Amber Archive Feb 2021: by author

accuratefreeenergy.gmail.com
- Re: [AMBER] GPU TI PROBLEM (Fri Feb 26 2021 - 10:07:32 PST)
- Re: [AMBER] GPU TI PROBLEM (Thu Feb 25 2021 - 06:12:48 PST)
Adrian Roitberg
- Re: [AMBER] Steered MD (Fri Feb 26 2021 - 08:14:12 PST)
- Re: [AMBER] Steered MD (Thu Feb 25 2021 - 12:22:18 PST)
- Re: [AMBER] maximum no of atoms for simulation (Wed Feb 10 2021 - 14:29:09 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Tue Feb 09 2021 - 07:37:35 PST)
Alain Arsene
- [AMBER] AmberTools20 parallel test errors (Thu Feb 25 2021 - 02:53:50 PST)
Alan
- Re: [AMBER] Acpype error: Timed out process killed (Mon Feb 22 2021 - 12:18:46 PST)
- Re: [AMBER] multi source calls in tleap (Sun Feb 14 2021 - 23:45:30 PST)
- [AMBER] multi source calls in tleap (Sun Feb 07 2021 - 11:50:12 PST)
- [AMBER] About changes in frcmod.parmbsc0 (Sat Feb 06 2021 - 00:12:55 PST)
Alysia Mandato
- Re: [AMBER] tLeap, Fatal: Atom does not have a type (Mon Feb 15 2021 - 13:17:10 PST)
- [AMBER] tLeap, Fatal: Atom does not have a type (Fri Feb 12 2021 - 11:08:52 PST)
Athena N
- [AMBER] Stacking energy calculation (Sat Feb 20 2021 - 00:52:04 PST)
Ayesha Fatima
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sun Feb 28 2021 - 01:38:34 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sat Feb 27 2021 - 22:56:56 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sat Feb 27 2021 - 02:38:36 PST)
- [AMBER] atom number difference in topology and simulated trajectory (Sat Feb 27 2021 - 00:10:20 PST)
- Re: [AMBER] Non zero ligand warning (Sun Jan 31 2021 - 08:41:24 PST)
- Re: [AMBER] Non zero ligand warning (Sun Jan 31 2021 - 08:12:55 PST)
Brian Radak
- Re: [AMBER] Sufficiently equilibrated or not (Sun Feb 21 2021 - 08:29:07 PST)
Carlos Simmerling
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Feb 25 2021 - 13:32:10 PST)
- Re: [AMBER] Steered MD (Thu Feb 25 2021 - 12:26:58 PST)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Feb 25 2021 - 09:15:54 PST)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Feb 25 2021 - 09:01:46 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Mon Feb 22 2021 - 10:00:49 PST)
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 03:48:01 PST)
- Re: [AMBER] Why do trajectories get corrupted? (Sun Feb 21 2021 - 08:31:42 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sun Feb 21 2021 - 08:29:37 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sun Feb 21 2021 - 05:58:27 PST)
- Re: [AMBER] Why do trajectories get corrupted? (Sun Feb 21 2021 - 05:51:19 PST)
- Re: [AMBER] Why do trajectories get corrupted? (Sun Feb 21 2021 - 05:17:40 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sun Feb 21 2021 - 04:08:13 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 15:56:24 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 12:35:24 PST)
- Re: [AMBER] tip3p water model in amber14 (Fri Feb 19 2021 - 09:33:45 PST)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions (Fri Feb 19 2021 - 07:30:49 PST)
- Re: [AMBER] High value for force constant is acceptable? (Thu Feb 18 2021 - 05:39:02 PST)
- Re: [AMBER] tLeap, Fatal: Atom does not have a type (Mon Feb 15 2021 - 13:23:31 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Tue Feb 09 2021 - 03:35:27 PST)
- Re: [AMBER] RAMD question (Xiaodong Wu) (Fri Feb 05 2021 - 03:39:34 PST)
