb 05 2019 - 09:44:39 PST)
[AMBER] Graphs Keiran Corbett (Tue Feb 05 2019 - 05:56:06 PST)
- Re: [AMBER] Graphs Gustaf Olsson (Tue Feb 05 2019 - 06:42:12 PST)
- Re: [AMBER] Graphs Daniel Roe (Tue Feb 05 2019 - 08:57:12 PST)
[AMBER] Ca in Amber14 vs Amber18 Keiran Corbett (Tue Feb 05 2019 - 06:07:53 PST)
- Re: [AMBER] Ca in Amber14 vs Amber18 Pengfei Li (Tue Feb 05 2019 - 08:37:26 PST)
[AMBER] hbonds solute with residue Rosellen, Martin (Tue Feb 05 2019 - 06:29:26 PST)
- Re: [AMBER] hbonds solute with residue Daniel Roe (Tue Feb 05 2019 - 08:34:54 PST)
[AMBER] cpptraj MYRIAN TORRES RICO (Tue Feb 05 2019 - 06:51:05 PST)
- Re: [AMBER] cpptraj Daniel Roe (Tue Feb 05 2019 - 08:17:36 PST)
Re: [AMBER] MCPB.py error with HEME containing protein Pengfei Li (Tue Feb 05 2019 - 08:00:19 PST)
Re: [AMBER] MCPB.py Error Pengfei Li (Tue Feb 05 2019 - 09:03:59 PST)
[AMBER] Use of LIE command in cpptraj error Debarati DasGupta (Tue Feb 05 2019 - 12:28:50 PST)
- Re: [AMBER] Use of LIE command in cpptraj error Debarati DasGupta (Tue Feb 05 2019 - 12:31:58 PST)
[AMBER] chamber problem Prabir Khatua (Tue Feb 05 2019 - 13:46:38 PST)
- Re: [AMBER] chamber problem Jason Swails (Wed Feb 06 2019 - 20:58:41 PST)
  - Re: [AMBER] chamber problem Prabir Khatua (Tue Feb 12 2019 - 10:30:22 PST)
    - Re: [AMBER] chamber problem David Case (Tue Feb 12 2019 - 14:34:45 PST)
    - Re: [AMBER] chamber problem Prabir Khatua (Wed Feb 13 2019 - 10:31:03 PST)
    - Re: [AMBER] chamber problem Jason Swails (Mon Feb 18 2019 - 12:32:46 PST)
    - Re: [AMBER] chamber problem Prabir Khatua (Tue Feb 19 2019 - 08:33:33 PST)
    - Re: [AMBER] chamber problem Jason Swails (Tue Feb 19 2019 - 19:37:38 PST)
    - Re: [AMBER] chamber problem Prabir Khatua (Wed Feb 20 2019 - 08:16:07 PST)
[AMBER] Creating PRMTOP and INPCRD in Amber 16 Fulbabu Sk (Wed Feb 06 2019 - 01:30:55 PST)
- Re: [AMBER] Creating PRMTOP and INPCRD in Amber 16 Pengfei Li (Fri Feb 08 2019 - 18:35:13 PST)
Re: [AMBER] FW: Building topology of a molecule with Antechamber David A Case (Wed Feb 06 2019 - 04:56:02 PST)
[AMBER] Change simulation box size Anthony Cruz-Balberdy (Wed Feb 06 2019 - 05:24:24 PST)
- Re: [AMBER] Change simulation box size David A Case (Wed Feb 06 2019 - 07:59:00 PST)
[AMBER] RESP charges for atoms/molecules which not included gaff, gaff2, exc..? Erdem Yeler (Wed Feb 06 2019 - 05:49:32 PST)
[AMBER] mmpbsa error Mehreen Ghufran (Wed Feb 06 2019 - 08:19:55 PST)
- [AMBER] mmpbsa error Mehreen Ghufran (Wed Feb 06 2019 - 08:28:29 PST)
[AMBER] The 3D-RISM-PC+ information for each atoms Eugene huh (Wed Feb 06 2019 - 23:49:04 PST)
- Re: [AMBER] The 3D-RISM-PC+ information for each atoms Tyler Luchko (Lists) (Thu Feb 07 2019 - 11:38:29 PST)
[AMBER] FW: Running Tempered + Hamiltonian replica exchange using pmemd.cuda.MPI BLUNTZER Marie (Thu Feb 07 2019 - 03:28:17 PST)
- Re: [AMBER] FW: Running Tempered + Hamiltonian replica exchange using pmemd.cuda.MPI Daniel Roe (Fri Feb 08 2019 - 07:30:59 PST)
[AMBER] Regarding constant pH MD Saikat Pal (Fri Feb 08 2019 - 07:29:38 PST)
