Amber Archive Mar 2018: by author

Aashish Bhatt
- Re: [AMBER] Regarding PLP and Lys parameter (Thu Mar 08 2018 - 06:38:57 PST)
- [AMBER] Regarding PLP and Lys parameter (Sat Mar 03 2018 - 03:35:05 PST)
Abdul-Rashid III Sampaco
- Re: [AMBER] disulfide bridge -reg (Mon Mar 05 2018 - 01:58:55 PST)
ABEL Stephane
- Re: [AMBER] Question about Parmbsc1 Force Field (Thu Mar 01 2018 - 08:32:54 PST)
Abhilash J
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Thu Mar 08 2018 - 04:31:25 PST)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Wed Mar 07 2018 - 02:37:22 PST)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Tue Mar 06 2018 - 05:53:01 PST)
Ahmed Mashaly
- Re: [AMBER] upper limit of water with solvateBox (Wed Mar 21 2018 - 07:07:18 PDT)
Andreas Tosstorff
- Re: [AMBER] Suitability of amber force fields for very low temperature MD simulations? (Sun Mar 11 2018 - 00:31:45 PST)
Angelo Rossi
- Re: [AMBER] Help With tinker_to_amber (Sun Mar 11 2018 - 14:48:15 PDT)
- [AMBER] Help With tinker_to_amber (Sat Mar 10 2018 - 10:49:03 PST)
ASMITA SEN
- Re: [AMBER] vlimit exceeded for step (Fri Mar 09 2018 - 12:11:00 PST)
- [AMBER] vlimit exceeded for step (Thu Mar 01 2018 - 05:32:53 PST)
- [AMBER] vlimit exceeded for step (Thu Mar 01 2018 - 05:31:26 PST)
balaahme
- [AMBER] van der Waals interactions, electrostatic interactions and long-range corrections (Tue Mar 06 2018 - 12:37:42 PST)
Barış Kurt
- Re: [AMBER] When will you update this tutorial? (Fri Mar 09 2018 - 10:01:37 PST)
- Re: [AMBER] When will you update this tutorial? (Fri Mar 09 2018 - 09:58:26 PST)
- [AMBER] How to Convert gaussian force constant to Gaff? (Fri Mar 09 2018 - 08:02:05 PST)
- [AMBER] When will you update this tutorial? (Thu Mar 08 2018 - 06:04:12 PST)
- Re: [AMBER] How to Develop New Amber ForceField For Borons (Thu Mar 08 2018 - 05:58:25 PST)
- Re: [AMBER] reaidt.f problem (Sun Mar 04 2018 - 12:19:12 PST)
- Re: [AMBER] reaidt.f problem (Sun Mar 04 2018 - 12:11:35 PST)
- [AMBER] reaidt.f problem (Sat Mar 03 2018 - 14:50:40 PST)
- [AMBER] How to Develop New Amber ForceField For Borons (Sat Mar 03 2018 - 08:00:20 PST)
Beale, John
- Re: [AMBER] peptide and bilayer membrane simulations (Wed Mar 28 2018 - 02:41:50 PDT)
Carlos Simmerling
- Re: [AMBER] Sudden termination of the heating simulation with sander.MPI (Wed Mar 21 2018 - 05:52:51 PDT)
- [AMBER] Fwd: ACS COMP Boston awards deadline set (Tue Mar 13 2018 - 12:00:21 PDT)
- Re: [AMBER] Created a new atom named: (Sat Mar 03 2018 - 06:57:27 PST)
- Re: [AMBER] Created a new atom named: (Sat Mar 03 2018 - 06:27:58 PST)
- Re: [AMBER] created a new atom named (is an error or we can ignore it) (Sat Mar 03 2018 - 04:27:35 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Fri Mar 02 2018 - 14:51:06 PST)
- Re: [AMBER] Replica Exchange Cut > 999.0 - Necessitates Very Large Water Box? (Fri Mar 02 2018 - 14:49:41 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Thu Mar 01 2018 - 16:02:45 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Thu Mar 01 2018 - 16:02:16 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Thu Mar 01 2018 - 11:37:46 PST)
Carolin Berner
- [AMBER] Suitability of amber force fields for very low temperature MD simulations? (Wed Mar 07 2018 - 06:28:43 PST)
Charles-Alexandre Mattelaer
