Amber Archive Mar 2020: by subject

[AMBER] "Error of reading the .dat file" in MCPB.py step 2
- Pengfei Li (Fri Mar 27 2020 - 15:14:19 PDT)
- Gustavo Seabra (Fri Mar 20 2020 - 14:42:18 PDT)
[AMBER] ** NFE-Error ** : Cannot read &colvar namelist!
- Feng Pan (Mon Mar 23 2020 - 12:18:32 PDT)
- Vishal Reddy (Mon Mar 23 2020 - 05:56:37 PDT)
[AMBER] 2DRMS before clustering
- Rodrigo Galindo-Murillo (Sat Mar 07 2020 - 13:10:01 PST)
- Debarati DasGupta (Sat Mar 07 2020 - 08:46:56 PST)
[AMBER] A problem of "Could not import Amber Python modules"
- David A Case (Wed Mar 18 2020 - 05:51:21 PDT)
- 唐元晖 (Wed Mar 18 2020 - 05:45:34 PDT)
- 唐元晖 (Tue Mar 17 2020 - 23:48:43 PDT)
[AMBER] Abasic Site and Leap Polymerization
- Christina Bergonzo (Mon Mar 30 2020 - 11:21:43 PDT)
- Carlos Simmerling (Mon Mar 30 2020 - 10:14:03 PDT)
- Robert Molt (Mon Mar 30 2020 - 10:08:06 PDT)
- Christina Bergonzo (Mon Mar 30 2020 - 08:07:58 PDT)
- Robert Molt (Mon Mar 30 2020 - 07:35:44 PDT)
[AMBER] About the D form amino amber force field
- Yeng-Tseng Wang (Sun Mar 15 2020 - 07:30:20 PDT)
- Carlos Simmerling (Sun Mar 15 2020 - 03:42:44 PDT)
- Yeng-Tseng Wang (Sun Mar 15 2020 - 01:53:07 PDT)
[AMBER] about TREE_CHAIN_CLASSIFICATION
- David A Case (Fri Mar 20 2020 - 06:11:51 PDT)
- Thomas Gaillard (Fri Mar 20 2020 - 05:16:40 PDT)
[AMBER] adding Na, K and Cl ions matching intracellular conc
- Vaibhav Dixit (Fri Mar 06 2020 - 07:50:09 PST)
- Matias Machado (Fri Mar 06 2020 - 07:32:57 PST)
- Matias Machado (Fri Mar 06 2020 - 07:29:54 PST)
- Vaibhav Dixit (Wed Mar 04 2020 - 20:19:41 PST)
- Matias Machado (Wed Mar 04 2020 - 16:24:40 PST)
- Matias Machado (Wed Mar 04 2020 - 16:23:01 PST)
- Vaibhav Dixit (Wed Mar 04 2020 - 04:49:40 PST)
[AMBER] AMBER 18 compilation error with CUDA 10.2
- Ruxi Qi (Wed Mar 04 2020 - 06:22:27 PST)
- Abhilash J (Sun Mar 01 2020 - 17:08:23 PST)
[AMBER] AMBER Digest, Vol 2934, Issue 1
- SATYAJIT KHATUA (Thu Mar 12 2020 - 12:51:53 PDT)
[AMBER] Amber parameters for heme b / d coordinated with deprotonated tyrosine
- HOCHEOL LIM (Thu Mar 05 2020 - 22:45:31 PST)
[AMBER] Amber restart simulation
- Carlos Simmerling (Tue Mar 31 2020 - 04:57:19 PDT)
- SUNITA MUDULI (Tue Mar 31 2020 - 04:55:33 PDT)
[AMBER] AMBER19: error in reading namelist cntrl
- Gustaf Olsson (Mon Mar 09 2020 - 03:10:58 PDT)
- geyushu.ustc.edu.cn (Mon Mar 09 2020 - 03:04:38 PDT)
[AMBER] AmberTools on Ubuntu 19.04: compilation
- emanuele falbo (Tue Mar 10 2020 - 08:43:32 PDT)
- David A Case (Tue Mar 10 2020 - 05:25:52 PDT)
- emanuele falbo (Tue Mar 10 2020 - 03:16:28 PDT)
[AMBER] AmberTools19 install error
- Raman Preet Singh (Mon Mar 09 2020 - 05:40:06 PDT)
- Gustaf Olsson (Sun Mar 08 2020 - 14:37:42 PDT)
- Raman Preet Singh (Sun Mar 08 2020 - 10:59:22 PDT)
- David A Case (Sun Mar 08 2020 - 09:39:48 PDT)
- Raman Preet Singh (Sun Mar 08 2020 - 07:03:00 PDT)