- Re: [AMBER] Regarding constant pH MD Saikat Pal (Sun Feb 10 2019 - 23:07:30 PST)
  - Re: [AMBER] Regarding constant pH MD LuxStyle International (Sun Feb 10 2019 - 23:08:05 PST)
    - Re: [AMBER] Regarding constant pH MD Bill Ross (Sun Feb 10 2019 - 23:33:58 PST)
- Re: [AMBER] Regarding constant pH MD Cruzeiro,Vinicius Wilian D (Mon Feb 11 2019 - 07:08:59 PST)
[AMBER] amber installation problem Rimon Riju (Fri Feb 08 2019 - 23:19:03 PST)
- Re: [AMBER] amber installation problem David Case (Sat Feb 09 2019 - 18:09:04 PST)
  - Re: [AMBER] amber installation problem Rimon Riju (Sat Feb 09 2019 - 22:05:16 PST)
[AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Sat Feb 09 2019 - 12:39:50 PST)
- Re: [AMBER] Convert prmtop to PSF file in Cpptraj Daniel Roe (Wed Feb 13 2019 - 05:34:42 PST)
  - Re: [AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Wed Feb 13 2019 - 06:10:37 PST)
    - Re: [AMBER] Convert prmtop to PSF file in Cpptraj Daniel Roe (Wed Feb 13 2019 - 06:29:58 PST)
    - Re: [AMBER] Convert prmtop to PSF file in Cpptraj Fulbabu Sk (Wed Feb 13 2019 - 06:58:22 PST)
[AMBER] 1D-RISM: *.xvv generation error Eugene huh (Mon Feb 11 2019 - 01:31:43 PST)
- Re: [AMBER] 1D-RISM: *.xvv generation error LuxStyle International (Mon Feb 11 2019 - 01:32:17 PST)
- Re: [AMBER] 1D-RISM: *.xvv generation error Tyler Luchko (Lists) (Mon Feb 11 2019 - 10:02:20 PST)
- Re: [AMBER] 1D-RISM: *.xvv generation error Eugene huh (Thu Feb 14 2019 - 02:08:01 PST)
  - Re: [AMBER] 1D-RISM: *.xvv generation error Tyler Luchko (Lists) (Thu Feb 14 2019 - 08:52:55 PST)
[AMBER] Behavior of MSD at different collision frequency values Abdullah Bin Faheem (Mon Feb 11 2019 - 02:13:07 PST)
- Re: [AMBER] Behavior of MSD at different collision frequency values LuxStyle International (Mon Feb 11 2019 - 02:13:28 PST)
- Re: [AMBER] Behavior of MSD at different collision frequency values David A Case (Mon Feb 11 2019 - 05:23:46 PST)
  - Re: [AMBER] Behavior of MSD at different collision frequency values Abdullah Bin Faheem (Mon Feb 11 2019 - 18:57:14 PST)
    - Re: [AMBER] Behavior of MSD at different collision frequency values Daniel Roe (Fri Feb 15 2019 - 05:24:05 PST)
[AMBER] Planarity of bound versus unbound ligand Tye Martin (Mon Feb 11 2019 - 12:36:42 PST)
- Re: [AMBER] Planarity of bound versus unbound ligand David Case (Mon Feb 11 2019 - 17:57:39 PST)
[AMBER] charmm psf to amber prmtop conversion problem Prabir Khatua (Mon Feb 11 2019 - 13:09:31 PST)
- Re: [AMBER] charmm psf to amber prmtop conversion problem David Case (Mon Feb 11 2019 - 18:00:54 PST)
[AMBER] Atom type of Calcium Sunita Patel (Mon Feb 11 2019 - 23:22:24 PST)
- Re: [AMBER] Atom type of Calcium Bill Ross (Mon Feb 11 2019 - 23:37:28 PST)
  - Re: [AMBER] Atom type of Calcium Sunita Patel (Mon Feb 11 2019 - 23:47:12 PST)
    - Re: [AMBER] Atom type of Calcium David Case (Tue Feb 12 2019 - 06:26:18 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Wed Feb 20 2019 - 04:05:06 PST)
    - Re: [AMBER] Atom type of Calcium David A Case (Wed Feb 20 2019 - 07:35:54 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Thu Feb 28 2019 - 04:21:23 PST)