- Re: [AMBER] Prmtop missing resid and resname info (Fri Feb 05 2021 - 03:38:44 PST)
- Re: [AMBER] GPU power usage drop for igb = 8 compared to igb = 2 (Wed Feb 03 2021 - 15:19:47 PST)
- Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem (Wed Feb 03 2021 - 09:17:26 PST)
- Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem (Wed Feb 03 2021 - 05:17:30 PST)
- Re: [AMBER] Random seed for restart files that have velocities? (Tue Feb 02 2021 - 18:42:50 PST)
- Re: [AMBER] Found bug in sander in restarting SGLD replica exchange runs (Tue Feb 02 2021 - 17:03:28 PST)
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! (Mon Feb 01 2021 - 15:27:34 PST)
- Re: [AMBER] how does tleap choose missing side chain conformations (Mon Feb 01 2021 - 03:23:01 PST)
Cato, Lee
- [AMBER] help with cpptraj error (segmentation fault) (Thu Feb 25 2021 - 10:12:20 PST)
Cavender, Chapin
- Re: [AMBER] OPC monovalent ion parameters (Sat Feb 13 2021 - 11:50:31 PST)
Ch Bilal
- [AMBER] ModuleNotFoundError: No module named 'MMPBSA_mods' (Wed Feb 03 2021 - 00:35:26 PST)
Charles Lin
- Re: [AMBER] RAMD question (Xiaodong Wu) (Fri Feb 05 2021 - 10:59:28 PST)
- Re: [AMBER] RAMD question (Xiaodong Wu) (Fri Feb 05 2021 - 10:53:31 PST)
Charo del Genio
- [AMBER] CPPTRAJ cannot open RXSGLD trajectories out of the box (Sun Feb 07 2021 - 05:59:33 PST)
- [AMBER] Solution to the replica exchange SGLD restart bug (Mon Feb 01 2021 - 13:40:41 PST)
Christina Bergonzo
- Re: [AMBER] CPPTRAJ - KMeans Value for K (Tue Feb 09 2021 - 05:45:22 PST)
Click, Timothy Howard
- Re: [AMBER] Calculating forces (Fri Feb 26 2021 - 07:27:20 PST)
Daniel Roe
- Re: [AMBER] cpptraj CMAP flag issue with charmm-gui parm7 files (Fri Feb 26 2021 - 17:50:17 PST)
- Re: [AMBER] Calculating pairwise RMSD of two proteins (Fri Feb 26 2021 - 12:36:12 PST)
- Re: [AMBER] Molecule volume in cpptraj? (Fri Feb 26 2021 - 06:44:45 PST)
- Re: [AMBER] help with cpptraj error (segmentation fault) (Thu Feb 25 2021 - 10:32:28 PST)
- Re: [AMBER] Calculating forces (Thu Feb 25 2021 - 02:32:52 PST)
- Re: [AMBER] CPPTRAJ mindist comand (Wed Feb 24 2021 - 04:15:26 PST)
- Re: [AMBER] Why do trajectories get corrupted? (Tue Feb 23 2021 - 11:26:33 PST)
- Re: [AMBER] single strand RNA parameters (Thu Feb 11 2021 - 12:38:25 PST)
- Re: [AMBER] single strand RNA parameters (Thu Feb 11 2021 - 10:08:41 PST)
- Re: [AMBER] single strand RNA parameters (Thu Feb 11 2021 - 06:28:49 PST)
- Re: [AMBER] CPPTRAJ cannot open RXSGLD trajectories out of the box (Sun Feb 07 2021 - 06:38:11 PST)
- Re: [AMBER] AMBER HREMD replica trajectory (Wed Feb 03 2021 - 06:46:39 PST)
David A Case
- Re: [AMBER] tip3p water model in amber14 (Fri Feb 26 2021 - 14:13:38 PST)
- Re: [AMBER] dimer shifts under NPT ensemble (Thu Feb 25 2021 - 18:02:24 PST)
- Re: [AMBER] tip3p water model in amber14 (Thu Feb 25 2021 - 17:54:45 PST)
- Re: [AMBER] tip3p water model in amber14 (Thu Feb 25 2021 - 12:04:35 PST)
- Re: [AMBER] Amber18 + Ambertools20 (Thu Feb 25 2021 - 08:49:15 PST)
- Re: [AMBER] AmberTools20 parallel test errors (Thu Feb 25 2021 - 04:20:18 PST)
- Re: [AMBER] How to recompile AmberTools (Wed Feb 24 2021 - 13:06:38 PST)
- Re: [AMBER] Problem with pmemd.MPI (Wed Feb 24 2021 - 04:24:52 PST)
- Re: [AMBER] Problem with pmemd.MPI (Tue Feb 23 2021 - 04:41:57 PST)
- Re: [AMBER] Acpype error: Timed out process killed (Mon Feb 22 2021 - 10:22:21 PST)