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 01:54:03 PST)
Chetna Tyagi
- Re: [AMBER] peptide and bilayer membrane simulations (Wed Mar 28 2018 - 08:54:51 PDT)
- Re: [AMBER] peptide and bilayer membrane simulations (Wed Mar 28 2018 - 02:46:39 PDT)
- [AMBER] peptide and bilayer membrane simulations (Wed Mar 28 2018 - 02:30:27 PDT)
- [AMBER] Problems with creating prmtop file from Charmm-GUI generated membrane system (Fri Mar 23 2018 - 03:55:00 PDT)
Chris Neale
- Re: [AMBER] Temperature-Based Replica Exchange: Number of Replicas (Wed Mar 21 2018 - 19:40:58 PDT)
Colin Brown
- [AMBER] PMEMD error: "Increase lin__limit in nb_pairlist.F90!!!" (Wed Mar 21 2018 - 07:42:01 PDT)
Cruzeiro,Vinicius Wilian D
- Re: [AMBER] Temperature-Based Replica Exchange: Number of Replicas (Wed Mar 21 2018 - 16:37:47 PDT)
- Re: [AMBER] constant pH simulations pemed.cuda (Thu Mar 08 2018 - 08:13:43 PST)
- Re: [AMBER] constant pH simulations pemed.cuda (Thu Mar 08 2018 - 07:48:02 PST)
Dai, Shuo
- Re: [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? (Fri Mar 23 2018 - 01:35:00 PDT)
- [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? (Thu Mar 22 2018 - 17:03:06 PDT)
Dan Gil
- Re: [AMBER] Question about Parmbsc1 Force Field (Fri Mar 02 2018 - 08:11:30 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field (Fri Mar 02 2018 - 07:24:45 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field (Thu Mar 01 2018 - 11:38:39 PST)
- [AMBER] Question about Parmbsc1 Force Field (Thu Mar 01 2018 - 07:09:53 PST)
Daniel Roe
- Re: [AMBER] cpptraj mask for hbond analysis (Fri Mar 30 2018 - 12:00:15 PDT)
- Re: [AMBER] Random seed reproducibility (Thu Mar 29 2018 - 06:17:41 PDT)
- Re: [AMBER] radial distribution function results (Tue Mar 13 2018 - 10:44:04 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 13 2018 - 09:34:30 PDT)
- Re: [AMBER] vlimit exceed error (Wed Mar 07 2018 - 10:07:09 PST)
- Re: [AMBER] can't compile (Wed Mar 07 2018 - 07:20:35 PST)
- Re: [AMBER] Question about using cpptraj - Script (Thu Mar 01 2018 - 03:30:53 PST)
daniele selli
- [AMBER] force-filed parametrization for dichloromethane (Wed Mar 21 2018 - 02:27:08 PDT)
David A Case
- Re: [AMBER] cpptraj mask for hbond analysis (Fri Mar 30 2018 - 11:58:07 PDT)
- Re: [AMBER] peptide and bilayer membrane simulations (Wed Mar 28 2018 - 06:56:07 PDT)
- Re: [AMBER] RMSD of individual sub unit of a protein complex. (Tue Mar 27 2018 - 15:15:14 PDT)
- Re: [AMBER] AMBER qualitatively compared to other packages (Tue Mar 27 2018 - 06:53:51 PDT)
- Re: [AMBER] Normal Mode Analysis - output from nmode? (Sun Mar 25 2018 - 08:13:41 PDT)
- Re: [AMBER] force-filed parametrization for dichloromethane (Fri Mar 23 2018 - 04:43:27 PDT)
- Re: [AMBER] pmemd.MPI with a single-entry group file? (Thu Mar 22 2018 - 18:52:30 PDT)
- Re: [AMBER] which geometry is used in am1bcc charge in antechamber in amber tools 17? (Thu Mar 22 2018 - 18:27:17 PDT)
- Re: [AMBER] prep to mol2 conversion (Thu Mar 22 2018 - 05:34:39 PDT)
- Re: [AMBER] Normal Mode Analysis in Amber (Thu Mar 22 2018 - 05:30:41 PDT)
- Re: [AMBER] pysmst code (Thu Mar 22 2018 - 05:21:00 PDT)
- Re: [AMBER] upper limit of water with solvateBox (Wed Mar 21 2018 - 07:35:21 PDT)