  - Re: [AMBER] Atom type of Calcium Bill Ross (Mon Feb 11 2019 - 23:52:33 PST)
    - Re: [AMBER] Atom type of Calcium Sunita Patel (Tue Feb 12 2019 - 02:13:00 PST)
[AMBER] Restart file is not formed until the simulation finishes Chetna Tyagi (Tue Feb 12 2019 - 02:55:30 PST)
- Re: [AMBER] Restart file is not formed until the simulation finishes Pratul Agarwal (Tue Feb 12 2019 - 05:03:24 PST)
- Re: [AMBER] Restart file is not formed until the simulation finishes Shayna Hilburg (Tue Feb 12 2019 - 06:23:49 PST)
  - Re: [AMBER] Restart file is not formed until the simulation finishes Chetna Tyagi (Wed Feb 13 2019 - 02:54:05 PST)
[AMBER] MM-GBSA for protein-sugar complex James Starlight (Tue Feb 12 2019 - 07:30:10 PST)
[AMBER] Cpptraj: PC1 and PC1 as function of residue number calculation Fulbabu Sk (Tue Feb 12 2019 - 11:30:42 PST)
- Re: [AMBER] Cpptraj: PC1 and PC1 as function of residue number calculation Daniel Roe (Wed Feb 13 2019 - 05:06:42 PST)
[AMBER] Interpreting QM MMPBSA results Sundar (Tue Feb 12 2019 - 14:50:25 PST)
- Re: [AMBER] Interpreting QM MMPBSA results David A Case (Mon Feb 18 2019 - 05:09:00 PST)
[AMBER] cpptraj PCA error Alen Ahmetovic (Tue Feb 12 2019 - 16:27:22 PST)
- Re: [AMBER] cpptraj PCA error Daniel Roe (Wed Feb 13 2019 - 05:11:02 PST)
[AMBER] Regarding population of hydrogen bond MOHD HOMAIDUR RAHMAN (Tue Feb 12 2019 - 17:24:14 PST)
- Re: [AMBER] Regarding population of hydrogen bond Wesley Michael Botello-Smith (Wed Feb 13 2019 - 11:24:31 PST)
[AMBER] Amber installation on Ubuntu 18.04 Rajarshi Roy (Tue Feb 12 2019 - 20:32:32 PST)
- Re: [AMBER] Amber installation on Ubuntu 18.04 Bill Ross (Tue Feb 12 2019 - 21:50:12 PST)
- Re: [AMBER] Amber installation on Ubuntu 18.04 David A Case (Wed Feb 13 2019 - 10:09:11 PST)
  - Re: [AMBER] Amber installation on Ubuntu 18.04 Rajarshi Roy (Wed Feb 13 2019 - 20:15:24 PST)
[AMBER] Amber18 TI on K10 - any known problem? Thomas Fox (Wed Feb 13 2019 - 04:06:28 PST)
- Re: [AMBER] Amber18 TI on K10 - any known problem? David A Case (Mon Feb 18 2019 - 05:07:45 PST)
[AMBER] gromacs .top file error fateme haghighi (Wed Feb 13 2019 - 06:52:06 PST)
- Re: [AMBER] gromacs .top file error Jason Swails (Tue Feb 19 2019 - 19:39:10 PST)
- Re: [AMBER] gromacs .top file error dhaval patel (Tue Feb 19 2019 - 20:45:50 PST)
[AMBER] A few issues Paul, Austin (Wed Feb 13 2019 - 06:55:12 PST)
- Re: [AMBER] A few issues Hai Nguyen (Wed Feb 13 2019 - 07:31:10 PST)
  - Re: [AMBER] A few issues Hai Nguyen (Thu Feb 14 2019 - 20:48:02 PST)
    - Re: [AMBER] A few issues David A Case (Fri Feb 15 2019 - 05:25:29 PST)
    - Re: [AMBER] A few issues Hai Nguyen (Fri Feb 15 2019 - 09:51:31 PST)
    - Re: [AMBER] A few issues Paul, Austin (Tue Feb 19 2019 - 11:59:42 PST)
    - Re: [AMBER] A few issues Hai Nguyen (Tue Feb 19 2019 - 12:59:29 PST)
    - Re: [AMBER] A few issues Hai Nguyen (Tue Feb 19 2019 - 16:29:35 PST)
- Re: [AMBER] A few issues David Case (Wed Feb 13 2019 - 18:18:07 PST)
[AMBER] reference.frc file from MMPBSA calculations Sundar (Wed Feb 13 2019 - 10:02:55 PST)