- Re: [AMBER] Odd number of electrons (Mon Feb 22 2021 - 10:19:50 PST)
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 10:13:13 PST)
- Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom (Mon Feb 22 2021 - 05:02:55 PST)
- Re: [AMBER] IEEE_OVERFLOW_FLAG (Mon Feb 22 2021 - 04:56:33 PST)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions (Mon Feb 22 2021 - 04:54:33 PST)
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 04:50:26 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 14:09:26 PST)
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center (Sat Feb 20 2021 - 06:24:25 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 06:16:08 PST)
- Re: [AMBER] query regarding heme forcefield parameters (Fri Feb 19 2021 - 07:38:35 PST)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions (Fri Feb 19 2021 - 07:33:25 PST)
- Re: [AMBER] Making sense of tip3p.frcmod (Thu Feb 18 2021 - 18:24:39 PST)
- Re: [AMBER] High value for force constant is acceptable? (Thu Feb 18 2021 - 05:25:37 PST)
- Re: [AMBER] Amber20 GPU plus PLUMED (Thu Feb 18 2021 - 05:24:04 PST)
- Re: [AMBER] Help with installation (Thu Feb 18 2021 - 05:16:32 PST)
- Re: [AMBER] error with AMBER installation (Wed Feb 17 2021 - 11:20:12 PST)
- Re: [AMBER] Altering ligand positions in Xleap (Tue Feb 16 2021 - 05:17:44 PST)
- Re: [AMBER] tLeap, Fatal: Atom does not have a type (Tue Feb 16 2021 - 05:13:40 PST)
- Re: [AMBER] Using divalent ions in LEaP (Sat Feb 13 2021 - 06:10:55 PST)
- Re: [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? (Fri Feb 12 2021 - 04:07:53 PST)
- Re: [AMBER] Questions about loading FF02 and MMGBSA (Thu Feb 11 2021 - 04:42:14 PST)
- Re: [AMBER] Probmlems compiling under macOS (Tue Feb 09 2021 - 05:30:57 PST)
- Re: [AMBER] Probmlems compiling under macOS (Mon Feb 08 2021 - 06:58:30 PST)
- Re: [AMBER] multi source calls in tleap (Mon Feb 08 2021 - 06:50:07 PST)
- Re: [AMBER] polarizable FF in amber18 or 20 (Sun Feb 07 2021 - 07:34:01 PST)
- Re: [AMBER] Fix the dihedral angle during the simulation (Sun Feb 07 2021 - 05:46:06 PST)
- Re: [AMBER] suggestion of a patch for building MPI version of MMPBSA.py (Sat Feb 06 2021 - 05:49:42 PST)
- Re: [AMBER] About changes in frcmod.parmbsc0 (Sat Feb 06 2021 - 05:25:31 PST)
- Re: [AMBER] suggestion of a patch for building MPI version of MMPBSA.py (Fri Feb 05 2021 - 11:53:12 PST)
- Re: [AMBER] Fwd: unreadable *.mdcrd (Fri Feb 05 2021 - 05:51:40 PST)
- Re: [AMBER] decompose running error (Fri Feb 05 2021 - 05:45:06 PST)
- Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem (Wed Feb 03 2021 - 06:00:45 PST)
- Re: [AMBER] ModuleNotFoundError: No module named 'MMPBSA_mods' (Wed Feb 03 2021 - 05:47:56 PST)
- Re: [AMBER] Random seed for restart files that have velocities? (Wed Feb 03 2021 - 05:44:00 PST)
- Re: [AMBER] error while building Amber20 with Intel + CUDA (Tue Feb 02 2021 - 13:27:40 PST)
- Re: [AMBER] QM/MM in Amber (Tue Feb 02 2021 - 05:30:39 PST)
- Re: [AMBER] erro free energy calculation (Mon Feb 01 2021 - 04:55:18 PST)
- Re: [AMBER] configure_mpich error (Mon Feb 01 2021 - 04:47:52 PST)
David Cerutti
- Re: [AMBER] [lsimon.usal.es: MDGX charge fitting with some charges fixed or restrained] (Wed Feb 24 2021 - 05:25:12 PST)
Delwakkada Liyanage, Senal Dinuka