- Re: [AMBER] FE atom in PARMCHK.DAT file (Wed Mar 21 2018 - 07:32:20 PDT)
- Re: [AMBER] Fwd: error while installing AMBER for GPU (Tue Mar 20 2018 - 05:04:09 PDT)
- Re: [AMBER] Inconsistency with the number of counter ions required for neutralization (Mon Mar 19 2018 - 05:07:34 PDT)
- Re: [AMBER] TI simulation with a solvateCap: vlimit exceeded for step (Sun Mar 18 2018 - 12:00:28 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Sun Mar 18 2018 - 11:52:25 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl (Sat Mar 17 2018 - 06:28:30 PDT)
- Re: [AMBER] Query regarding minimization (Thu Mar 15 2018 - 04:50:02 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl (Wed Mar 14 2018 - 13:09:39 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 13:07:36 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 13:01:57 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Mon Mar 12 2018 - 10:24:15 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Mon Mar 12 2018 - 10:22:33 PDT)
- Re: [AMBER] Help With tinker_to_amber (Sat Mar 10 2018 - 12:57:07 PST)
- Re: [AMBER] vlimit exceeded for step (Fri Mar 09 2018 - 18:37:00 PST)
- Re: [AMBER] Regarding PLP and Lys parameter (Fri Mar 09 2018 - 05:06:58 PST)
- Re: [AMBER] When will you update this tutorial? (Fri Mar 09 2018 - 04:53:29 PST)
- Re: [AMBER] Suitability of amber force fields for very low temperature MD simulations? (Thu Mar 08 2018 - 11:10:56 PST)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Wed Mar 07 2018 - 05:52:36 PST)
- Re: [AMBER] amber16 sander can't read the box information from restart file (Wed Mar 07 2018 - 05:47:41 PST)
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Tue Mar 06 2018 - 15:53:39 PST)
- Re: [AMBER] van der Waals interactions, electrostatic interactions and long-range corrections (Tue Mar 06 2018 - 15:47:57 PST)
- Re: [AMBER] Amber16/AmberTools17 CUDA version (Mon Mar 05 2018 - 05:17:28 PST)
- Re: [AMBER] Creating gaff-suitable PDB file for SO2 (Mon Mar 05 2018 - 05:13:25 PST)
- Re: [AMBER] vlimit exceeded for step (Mon Mar 05 2018 - 05:09:28 PST)
- Re: [AMBER] Energy Calculations in Amber (Mon Mar 05 2018 - 05:04:30 PST)
- Re: [AMBER] disulfide bridge -reg (Mon Mar 05 2018 - 05:00:46 PST)
- Re: [AMBER] reaidt.f problem (Sun Mar 04 2018 - 05:41:43 PST)
- Re: [AMBER] Penalty score (Sat Mar 03 2018 - 14:29:40 PST)
- Re: [AMBER] created a new atom named (is an error or we can ignore it) (Sat Mar 03 2018 - 14:25:37 PST)
- Re: [AMBER] mm_pbsa.pl error (Sat Mar 03 2018 - 14:21:38 PST)
- Re: [AMBER] How to Develop New Amber ForceField For Borons (Sat Mar 03 2018 - 14:14:26 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Sat Mar 03 2018 - 14:07:35 PST)
- Re: [AMBER] Using center of mass dihedral restraints using PMEMD (Sat Mar 03 2018 - 06:06:47 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field (Sat Mar 03 2018 - 05:59:36 PST)
David Cerutti
- Re: [AMBER] MacOS pmemd.cuda (Thu Mar 29 2018 - 12:54:34 PDT)
- Re: [AMBER] How to Develop New Amber ForceField For Borons (Thu Mar 08 2018 - 09:40:10 PST)
David Sáez
- [AMBER] Turn of SMD after reaching target. (Fri Mar 02 2018 - 08:19:40 PST)
diego.soler.uam.es
- Re: [AMBER] Reaction Coordinate that is the Difference of two Distances (Wed Mar 14 2018 - 09:19:21 PDT)