[AMBER] NMR restraints in AmberTools? Istvan Kolossvary (Wed Feb 13 2019 - 15:34:45 PST)
- Re: [AMBER] NMR restraints in AmberTools? David Case (Wed Feb 13 2019 - 18:30:31 PST)
  - Re: [AMBER] NMR restraints in AmberTools? Istvan Kolossvary (Wed Feb 13 2019 - 18:38:31 PST)
[AMBER] Dihedral configuration entropy Lod King (Wed Feb 13 2019 - 16:02:50 PST)
- Re: [AMBER] Dihedral configuration entropy Daniel Roe (Tue Feb 19 2019 - 11:41:56 PST)
[AMBER] Calculation of Entropy using MMPBSA AMBER 18 DHEERAJ CHITARA (Wed Feb 13 2019 - 21:43:48 PST)
- Re: [AMBER] Calculation of Entropy using MMPBSA AMBER 18 David A Case (Thu Feb 14 2019 - 06:04:58 PST)
[AMBER] MMPBSA Nisha Amarnath Jonniya (Wed Feb 13 2019 - 23:06:08 PST)
- Re: [AMBER] MMPBSA David A Case (Mon Feb 18 2019 - 04:55:49 PST)
  - Re: [AMBER] MMPBSA Nisha Amarnath Jonniya (Mon Feb 18 2019 - 05:42:04 PST)
[AMBER] making force fields files from topology Hadi Rahmaninejad (Thu Feb 14 2019 - 07:31:45 PST)
- [AMBER] Fwd: making force fields files from topology Hadi Rahmaninejad (Sun Feb 17 2019 - 15:22:21 PST)
- [AMBER] Fwd: making force fields files from topology Hadi Rahmaninejad (Sun Feb 17 2019 - 15:28:06 PST)
- Re: [AMBER] making force fields files from topology David A Case (Mon Feb 18 2019 - 04:51:58 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Thu Feb 14 2019 - 08:36:17 PST)
- Re: [AMBER] MBAR from TI on pmemd Jason Swails (Wed Feb 27 2019 - 22:13:56 PST)
Re: [AMBER] OpenMPI 4.0.0 support Stephan Schott (Thu Feb 14 2019 - 16:54:02 PST)
- Re: [AMBER] OpenMPI 4.0.0 support viktor drobot (Thu Feb 14 2019 - 22:32:03 PST)
- Re: [AMBER] OpenMPI 4.0.0 support David A Case (Fri Feb 15 2019 - 05:16:01 PST)
- Re: [AMBER] OpenMPI 4.0.0 support David A Case (Fri Feb 15 2019 - 11:07:29 PST)
- Re: [AMBER] OpenMPI 4.0.0 support Stephan Schott (Fri Feb 15 2019 - 11:28:49 PST)
[AMBER] Dihedral configuration entropy Lod King (Thu Feb 14 2019 - 17:48:27 PST)
- Re: [AMBER] Dihedral configuration entropy Daniel Roe (Fri Feb 15 2019 - 10:33:45 PST)
[AMBER] Generating spherical macro-ion in amber ATUL KUMAR (Thu Feb 14 2019 - 23:20:18 PST)
- Re: [AMBER] Generating spherical macro-ion in amber David A Case (Fri Feb 15 2019 - 05:29:16 PST)
  - Re: [AMBER] Generating spherical macro-ion in amber ATUL KUMAR (Fri Feb 15 2019 - 05:55:22 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Fri Feb 15 2019 - 00:38:46 PST)
[AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Sat Feb 16 2019 - 20:54:52 PST)
- Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Robin Betz (Mon Feb 18 2019 - 13:51:52 PST)
  - Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Tue Feb 19 2019 - 01:49:52 PST)
- Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Daniel Roe (Thu Feb 21 2019 - 07:43:02 PST)
  - Re: [AMBER] xleap "impose" and addAtomtypes command for paramfit gen_conformers.sh Erdem Yeler (Fri Feb 22 2019 - 02:33:30 PST)
[AMBER] peptide-bilayer MD simulation analysis golshan bakrani (Sun Feb 17 2019 - 21:50:35 PST)
[AMBER] Speed-up calculation of Entropy with MMPBSA James Starlight (Mon Feb 18 2019 - 01:34:22 PST)