- Re: [AMBER] Sufficiently equilibrated or not (Mon Feb 22 2021 - 09:27:01 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 18:33:52 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 11:58:31 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 11:46:01 PST)
- [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 11:17:14 PST)
Demian Riccardi
- [AMBER] GPU power usage drop for igb = 8 compared to igb = 2 (Wed Feb 03 2021 - 14:48:45 PST)
divyabharathi korlepara
- Re: [AMBER] Odd number of electrons (Tue Feb 23 2021 - 20:43:25 PST)
- [AMBER] Odd number of electrons (Mon Feb 22 2021 - 05:57:27 PST)
Domenico Marson
- [AMBER] Amber20 GPU plus PLUMED (Fri Feb 12 2021 - 04:02:46 PST)
Elvis A F Martis
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sun Feb 28 2021 - 03:01:27 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sat Feb 27 2021 - 23:07:30 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sat Feb 27 2021 - 03:26:21 PST)
- Re: [AMBER] atom number difference in topology and simulated trajectory (Sat Feb 27 2021 - 01:46:44 PST)
- Re: [AMBER] Fwd: unreadable *.mdcrd (Fri Feb 05 2021 - 17:01:30 PST)
Gabriel Jara
- [AMBER] theoretical doubt about TI (Wed Feb 17 2021 - 05:54:14 PST)
Gordon Richard Chalmers
- Re: [AMBER] Sufficiently equilibrated or not (Sun Feb 21 2021 - 09:00:45 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sun Feb 21 2021 - 08:12:59 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 22:24:29 PST)
- Re: [AMBER] Altering ligand positions in Xleap (Tue Feb 16 2021 - 05:20:46 PST)
Gustaf Olsson
- Re: [AMBER] How to recompile AmberTools (Thu Feb 25 2021 - 00:02:54 PST)
- Re: [AMBER] How to recompile AmberTools (Wed Feb 24 2021 - 00:11:14 PST)
- Re: [AMBER] Odd number of electrons (Wed Feb 24 2021 - 00:08:47 PST)
- Re: [AMBER] Probmlems compiling under macOS (Wed Feb 10 2021 - 02:32:47 PST)
- Re: [AMBER] Probmlems compiling under macOS (Tue Feb 09 2021 - 07:42:17 PST)
- Re: [AMBER] Probmlems compiling under macOS (Tue Feb 09 2021 - 00:17:36 PST)
- Re: [AMBER] Probmlems compiling under macOS (Mon Feb 08 2021 - 23:50:07 PST)
- Re: [AMBER] Probmlems compiling under macOS (Mon Feb 08 2021 - 02:26:48 PST)
Gustavo Seabra
- Re: [AMBER] Molecule volume in cpptraj? (Fri Feb 26 2021 - 13:01:02 PST)
- [AMBER] Molecule volume in cpptraj? (Thu Feb 25 2021 - 10:56:10 PST)
Holly Freedman
- [AMBER] TI with igb. = 6 (Mon Feb 08 2021 - 09:47:02 PST)
jacob wick
- [AMBER] Fwd: GaMD output (gamd.log) file analysis (Sun Feb 21 2021 - 00:51:31 PST)
- [AMBER] GaMD output (gamd.log) file analysis (Fri Feb 19 2021 - 01:08:20 PST)
Jason Swails
- Re: [AMBER] Error while setting up constant pH MD simulations (Fri Feb 26 2021 - 05:44:50 PST)
Jiri Sponer
- Re: [AMBER] single strand RNA parameters (Thu Feb 11 2021 - 10:59:27 PST)
- Re: [AMBER] single strand RNA parameters (Thu Feb 11 2021 - 07:39:45 PST)
Jorge Iulek
- Re: [AMBER] single strand RNA parameters (Sat Feb 13 2021 - 01:59:39 PST)
- Re: [AMBER] single strand RNA parameters (Sat Feb 13 2021 - 02:03:10 PST)
- Re: [AMBER] single strand RNA parameters (Thu Feb 11 2021 - 08:41:54 PST)
- [AMBER] single strand RNA parameters (Wed Feb 10 2021 - 09:41:56 PST)
Junmei Wang
- Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom (Mon Feb 08 2021 - 06:26:44 PST)
Karl Kirschner
- Re: [AMBER] High value for force constant is acceptable? (Fri Feb 19 2021 - 10:39:29 PST)
Kenneth Huang