- [AMBER] Reaction Coordinate that is the Difference of two Distances (Wed Mar 14 2018 - 08:24:01 PDT)
Dmitry Suplatov
- [AMBER] AMBER qualitatively compared to other packages (Fri Mar 23 2018 - 04:24:37 PDT)
Dr. M. Shahid
- Re: [AMBER] restraintmask, error in reading namelist cntrl (Wed Mar 14 2018 - 08:51:25 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 08:49:29 PDT)
Edjan Silva
- Re: [AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files (Fri Mar 23 2018 - 22:47:14 PDT)
- [AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files (Fri Mar 23 2018 - 10:16:30 PDT)
Eric Lang
- Re: [AMBER] Problem with cphstat (Mon Mar 12 2018 - 08:33:03 PDT)
- Re: [AMBER] Problem with cphstat (Mon Mar 12 2018 - 05:14:15 PDT)
- Re: [AMBER] constant pH simulations pemed.cuda (Thu Mar 08 2018 - 08:19:10 PST)
Feng Pan
- Re: [AMBER] center of mass restraint in pmemd.cuda (Mon Mar 26 2018 - 12:35:39 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 20:41:50 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 18:44:30 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 14:46:49 PDT)
- Re: [AMBER] NFE, PMD, and MULTI_RMSD questions (Wed Mar 14 2018 - 11:31:32 PDT)
- Re: [AMBER] Turn of SMD after reaching target. (Fri Mar 02 2018 - 15:55:55 PST)
FyD
- Re: [AMBER] How to Develop New Amber ForceField For Borons (Thu Mar 08 2018 - 11:14:44 PST)
- Re: [AMBER] How to Develop New Amber ForceField For Borons (Sat Mar 03 2018 - 22:44:48 PST)
George M. Giambasu
- Re: [AMBER] AMBER qualitatively compared to other packages (Wed Mar 28 2018 - 06:35:21 PDT)
George Tzotzos
- Re: [AMBER] Calculating ligand contribution is failing- MMPBSA method (Tue Mar 27 2018 - 03:15:05 PDT)
Goetz, Andreas
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account (Thu Mar 08 2018 - 12:01:57 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Sat Mar 03 2018 - 19:35:30 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Fri Mar 02 2018 - 23:29:31 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 18:04:23 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 03:02:35 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 00:25:54 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Wed Feb 28 2018 - 20:10:34 PST)
Gu, Wenze
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Sun Mar 04 2018 - 07:45:20 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Sat Mar 03 2018 - 06:57:22 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Thu Mar 01 2018 - 16:20:21 PST)
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Thu Mar 01 2018 - 15:43:56 PST)
- [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Thu Mar 01 2018 - 11:16:09 PST)
Hector A. Baldoni
- Re: [AMBER] How to Convert gaussian force constant to Gaff? (Mon Mar 19 2018 - 18:44:54 PDT)
Henrik Hariman
- Re: [AMBER] Penalty score (Sun Mar 04 2018 - 07:15:18 PST)
- [AMBER] Penalty score (Sat Mar 03 2018 - 11:24:34 PST)
Hugo Macdermott-Opeskin
- [AMBER] ABMD write error to MDOUT (Wed Feb 28 2018 - 20:28:49 PST)
Ikuo KURISAKI
- Re: [AMBER] upper limit of water with solvateBox (Wed Mar 21 2018 - 17:54:18 PDT)
- [AMBER] upper limit of water with solvateBox (Wed Mar 21 2018 - 06:06:28 PDT)
Jacopo Sgrignani
- Re: [AMBER] constant pH simulations pemed.cuda (Thu Mar 08 2018 - 07:50:53 PST)