- Re: [AMBER] Speed-up calculation of Entropy with MMPBSA David A Case (Mon Feb 18 2019 - 04:50:12 PST)
  - Re: [AMBER] Speed-up calculation of Entropy with MMPBSA James Starlight (Mon Feb 18 2019 - 05:16:41 PST)
[AMBER] Umbrella Sampling and WHAM analysis mish (Mon Feb 18 2019 - 03:29:31 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Mon Feb 18 2019 - 04:57:17 PST)
[AMBER] ChamberParm objects are not supported by this action Hadi Rahmaninejad (Mon Feb 18 2019 - 09:13:22 PST)
- Re: [AMBER] ChamberParm objects are not supported by this action David A Case (Mon Feb 18 2019 - 11:21:07 PST)
  - Re: [AMBER] ChamberParm objects are not supported by this action Jason Swails (Mon Feb 18 2019 - 12:26:44 PST)
    - Re: [AMBER] ChamberParm objects are not supported by this action Hadi Rahmaninejad (Mon Feb 18 2019 - 13:07:12 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Mon Feb 18 2019 - 09:54:13 PST)
- Re: [AMBER] puckering coordinates Pratul Agarwal (Tue Feb 19 2019 - 05:52:31 PST)
  - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 08:02:25 PST)
    - Re: [AMBER] puckering coordinates MYRIAN TORRES RICO (Tue Feb 19 2019 - 08:25:03 PST)
    - Re: [AMBER] puckering coordinates Daniel Roe (Tue Feb 19 2019 - 08:42:24 PST)
    - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 08:58:22 PST)
    - Re: [AMBER] puckering coordinates MYRIAN TORRES RICO (Tue Feb 19 2019 - 09:47:44 PST)
    - Re: [AMBER] puckering coordinates Charles-Alexandre Mattelaer (Tue Feb 19 2019 - 09:54:27 PST)
    - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 10:04:23 PST)
    - Re: [AMBER] puckering coordinates mish (Tue Feb 19 2019 - 10:09:38 PST)
    - Re: [AMBER] puckering coordinates Daniel Roe (Tue Feb 19 2019 - 10:42:57 PST)
    - Re: [AMBER] puckering coordinates Pratul Agarwal (Tue Feb 19 2019 - 10:19:18 PST)
Re: [AMBER] Speed-up calculation of Entropy with MMPBSA (James Starlight) David Minh (Mon Feb 18 2019 - 12:22:08 PST)
[AMBER] ff99SBi force field in Amber Advanced Tutorial A22 Michiel de Hoon (Mon Feb 18 2019 - 18:30:06 PST)
[AMBER] Problem during parallel installation Sunita Patel (Tue Feb 19 2019 - 07:05:49 PST)
- Re: [AMBER] Problem during parallel installation Pratul Agarwal (Tue Feb 19 2019 - 05:45:39 PST)
- Re: [AMBER] Problem during parallel installation David A Case (Tue Feb 19 2019 - 05:50:49 PST)
  - Re: [AMBER] Problem during parallel installation Sunita Patel (Wed Feb 20 2019 - 03:04:47 PST)
[AMBER] Bad atom type i Keiran Corbett (Tue Feb 19 2019 - 02:04:52 PST)
- Re: [AMBER] Bad atom type i David Case (Wed Feb 20 2019 - 18:11:13 PST)
[AMBER] puckering MYRIAN TORRES RICO (Tue Feb 19 2019 - 07:23:43 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:37:39 PST)
- Re: [AMBER] gas phase TI David A Case (Tue Feb 19 2019 - 10:35:43 PST)
  - Re: [AMBER] gas phase TI Hosein Geraili Daronkola (Wed Feb 20 2019 - 06:33:17 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:42:00 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 07:52:58 PST)
[AMBER] gas phase TI Hosein Geraili Daronkola (Tue Feb 19 2019 - 08:06:54 PST)