- Re: [AMBER] tLeap, Fatal: Atom does not have a type (Fri Feb 12 2021 - 14:32:32 PST)
- Re: [AMBER] Using divalent ions in LEaP (Fri Feb 12 2021 - 14:23:30 PST)
- Re: [AMBER] leap hangs on dihedral in frcmod? (Fri Feb 12 2021 - 14:09:22 PST)
- [AMBER] leap hangs on dihedral in frcmod? (Thu Feb 11 2021 - 14:08:58 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Tue Feb 09 2021 - 08:15:35 PST)
- Re: [AMBER] Prmtop missing resid and resname info (Fri Feb 05 2021 - 07:21:00 PST)
Lachele Foley
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 23:04:17 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 13:30:56 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 11:55:15 PST)
- Re: [AMBER] Sufficiently equilibrated or not (Sat Feb 20 2021 - 11:41:24 PST)
Li,Haoxi
- [AMBER] Multiple Harmonic Restraints (Tue Feb 23 2021 - 08:44:27 PST)
Liao
- Re: [AMBER] Random seed for restart files that have velocities? (Tue Feb 02 2021 - 19:58:02 PST)
- [AMBER] Random seed for restart files that have velocities? (Tue Feb 02 2021 - 18:15:57 PST)
liu junjun
- Re: [AMBER] Bug in the Mol2 format: space converted into a new oxygen atom (Thu Feb 04 2021 - 12:22:25 PST)
Luis Simon
- Re: [AMBER] [lsimon.usal.es: MDGX charge fitting with some charges fixed or restrained] (Wed Feb 24 2021 - 09:20:24 PST)
- [AMBER] MDGX charge fitting with some charges fixed or restrained (Wed Feb 24 2021 - 00:34:30 PST)
- [AMBER] mdgx ipolQ charges of a charged residue (Mon Feb 08 2021 - 01:23:05 PST)
- Re: [AMBER] problem deriving implicit polarised charges charges with mdgx (Sun Feb 07 2021 - 13:29:15 PST)
- [AMBER] problem deriving implicit polarised charges charges with mdgx (Fri Feb 05 2021 - 13:10:59 PST)
Maria Nagan
- Re: [AMBER] Why do trajectories get corrupted? (Sat Feb 20 2021 - 09:09:34 PST)
- Re: [AMBER] Parameters for Iron Oxide (Fri Feb 12 2021 - 14:49:07 PST)
- Re: [AMBER] tLeap, Fatal: Atom does not have a type (Fri Feb 12 2021 - 14:41:58 PST)
- Re: [AMBER] Using divalent ions in LEaP (Fri Feb 12 2021 - 14:14:44 PST)
- Re: [AMBER] Using divalent ions in LEaP (Fri Feb 12 2021 - 13:45:32 PST)
- Re: [AMBER] Hydrogen bond analysis tutorial (Tue Feb 02 2021 - 11:21:07 PST)
Matias Machado
- Re: [AMBER] Membrane protein-ligand simulation - application of multiple FF - compatibility and reliability (Mon Feb 22 2021 - 17:16:54 PST)
- Re: [AMBER] OPC monovalent ion parameters (Mon Feb 22 2021 - 11:16:46 PST)
- Re: [AMBER] multi source calls in tleap (Mon Feb 22 2021 - 11:09:00 PST)
- Re: [AMBER] leap hangs on dihedral in frcmod? (Fri Feb 12 2021 - 04:13:31 PST)
- Re: [AMBER] multi source calls in tleap (Thu Feb 11 2021 - 05:52:23 PST)
Matthew Guberman-Pfeffer
- [AMBER] MMPBSA, signal SIGSEGV failure (Thu Feb 25 2021 - 08:11:29 PST)
- Re: [AMBER] How to recompile AmberTools (Wed Feb 24 2021 - 12:04:58 PST)
- [AMBER] How to recompile AmberTools (Tue Feb 23 2021 - 21:41:46 PST)
- [AMBER] Parameters for Iron Oxide (Thu Feb 11 2021 - 02:42:10 PST)
- [AMBER] Questions about loading FF02 and MMGBSA (Wed Feb 10 2021 - 18:40:46 PST)
Ming Tang
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Feb 25 2021 - 14:25:49 PST)
- Re: [AMBER] Apply Lennar-Jones potential between small molecules (Thu Feb 25 2021 - 13:17:00 PST)
- [AMBER] Apply Lennar-Jones potential between small molecules (Wed Feb 24 2021 - 14:51:46 PST)
mish
