Amber Archive Feb 2019: by author

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

Amber Archive Feb 2019 by author