[AMBER] MMPBSA Calculation Error: Order of protein and ligand M RCC (Tue Feb 19 2019 - 09:17:07 PST)
- Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand Sundar (Tue Feb 19 2019 - 09:35:52 PST)
- Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand David A Case (Tue Feb 19 2019 - 10:39:34 PST)
- Re: [AMBER] MMPBSA Calculation Error: Order of protein and ligand M RCC (Wed Feb 20 2019 - 03:32:50 PST)
[AMBER] Silica in antechamber Hadi Rahmaninejad (Tue Feb 19 2019 - 09:46:42 PST)
- Re: [AMBER] Silica in antechamber David A Case (Tue Feb 19 2019 - 10:42:51 PST)
  - Re: [AMBER] Silica in antechamber Hadi Rahmaninejad (Tue Feb 19 2019 - 11:23:27 PST)
[AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Antonio Amber Carlesso (Tue Feb 19 2019 - 10:57:26 PST)
- Re: [AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Christina Bergonzo (Thu Feb 21 2019 - 07:01:52 PST)
  - Re: [AMBER] Protein_plus_ADP_plus_Mg2+_preparation_general_rule Adrian Roitberg (Thu Feb 21 2019 - 11:41:01 PST)
[AMBER] Ovito visualization Shayna Hilburg (Tue Feb 19 2019 - 12:48:46 PST)
[AMBER] Suggestions for Analysis Souvik Dey (Tue Feb 19 2019 - 15:49:27 PST)
- Re: [AMBER] Suggestions for Analysis dhaval patel (Tue Feb 19 2019 - 20:49:58 PST)
  - Re: [AMBER] Suggestions for Analysis Souvik Dey (Thu Feb 21 2019 - 11:50:00 PST)
[AMBER] MMGBSA Angew Chemie (Tue Feb 19 2019 - 20:21:34 PST)
[AMBER] overestimate hydrogen bonding distance Niko Prasetyo (Wed Feb 20 2019 - 01:36:40 PST)
- Re: [AMBER] overestimate hydrogen bonding distance Maciej Maciejczyk (Wed Feb 20 2019 - 02:22:48 PST)
  - Re: [AMBER] overestimate hydrogen bonding distance Niko Prasetyo (Wed Feb 20 2019 - 02:47:40 PST)
    - Re: [AMBER] overestimate hydrogen bonding distance Daniel Roe (Mon Feb 25 2019 - 05:31:58 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Wed Feb 20 2019 - 03:17:48 PST)
- Re: [AMBER] puckering coordinates Daniel Roe (Wed Feb 20 2019 - 04:51:57 PST)
[AMBER] Bond breakage modelling Ali Khodayari (Wed Feb 20 2019 - 05:04:13 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Wed Feb 20 2019 - 06:22:34 PST)
- Re: [AMBER] puckering coordinates Daniel Roe (Thu Feb 21 2019 - 11:18:29 PST)
[AMBER] Amber14 installation issue Alexey Orlov (Wed Feb 20 2019 - 09:56:56 PST)
- Re: [AMBER] Amber14 installation issue David A Case (Wed Feb 20 2019 - 11:14:19 PST)
[AMBER] XMIN internal output suppressed Istvan Kolossvary (Wed Feb 20 2019 - 15:45:51 PST)
- Re: [AMBER] XMIN internal output suppressed David Case (Wed Feb 20 2019 - 18:03:34 PST)
  - Re: [AMBER] XMIN internal output suppressed Istvan Kolossvary (Wed Feb 20 2019 - 19:19:00 PST)
[AMBER] Can cpptraj multidihedral use nonbonded atoms? Michael F. Bruist (Wed Feb 20 2019 - 15:48:29 PST)
- Re: [AMBER] Can cpptraj multidihedral use nonbonded atoms? Daniel Roe (Thu Feb 21 2019 - 11:16:25 PST)
  - Re: [AMBER] Can cpptraj multidihedral use nonbonded atoms? Michael F. Bruist (Thu Feb 28 2019 - 15:01:15 PST)
[AMBER] About clusterdihedral Gilberto Pereira (Thu Feb 21 2019 - 01:06:47 PST)