- Re: [AMBER] Disparities between dG solv from GB and PB Models (Sat Feb 13 2021 - 15:23:24 PST)
- [AMBER] Disparities between dG solv from GB and PB Models (Sat Feb 13 2021 - 13:55:33 PST)
Mohammad Alaraby
- [AMBER] error with AMBER installation (Wed Feb 17 2021 - 04:50:46 PST)
Mudrovcic, Korana
- [AMBER] IEEE_OVERFLOW_FLAG (Tue Feb 09 2021 - 06:22:56 PST)
neildancer.sina.com
- Re: [AMBER] Thermodynamic integration for protein-protein interactions (Mon Feb 22 2021 - 05:32:14 PST)
- Re: [AMBER] Thermodynamic integration for protein-protein interactions (Fri Feb 19 2021 - 08:02:29 PST)
Nikolay N. Kuzmich
- Re: [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? (Fri Feb 12 2021 - 08:57:35 PST)
- [AMBER] Testing pmemd.cuda.MPI - how many failed file comparisons are innocuous? (Fri Feb 12 2021 - 01:44:56 PST)
- Re: [AMBER] configure_mpich error (Tue Feb 02 2021 - 08:29:49 PST)
- [AMBER] configure_mpich error (Mon Feb 01 2021 - 03:36:23 PST)
Nisha Amarnath Jonniya
- Re: [AMBER] decompose running error (Mon Feb 08 2021 - 21:31:45 PST)
- Re: [AMBER] decompose running error (Mon Feb 08 2021 - 21:25:41 PST)
- [AMBER] decompose running error (Thu Feb 04 2021 - 22:23:23 PST)
Patil Pranita Uttamrao
- [AMBER] query regarding heme forcefield parameters (Fri Feb 19 2021 - 02:07:27 PST)
Paul, Austin
- [AMBER] Making sense of tip3p.frcmod (Thu Feb 18 2021 - 16:18:12 PST)
Pengfei Li
- Re: [AMBER] Sufficiently equilibrated or not (Fri Feb 26 2021 - 15:31:15 PST)
- Re: [AMBER] ZAFF force field (Fri Feb 26 2021 - 15:12:51 PST)
- Re: [AMBER] OPC monovalent ion parameters (Fri Feb 26 2021 - 15:08:06 PST)
- Re: [AMBER] OPC monovalent ion parameters (Mon Feb 15 2021 - 08:54:28 PST)
- Re: [AMBER] OPC monovalent ion parameters (Sat Feb 13 2021 - 15:58:03 PST)
Petr Stadlbauer
- Re: [AMBER] Preparation of i-Motif structures (Wed Feb 10 2021 - 09:34:15 PST)
Pinky Mazumder
- Re: [AMBER] Steered MD (Sat Feb 27 2021 - 06:37:50 PST)
- Re: [AMBER] Steered MD (Sat Feb 27 2021 - 06:29:17 PST)
- Re: [AMBER] Steered MD (Fri Feb 26 2021 - 07:43:20 PST)
- Re: [AMBER] Steered MD (Thu Feb 25 2021 - 16:13:19 PST)
- [AMBER] Steered MD (Thu Feb 25 2021 - 12:14:30 PST)
- Re: [AMBER] maximum no of atoms for simulation (Wed Feb 10 2021 - 15:01:44 PST)
- [AMBER] maximum no of atoms for simulation (Wed Feb 10 2021 - 14:11:14 PST)
- Re: [AMBER] max pairlist cutoff must be less than unit cell max sphere radius! (Mon Feb 01 2021 - 14:27:11 PST)
Piotr Fajer
- Re: [AMBER] CPPTRAJ - KMeans Value for K (Mon Feb 08 2021 - 10:15:33 PST)
Pranjal Bhuyan
- Re: [AMBER] Problem with pmemd.MPI (Tue Feb 23 2021 - 21:45:21 PST)
- [AMBER] Problem with pmemd.MPI (Tue Feb 23 2021 - 02:36:56 PST)
Prasanth G, Research Scholar
- [AMBER] Membrane protein-ligand simulation - application of multiple FF - compatibility and reliability (Tue Feb 16 2021 - 09:49:09 PST)
Qinghua Liao
- Re: [AMBER] dimer shifts under NPT ensemble (Fri Feb 26 2021 - 15:25:49 PST)
- Re: [AMBER] dimer shifts under NPT ensemble (Fri Feb 26 2021 - 14:58:29 PST)
- Re: [AMBER] dimer shifts under NPT ensemble (Thu Feb 25 2021 - 23:59:59 PST)
- Re: [AMBER] dimer shifts under NPT ensemble (Thu Feb 25 2021 - 23:31:16 PST)
- [AMBER] dimer shifts under NPT ensemble (Thu Feb 25 2021 - 16:04:23 PST)
Rafał Bachorz
- [AMBER] Amber18 + Ambertools20 (Thu Feb 25 2021 - 06:04:39 PST)
raissa.conceicao.bol.com.br