- [AMBER] constant pH simulations pemed.cuda (Thu Mar 08 2018 - 07:45:53 PST)
Jag Silwal
- [AMBER] RMSD of individual sub unit of a protein complex. (Tue Mar 27 2018 - 14:40:20 PDT)
James Kress
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account (Thu Mar 08 2018 - 09:03:15 PST)
Jan Brezovsky
- [AMBER] Additional Ph.D. and Post-doc positions in MD simulations of enzymes (Mon Mar 05 2018 - 09:04:16 PST)
Jason Ku Wang
- [AMBER] Temperature-Based Replica Exchange: Number of Replicas (Wed Mar 21 2018 - 16:15:12 PDT)
- [AMBER] Replica Exchange Cut > 999.0 - Necessitates Very Large Water Box? (Fri Mar 02 2018 - 14:42:31 PST)
Jason Swails
- Re: [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types (Sun Mar 18 2018 - 15:07:13 PDT)
Jeyaram R A
- Re: [AMBER] disulfide bridge -reg (Mon Mar 05 2018 - 21:56:51 PST)
- [AMBER] disulfide bridge -reg (Mon Mar 05 2018 - 01:46:14 PST)
jixiaofeng
- [AMBER] MM-GBSA for membrane protein (Wed Mar 21 2018 - 18:59:02 PDT)
Jonathan David
- Re: [AMBER] FW: AMBER support and extra-point of charge (RESP) issue (Sun Mar 18 2018 - 23:21:37 PDT)
- [AMBER] FW: AMBER support and extra-point of charge (RESP) issue (Thu Mar 08 2018 - 23:33:53 PST)
Kadir Ozcan
- [AMBER] MacOS pmemd.cuda (Thu Mar 29 2018 - 12:21:22 PDT)
Kevin Keane
- Re: [AMBER] pmemd.MPI with a single-entry group file? (Thu Mar 22 2018 - 20:30:02 PDT)
- [AMBER] pmemd.MPI with a single-entry group file? (Thu Mar 22 2018 - 16:12:25 PDT)
koushik kasavajhala
- Re: [AMBER] After running MD, the number of atom in mdcrd file becomes 0 (Fri Mar 02 2018 - 14:57:50 PST)
Lenz, Stefan
- [AMBER] Using center of mass dihedral restraints using PMEMD (Fri Mar 02 2018 - 15:34:42 PST)
Lillian Chong
- [AMBER] WESTPA workshop August 2-3, 2018 (Tue Mar 27 2018 - 10:54:13 PDT)
liu junjun
- Re: [AMBER] mm_pbsa.pl error (Sat Mar 03 2018 - 08:17:21 PST)
Lizelle Lubbe
- [AMBER] Volume occupied during MD (Thu Mar 15 2018 - 06:31:28 PDT)
- [AMBER] Count water in active site (Thu Mar 15 2018 - 06:22:57 PDT)
- Re: [AMBER] radial distribution function results (Tue Mar 13 2018 - 12:16:17 PDT)
- [AMBER] radial distribution function results (Thu Mar 08 2018 - 09:52:45 PST)
Luka Bilić
- Re: [AMBER] Fwd: error while installing AMBER for GPU (Tue Mar 20 2018 - 00:12:36 PDT)
M Conte
- Re: [AMBER] Creating gaff-suitable PDB file for SO2 (Mon Mar 05 2018 - 23:27:39 PST)
- [AMBER] Slab of water (Mon Mar 05 2018 - 15:28:18 PST)
- [AMBER] Creating gaff-suitable PDB file for SO2 (Wed Feb 28 2018 - 22:24:30 PST)
Maciej Maciejczyk
- Re: [AMBER] Fwd: error while installing AMBER for GPU (Tue Mar 20 2018 - 05:15:36 PDT)
Mahmoud A. A. Ibrahim
- Re: [AMBER] FW: AMBER support and extra-point of charge (RESP) issue (Thu Mar 15 2018 - 06:46:13 PDT)
malkeet singh Bahia
- Re: [AMBER] Sudden termination of the heating simulation with sander.MPI (Wed Mar 21 2018 - 05:47:44 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 20 2018 - 07:51:30 PDT)
- Re: [AMBER] Fwd: error while installing AMBER for GPU (Tue Mar 20 2018 - 03:13:47 PDT)