- Re: [AMBER] About clusterdihedral Daniel Roe (Thu Feb 21 2019 - 11:12:10 PST)
[AMBER] Error and sudden halt in equilibration senal dinuka (Thu Feb 21 2019 - 03:00:00 PST)
- Re: [AMBER] Error and sudden halt in equilibration Bill Ross (Thu Feb 21 2019 - 03:32:19 PST)
- Re: [AMBER] Error and sudden halt in equilibration David A Case (Thu Feb 21 2019 - 05:22:24 PST)
  - Re: [AMBER] Error and sudden halt in equilibration senal dinuka (Thu Feb 21 2019 - 20:07:35 PST)
    - Re: [AMBER] Error and sudden halt in equilibration Bill Ross (Thu Feb 21 2019 - 21:47:04 PST)
- Re: [AMBER] Error and sudden halt in equilibration Stephan Schott (Fri Feb 22 2019 - 10:21:32 PST)
[AMBER] Problem in running pmemd.cuda ATUL KUMAR (Thu Feb 21 2019 - 03:00:03 PST)
- Re: [AMBER] Problem in running pmemd.cuda David A Case (Thu Feb 21 2019 - 05:27:53 PST)
- Re: [AMBER] Problem in running pmemd.cuda Stejskal, Lenka (Thu Feb 21 2019 - 13:16:05 PST)
  - Re: [AMBER] Problem in running pmemd.cuda ATUL KUMAR (Thu Feb 21 2019 - 22:43:23 PST)
[AMBER] Reference energies in CpHMD (constant pH MD) for HIP Rodrigo Pérez Cossio (Thu Feb 21 2019 - 16:16:48 PST)
- Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Cruzeiro,Vinicius Wilian D (Thu Feb 21 2019 - 17:41:16 PST)
  - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Cruzeiro,Vinicius Wilian D (Thu Feb 21 2019 - 18:11:17 PST)
    - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Jason Swails (Wed Feb 27 2019 - 22:08:33 PST)
    - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Brian Radak (Thu Feb 28 2019 - 09:14:41 PST)
  - Re: [AMBER] Reference energies in CpHMD (constant pH MD) for HIP Jason Swails (Wed Feb 27 2019 - 22:00:26 PST)
[AMBER] Does NVIDIA RTX 2080 Ti support Amber16 with cuda-8? M RCC (Fri Feb 22 2019 - 00:20:29 PST)
- Re: [AMBER] Does NVIDIA RTX 2080 Ti support Amber16 with cuda-8? Ross Walker (Fri Feb 22 2019 - 13:05:08 PST)
[AMBER] puckering coordinates MYRIAN TORRES RICO (Fri Feb 22 2019 - 01:40:41 PST)
[AMBER] MBAR from TI on pmemd Hosein Geraili Daronkola (Fri Feb 22 2019 - 02:33:31 PST)
- Re: [AMBER] MBAR from TI on pmemd accuratefreeenergy.gmail.com (Fri Feb 22 2019 - 06:25:23 PST)
[AMBER] Dihedral Kb Value when IDIVF=1 Erdem Yeler (Fri Feb 22 2019 - 03:17:57 PST)
[AMBER] QM/MM - gaussian interface query Abhilash J (Sat Feb 23 2019 - 04:02:31 PST)
[AMBER] Potential bug in sander/LMOD Istvan Kolossvary (Sun Feb 24 2019 - 14:29:11 PST)
[AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation Prasanth G, Research Scholar (Mon Feb 25 2019 - 04:53:34 PST)
- Re: [AMBER] Protein-ligand simulation and help w.r.t files for carrying out simulation David A Case (Mon Feb 25 2019 - 08:07:47 PST)
[AMBER] pytraj distance image Antoine MARION (Mon Feb 25 2019 - 07:53:56 PST)
- Re: [AMBER] pytraj distance image Hai Nguyen (Mon Feb 25 2019 - 08:36:19 PST)
  - Re: [AMBER] pytraj distance image Hai Nguyen (Mon Feb 25 2019 - 11:23:54 PST)
- Re: [AMBER] pytraj distance image Hai Nguyen (Mon Feb 25 2019 - 15:47:37 PST)
  - Re: [AMBER] pytraj distance image Antoine MARION (Tue Feb 26 2019 - 02:29:02 PST)