- Re: [AMBER] tLeap, Fatal: Atom does not have a type (Tue Feb 16 2021 - 03:40:18 PST)
Ray Luo
- Re: [AMBER] MMPBSA, signal SIGSEGV failure (Thu Feb 25 2021 - 09:09:36 PST)
- Re: [AMBER] Disparities between dG solv from GB and PB Models (Sat Feb 13 2021 - 14:21:27 PST)
Renato Araujo
- [AMBER] Hydrogen bond analysis tutorial (Tue Feb 02 2021 - 11:13:29 PST)
- [AMBER] erro free energy calculation (Mon Feb 01 2021 - 03:56:21 PST)
Richard Kullmann
- [AMBER] CPPTRAJ mindist comand (Wed Feb 24 2021 - 03:07:41 PST)
- [AMBER] AMBER HREMD replica trajectory (Wed Feb 03 2021 - 06:34:11 PST)
Rinsha Chk
- Re: [AMBER] High value for force constant is acceptable? (Thu Feb 18 2021 - 22:52:37 PST)
- [AMBER] High value for force constant is acceptable? (Thu Feb 11 2021 - 03:50:58 PST)
- Re: [AMBER] Fix the dihedral angle during the simulation (Sun Feb 07 2021 - 05:48:52 PST)
- [AMBER] Fix the dihedral angle during the simulation (Sun Feb 07 2021 - 01:06:16 PST)
Sadaf Rani
- [AMBER] Calculating pairwise RMSD of two proteins (Fri Feb 26 2021 - 10:31:20 PST)
- [AMBER] Fwd: MMPBSA Error (Fri Feb 12 2021 - 05:13:17 PST)
Sam Walsworth (Researcher)
- Re: [AMBER] Using divalent ions in LEaP (Fri Feb 12 2021 - 14:04:26 PST)
- [AMBER] Using divalent ions in LEaP (Fri Feb 12 2021 - 13:30:36 PST)
SATYAJIT KHATUA
- Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center (Tue Feb 23 2021 - 21:20:23 PST)
- [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center (Fri Feb 19 2021 - 09:56:53 PST)
Seibold, Steve Allan
- [AMBER] CUDE upgrade question and AMBER (Thu Feb 04 2021 - 10:00:30 PST)
Shilpa Gupta
- [AMBER] Acpype error: Timed out process killed (Mon Feb 22 2021 - 07:24:04 PST)
Sruthi Sudhakar
- [AMBER] Regarding restarting of Gaussian Accelerated MD. (Mon Feb 22 2021 - 20:39:04 PST)
- [AMBER] Altering ligand positions in Xleap (Tue Feb 16 2021 - 02:44:10 PST)
- [AMBER] Preparation of i-Motif structures (Tue Feb 09 2021 - 13:30:41 PST)
Susan Chacko
- Re: [AMBER] error while building Amber20 with Intel + CUDA (Tue Feb 02 2021 - 13:33:46 PST)
- [AMBER] error while building Amber20 with Intel + CUDA (Tue Feb 02 2021 - 12:20:43 PST)
Swisher, Justin S
- Re: [AMBER] tip3p water model in amber14 (Fri Feb 26 2021 - 08:59:07 PST)
- Re: [AMBER] tip3p water model in amber14 (Thu Feb 25 2021 - 16:29:06 PST)
- Re: [AMBER] tip3p water model in amber14 (Thu Feb 25 2021 - 10:36:55 PST)
- [AMBER] tip3p water model in amber14 (Fri Feb 19 2021 - 08:48:24 PST)
Thomas Cheatham
- Re: [AMBER] dimer shifts under NPT ensemble (Thu Feb 25 2021 - 19:44:07 PST)
- Re: [AMBER] OPC monovalent ion parameters (Sat Feb 13 2021 - 20:33:41 PST)
- Re: [AMBER] About changes in frcmod.parmbsc0 (Sat Feb 06 2021 - 00:28:39 PST)
Thomas Gaillard
- Re: [AMBER] dimer shifts under NPT ensemble (Fri Feb 26 2021 - 04:41:54 PST)
- Re: [AMBER] Multiple Harmonic Restraints (Tue Feb 23 2021 - 09:20:41 PST)
Tomasz Miernik
- Re: [AMBER] Fwd: unreadable *.mdcrd (Fri Feb 05 2021 - 14:07:04 PST)
Umut Çağan Uçar
- Re: [AMBER] GPU TI PROBLEM (Fri Feb 26 2021 - 00:46:09 PST)
- [AMBER] GPU TI PROBLEM (Thu Feb 25 2021 - 05:36:25 PST)
Vaibhav Dixit
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 20:50:12 PST)
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 07:30:42 PST)
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 03:58:36 PST)
- Re: [AMBER] MAXPR error in sander sp job (Mon Feb 22 2021 - 02:36:40 PST)