- [AMBER] Fwd: error while installing AMBER for GPU (Mon Mar 19 2018 - 23:29:40 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Mon Mar 19 2018 - 11:14:23 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Mon Mar 19 2018 - 11:11:23 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 11:59:46 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 11:47:51 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 11:10:45 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 11:08:59 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 07:53:09 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 13 2018 - 11:31:15 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 13 2018 - 11:28:15 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 13 2018 - 11:08:29 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 13 2018 - 09:14:47 PDT)
- [AMBER] error while installing AMBER for GPU (Mon Mar 12 2018 - 07:59:33 PDT)
Manivel Panneerselvam
- [AMBER] Selection of interactions that persisted for over 75% of MD time (Mon Mar 26 2018 - 22:39:30 PDT)
maryam azimzadehirani
- [AMBER] Accelerated MD - Please advice (Thu Mar 22 2018 - 07:41:41 PDT)
- Re: [AMBER] Inconsistency with the number of counter ions required for neutralization (Mon Mar 19 2018 - 07:48:16 PDT)
- [AMBER] Inconsistency with the number of counter ions required for neutralization (Mon Mar 19 2018 - 04:01:35 PDT)
Meiting Wang
- [AMBER] TI simulation with a solvateCap: vlimit exceeded for step (Tue Mar 13 2018 - 08:31:38 PDT)
meryem m'hachi
- [AMBER] Force Fields and Water Models (Wed Mar 07 2018 - 02:08:07 PST)
Michael Yonkunas
- [AMBER] cpptraj mask for hbond analysis (Fri Mar 30 2018 - 09:09:27 PDT)
micheal lop
- [AMBER] Convertion between Gaussian and Gaff ANGULAR Force Constant Units (Thu Mar 15 2018 - 09:43:15 PDT)
MinYuan
- Re: [AMBER] AMBER/ORCA for QM/MM (Fri Mar 02 2018 - 02:22:38 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 17:13:59 PST)
minyuan.mail.ustc.edu.cn
- [AMBER] Energy Calculations in Amber (Sun Mar 04 2018 - 06:10:54 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Sun Mar 04 2018 - 04:18:38 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Sat Mar 03 2018 - 16:53:58 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 01:45:40 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Thu Mar 01 2018 - 00:09:39 PST)
- Re: [AMBER] AMBER/ORCA for QM/MM (Wed Feb 28 2018 - 19:23:16 PST)
Morrow,John Kenneth
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C (Thu Mar 01 2018 - 14:15:24 PST)
Nikolay N. Kuzmich
- Re: [AMBER] Sudden termination of the heating simulation with sander.MPI (Thu Mar 22 2018 - 08:42:47 PDT)
- [AMBER] Sudden termination of the heating simulation with sander.MPI (Wed Mar 21 2018 - 05:24:44 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl (Mon Mar 19 2018 - 02:14:17 PDT)
- Re: [AMBER] restraintmask, error in reading namelist cntrl (Fri Mar 16 2018 - 08:53:38 PDT)
- [AMBER] restraintmask, error in reading namelist cntrl (Wed Mar 14 2018 - 08:10:37 PDT)
Pengfei Li
- Re: [AMBER] MCPB.py (Tue Mar 27 2018 - 14:13:27 PDT)
- Re: [AMBER] generating solvated Fe2+ (Mon Mar 26 2018 - 09:30:56 PDT)
- Re: [AMBER] MCPB.py (Mon Mar 26 2018 - 09:24:03 PDT)
- Re: [AMBER] How to Convert gaussian force constant to Gaff? (Tue Mar 20 2018 - 06:14:03 PDT)
- Re: [AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py (Mon Mar 19 2018 - 16:08:30 PDT)
- Re: [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types (Mon Mar 19 2018 - 16:03:36 PDT)