    - Re: [AMBER] pytraj distance image Hai Nguyen (Tue Feb 26 2019 - 06:10:43 PST)
    - Re: [AMBER] pytraj distance image Antoine MARION (Wed Feb 27 2019 - 00:02:02 PST)
[AMBER] Nothing returned in aMD simulation of membrane protein Meng Wu (Mon Feb 25 2019 - 21:42:52 PST)
[AMBER] confusion of choosing force field Sasthi Charan Mandal (Tue Feb 26 2019 - 04:54:13 PST)
- Re: [AMBER] confusion of choosing force field David A Case (Tue Feb 26 2019 - 06:13:50 PST)
- Re: [AMBER] confusion of choosing force field Pavlína Pokorná (Tue Feb 26 2019 - 06:41:19 PST)
  - Re: [AMBER] confusion of choosing force field Sasthi Charan Mandal (Tue Feb 26 2019 - 09:18:32 PST)
    - Re: [AMBER] confusion of choosing force field David Case (Thu Feb 28 2019 - 15:48:15 PST)
[AMBER] Changing ligand coordinates D. Yousefi (Tue Feb 26 2019 - 05:29:04 PST)
- Re: [AMBER] Changing ligand coordinates Daniel Roe (Tue Feb 26 2019 - 07:08:19 PST)
  - Re: [AMBER] Changing ligand coordinates D. Yousefi (Wed Feb 27 2019 - 03:33:10 PST)
[AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Tue Feb 26 2019 - 09:29:30 PST)
- Re: [AMBER] command from ambertools tutorial does not working Daniel Roe (Tue Feb 26 2019 - 09:41:38 PST)
  - Re: [AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Tue Feb 26 2019 - 09:48:51 PST)
    - Re: [AMBER] command from ambertools tutorial does not working David A Case (Wed Feb 27 2019 - 11:10:37 PST)
    - Re: [AMBER] command from ambertools tutorial does not working Erdem Yeler (Wed Feb 27 2019 - 13:45:54 PST)
    - Re: [AMBER] command from ambertools tutorial does not working Sasthi Charan Mandal (Thu Feb 28 2019 - 00:12:26 PST)
[AMBER] protein function Hosein Geraili Daronkola (Tue Feb 26 2019 - 10:30:12 PST)
[AMBER] Error in generating the residue topology for non-standard amino acid residues RITUPARNA ROY (Wed Feb 27 2019 - 06:48:10 PST)
- Re: [AMBER] Error in generating the residue topology for non-standard amino acid residues David Case (Thu Feb 28 2019 - 15:40:58 PST)
[AMBER] antechamber error Chang Woon Jang (Wed Feb 27 2019 - 09:38:14 PST)
- Re: [AMBER] antechamber error David A Case (Wed Feb 27 2019 - 11:17:08 PST)
[AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Feng, Zimin (Wed Feb 27 2019 - 12:25:02 PST)
- Re: [AMBER] is this reference energy dG ~34 kcal/mol reasonable for acetic acid? Cruzeiro,Vinicius Wilian D (Wed Feb 27 2019 - 14:41:43 PST)
[AMBER] CPPTRAJ Center of Mass binning Debarati DasGupta (Wed Feb 27 2019 - 12:49:54 PST)
[AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Wed Feb 27 2019 - 14:11:54 PST)
- Re: [AMBER] CPPTRAJ grid unknown command Daniel Roe (Wed Feb 27 2019 - 14:21:00 PST)
  - Re: [AMBER] CPPTRAJ grid unknown command Debarati DasGupta (Thu Feb 28 2019 - 07:31:10 PST)
[AMBER] Two dimensional replica exchange MD: Success rate Stephan Eismann (Wed Feb 27 2019 - 17:30:20 PST)
[AMBER] alchemical_analysis Hosein Geraili Daronkola (Thu Feb 28 2019 - 08:24:01 PST)
- Re: [AMBER] alchemical_analysis accuratefreeenergy.gmail.com (Thu Feb 28 2019 - 10:55:21 PST)

Amber Archive Feb 2019 by thread