- [AMBER] case studies of MD based drug discovery (Sun Feb 21 2021 - 05:05:28 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 22:58:02 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 16:26:31 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 15:31:38 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 06:49:52 PST)
- Re: [AMBER] MAXPR error in sander sp job (Sat Feb 20 2021 - 05:10:05 PST)
- [AMBER] MAXPR error in sander sp job (Fri Feb 19 2021 - 20:06:57 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Wed Feb 10 2021 - 02:51:53 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Wed Feb 10 2021 - 02:41:39 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Tue Feb 09 2021 - 04:14:06 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Mon Feb 08 2021 - 20:39:57 PST)
- [AMBER] polarizable FF in amber18 or 20 (Sun Feb 07 2021 - 02:01:37 PST)
- Re: [AMBER] curiosity about sander reading a traj being written by GPU code (Sat Feb 06 2021 - 05:15:31 PST)
- [AMBER] curiosity about sander reading a traj being written by GPU code (Fri Feb 05 2021 - 08:39:10 PST)
- Re: [AMBER] how does tleap choose missing side chain conformations (Tue Feb 02 2021 - 03:07:48 PST)
- [AMBER] how does tleap choose missing side chain conformations (Sun Jan 31 2021 - 19:51:51 PST)
Victoria E Hill
- Re: [AMBER] Why do trajectories get corrupted? (Sun Feb 21 2021 - 06:12:56 PST)
- Re: [AMBER] Why do trajectories get corrupted? (Sun Feb 21 2021 - 05:36:06 PST)
- Re: [AMBER] Why do trajectories get corrupted? (Sun Feb 21 2021 - 04:58:10 PST)
- [AMBER] Why do trajectories get corrupted? (Sat Feb 20 2021 - 08:36:44 PST)
Violeta Burns Casamayor
- [AMBER] Prmtop missing resid and resname info (Fri Feb 05 2021 - 01:55:31 PST)
Vitor Rabelo
- [AMBER] MMPBSA.py Error: Could not import Amber Python modules (Thu Feb 04 2021 - 11:08:49 PST)
Wesley Michael Botello-Smith
- [AMBER] cpptraj CMAP flag issue with charmm-gui parm7 files (Fri Feb 26 2021 - 13:40:53 PST)
WW
- [AMBER] Thermodynamic integration for protein-protein interactions (Fri Feb 19 2021 - 06:35:25 PST)
Yashraj Kulkarni
- [AMBER] Error while setting up constant pH MD simulations (Sat Feb 13 2021 - 06:55:57 PST)
Yoshitaka Moriwaki
- Re: [AMBER] suggestion of a patch for building MPI version of MMPBSA.py (Sat Feb 06 2021 - 02:18:28 PST)
- [AMBER] suggestion of a patch for building MPI version of MMPBSA.py (Fri Feb 05 2021 - 09:43:17 PST)
Åke Sandgren
- Re: [AMBER] IEEE_OVERFLOW_FLAG (Mon Feb 22 2021 - 05:52:17 PST)
Женя Елизарова
- Re: [AMBER] QM/MM in Amber (Tue Feb 02 2021 - 01:31:05 PST)
- [AMBER] QM/MM in Amber (Tue Feb 02 2021 - 01:25:23 PST)
Игорь Злотников
- [AMBER] Fwd: Prepare pbd file modified cyclodextrin (Sun Feb 14 2021 - 04:16:16 PST)
- [AMBER] Prepare pbd file modified cyclodextrin (Thu Feb 04 2021 - 00:52:45 PST)
吴晓东
- [AMBER] RAMD simulation (Xiaodong) (Sat Feb 06 2021 - 23:00:28 PST)
- [AMBER] RAMD question (Xiaodong Wu) (Fri Feb 05 2021 - 01:19:57 PST)
李明玉
- [AMBER] External electric fields cannot be used when npt > 0 (Fri Feb 05 2021 - 09:19:49 PST)
- Re: [AMBER] Nudged Elastic Band solvent choice and initial heating problem (Wed Feb 03 2021 - 09:01:09 PST)
- [AMBER] Nudged Elastic Band solvent choice and initial heating problem (Wed Feb 03 2021 - 04:12:45 PST)

Amber Archive Feb 2021 by author