- Re: [AMBER] How to Convert gaussian force constant to Gaff? (Mon Mar 19 2018 - 15:52:13 PDT)
- Re: [AMBER] How to Convert gaussian force constant to Gaff? (Mon Mar 19 2018 - 15:43:30 PDT)
- Re: [AMBER] Can I include Mg ions in receptor mask when using MMPBSA.py (Mon Mar 19 2018 - 15:29:59 PDT)
Premila Samuel Mohan Dass
- Re: [AMBER] reaidt.f problem (Sun Mar 04 2018 - 12:54:10 PST)
- Re: [AMBER] reaidt.f problem (Sun Mar 04 2018 - 12:26:52 PST)
rabi1993.iitg.ernet.in
- [AMBER] Query for force field parameters of 'R' and 'S' enantiomers (Fri Mar 30 2018 - 22:05:17 PDT)
- [AMBER] CUDA (GPU): Implementation does not currently support the use of COM simulations.Require iat(1) >= 0. (Fri Mar 30 2018 - 22:03:23 PDT)
Rajarshi Roy
- Re: [AMBER] center of mass restraint in pmemd.cuda (Wed Mar 21 2018 - 04:41:17 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 20:54:15 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 20:39:05 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 18:34:08 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 08:15:25 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Mon Mar 19 2018 - 03:39:57 PDT)
- [AMBER] center of mass restraint in pmemd.cuda (Thu Mar 15 2018 - 03:07:49 PDT)
Rakesh Srivastava
- Re: [AMBER] Query regarding minimization (Thu Mar 15 2018 - 05:17:24 PDT)
- [AMBER] Query regarding minimization (Thu Mar 15 2018 - 00:37:44 PDT)
Rana Rehan Khalid
- Re: [AMBER] prep to mol2 conversion (Thu Mar 22 2018 - 07:11:15 PDT)
- Re: [AMBER] prep to mol2 conversion (Thu Mar 22 2018 - 06:12:05 PDT)
- Re: [AMBER] prep to mol2 conversion (Thu Mar 22 2018 - 05:55:42 PDT)
- [AMBER] prep to mol2 conversion (Thu Mar 22 2018 - 04:45:03 PDT)
- Re: [AMBER] created a new atom named (is an error or we can ignore it) (Sat Mar 03 2018 - 14:47:11 PST)
- Re: [AMBER] created a new atom named (is an error or we can ignore it) (Sat Mar 03 2018 - 09:56:12 PST)
- Re: [AMBER] Created a new atom named: (Sat Mar 03 2018 - 06:40:15 PST)
- [AMBER] Created a new atom named: (Sat Mar 03 2018 - 06:23:22 PST)
- [AMBER] created a new atom named (is an error or we can ignore it) (Sat Mar 03 2018 - 02:43:16 PST)
- Re: [AMBER] How to generate parameters for two MG 2+ ions ---GTP (Thu Mar 01 2018 - 08:09:52 PST)
Ray Luo
- Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom 7 CB 3C (Thu Mar 01 2018 - 16:56:52 PST)
Robert DeLisle
- [AMBER] Normal Mode Analysis - output from nmode? (Sat Mar 24 2018 - 10:42:51 PDT)
- Re: [AMBER] Normal Mode Analysis in Amber (Thu Mar 22 2018 - 07:59:25 PDT)
- [AMBER] Normal Mode Analysis in Amber (Wed Mar 21 2018 - 19:59:24 PDT)
Roitberg,Adrian E
- Re: [AMBER] error while installing AMBER for GPU (Wed Mar 14 2018 - 11:15:36 PDT)
roja rahmani
- [AMBER] Position of amino acid from surface (Sat Mar 24 2018 - 05:21:46 PDT)
Rosellen, Martin
- [AMBER] Resume AMD simulation (Wed Mar 21 2018 - 06:24:35 PDT)
Ross Walker
- Re: [AMBER] CUDA (GPU): Implementation does not currently support the use of COM simulations.Require iat(1) >= 0. (Sat Mar 31 2018 - 06:06:05 PDT)
- Re: [AMBER] error while installing AMBER for GPU (Tue Mar 20 2018 - 07:46:36 PDT)
- Re: [AMBER] center of mass restraint in pmemd.cuda (Tue Mar 20 2018 - 07:42:42 PDT)
Ruchika Bhat
- Re: [AMBER] Simulation does not restart from restart file written in previous step. (Tue Mar 06 2018 - 23:13:49 PST)
Russell Davidson
- [AMBER] NFE, PMD, and MULTI_RMSD questions (Tue Mar 13 2018 - 16:26:53 PDT)
Ruth Helena Tichauer
- Re: [AMBER] Reaction Coordinate that is the Difference of two Distances (Wed Mar 14 2018 - 08:40:23 PDT)
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account (Mon Mar 12 2018 - 03:51:51 PDT)
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account (Fri Mar 09 2018 - 00:44:28 PST)
- Re: [AMBER] QM/MM with Orca: selected input parameters not taken into account (Thu Mar 08 2018 - 14:11:55 PST)
- [AMBER] QM/MM with Orca: selected input parameters not taken into account (Thu Mar 08 2018 - 01:54:35 PST)
Ryan Richter
- [AMBER] can't compile (Wed Mar 07 2018 - 07:02:05 PST)
sangita kachhap
- [AMBER] vlimit exceed error (Tue Mar 06 2018 - 07:47:16 PST)
Scott Brozell
- Re: [AMBER] upper limit of water with solvateBox (Fri Mar 23 2018 - 09:38:23 PDT)
Seitz, Anthony Joseph
- [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types (Fri Mar 09 2018 - 11:28:19 PST)
Sergey Samsonov
- [AMBER] Random seed reproducibility (Thu Mar 29 2018 - 01:32:04 PDT)
Setyanto Md
- [AMBER] Need advice with GPU choice. (Sat Mar 31 2018 - 01:54:08 PDT)
Smith, Micholas D.
- Re: [AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) (Mon Mar 19 2018 - 10:59:09 PDT)
- [AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) (Mon Mar 19 2018 - 07:40:12 PDT)
Stefan Lenz
- Re: [AMBER] Using center of mass dihedral restraints using PMEMD (Sat Mar 03 2018 - 06:19:37 PST)
Tasneem Kausar
- Re: [AMBER] Problem with cphstat (Mon Mar 12 2018 - 09:12:09 PDT)
- Re: [AMBER] Problem with cphstat (Mon Mar 12 2018 - 07:53:28 PDT)
- [AMBER] Problem with cphstat (Sun Mar 11 2018 - 22:29:49 PDT)
Thakur, Abhishek
- Re: [AMBER] MCPB.py (Mon Mar 26 2018 - 09:39:25 PDT)
- [AMBER] MCPB.py (Thu Mar 22 2018 - 12:12:54 PDT)
Thomas Evangelidis
- Re: [AMBER] AMBER qualitatively compared to other packages (Wed Mar 28 2018 - 04:38:44 PDT)
Thomas Pochapsky
- [AMBER] generating solvated Fe2+ (Thu Mar 22 2018 - 12:48:53 PDT)
Tyler Luchko (Lists)
- Re: [AMBER] 3D-RISM solvation free energy of a molecule in an organic solvent (not water) (Mon Mar 19 2018 - 10:53:36 PDT)
varun dewaker
- [AMBER] Calculating ligand contribution is failing- MMPBSA method (Sun Mar 25 2018 - 22:20:24 PDT)
Vikram Dalal
- [AMBER] Help with mdcrd in VMD (Sat Mar 31 2018 - 10:16:49 PDT)
Vlad Cojocaru
- Re: [AMBER] Force Fields and Water Models (Wed Mar 07 2018 - 03:17:54 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field (Fri Mar 02 2018 - 07:44:21 PST)
- Re: [AMBER] Question about Parmbsc1 Force Field (Thu Mar 01 2018 - 08:09:35 PST)
Wu Xu
- Re: [AMBER] mm_pbsa.pl error (Sun Mar 04 2018 - 16:25:47 PST)
- Re: [AMBER] mm_pbsa.pl error (Sat Mar 03 2018 - 10:01:16 PST)
- [AMBER] mm_pbsa.pl error (Sat Mar 03 2018 - 08:08:26 PST)
Yuliana Bosken
- Re: [AMBER] ERROR TUTORIAL AMBER - creating PDB files from the AMBER coordinate files (Fri Mar 23 2018 - 15:41:52 PDT)
张玥
- [AMBER] Calculate water density in the protein water channel by Amber 16 (Mon Mar 26 2018 - 22:52:22 PDT)
- [AMBER] Calculate water density in the protein water channel by Amber 16 (Mon Mar 26 2018 - 06:20:26 PDT)

Amber Archive Mar 2018 by author