[AMBER] AmberTools19 serial installation test errors
- Gustaf Olsson (Fri Mar 13 2020 - 01:52:28 PDT)
- Mariana Simoes Ferreira (Thu Mar 12 2020 - 12:57:39 PDT)
[AMBER] AmberTools19 update.8 fails to install
- David A Case (Sat Mar 28 2020 - 08:21:49 PDT)
- mark.bergman.uphs.upenn.edu (Fri Mar 27 2020 - 14:49:04 PDT)
[AMBER] Ambmask Error in group input::atommask.f::pop_evalstack stack underflow
- Daniel Roe (Wed Mar 25 2020 - 12:30:44 PDT)
- Oliver Grant (Fri Mar 20 2020 - 02:35:20 PDT)
[AMBER] Are the 6-character atom types of CGenFF compatible with parmed-chamber
- David Sáez (Thu Mar 05 2020 - 15:58:18 PST)
- David Sáez (Thu Mar 05 2020 - 13:40:46 PST)
- David Sáez (Wed Mar 04 2020 - 11:33:42 PST)
[AMBER] Boron compunds with "pdb" file with novel frcmod file
- Erdem Yeler (Tue Mar 17 2020 - 05:56:31 PDT)
- David A Case (Sun Mar 15 2020 - 09:41:26 PDT)
- Erdem Yeler (Sat Mar 14 2020 - 13:43:33 PDT)
[AMBER] checkstructure with cpptraj
- Nicolas Feldman (Tue Mar 31 2020 - 13:00:19 PDT)
- Nicolas Feldman (Tue Mar 31 2020 - 12:58:17 PDT)
- David Sáez (Tue Mar 31 2020 - 12:55:49 PDT)
- Ahmed Elrashedy (Tue Mar 31 2020 - 11:29:41 PDT)
- Nicolas Feldman (Tue Mar 31 2020 - 11:08:08 PDT)
- Daniel Roe (Tue Mar 31 2020 - 10:31:51 PDT)
- Nicolas Feldman (Sun Mar 29 2020 - 16:18:02 PDT)
- Gustaf Olsson (Sun Mar 29 2020 - 12:47:08 PDT)
- Nicolas Feldman (Sun Mar 29 2020 - 08:26:34 PDT)
[AMBER] Citing DNA OL15 forcefield
- Sruthi Sudhakar (Thu Mar 05 2020 - 01:00:18 PST)
- Christina Bergonzo (Wed Mar 04 2020 - 11:55:02 PST)
- Sruthi Sudhakar (Wed Mar 04 2020 - 11:14:40 PST)
[AMBER] Clustering analysis
- Daniel Roe (Wed Mar 25 2020 - 12:27:27 PDT)
- Debarati DasGupta (Wed Mar 18 2020 - 15:33:59 PDT)
[AMBER] Clustering query
- Elvis Martis (Sun Mar 22 2020 - 11:14:19 PDT)
- Debarati DasGupta (Sun Mar 22 2020 - 10:37:06 PDT)
[AMBER] cross angle analysis
- Daniel Roe (Wed Mar 25 2020 - 12:39:23 PDT)
- Antonio Amber Carlesso (Tue Mar 24 2020 - 05:56:28 PDT)
[AMBER] CUDA single gpu usage issue
- Abhilash J (Fri Mar 06 2020 - 13:48:38 PST)
- Nicholas Moyer (Fri Mar 06 2020 - 06:15:43 PST)
- Ray Luo (Thu Mar 05 2020 - 22:33:43 PST)
- Ray Luo (Wed Mar 04 2020 - 10:03:55 PST)
- Abhilash J (Wed Mar 04 2020 - 09:32:00 PST)
- Nicholas Moyer (Wed Mar 04 2020 - 08:24:59 PST)
- Ruxi Qi (Wed Mar 04 2020 - 01:22:42 PST)
- Ruxi Qi (Wed Mar 04 2020 - 01:05:57 PST)
- Manish Manish (Tue Mar 03 2020 - 21:54:16 PST)
- Ray Luo (Tue Mar 03 2020 - 19:06:19 PST)
- Nicholas Moyer (Tue Mar 03 2020 - 14:04:07 PST)
- Abhilash J (Tue Mar 03 2020 - 13:58:03 PST)
- Ray Luo (Tue Mar 03 2020 - 10:26:35 PST)
- Nicholas Moyer (Tue Mar 03 2020 - 10:21:56 PST)
- Nicholas Moyer (Tue Mar 03 2020 - 10:20:30 PST)
- Ray Luo (Tue Mar 03 2020 - 10:16:22 PST)
- David A Case (Tue Mar 03 2020 - 07:09:18 PST)
- Nicholas Moyer (Tue Mar 03 2020 - 06:03:58 PST)
[AMBER] CUDA version for AMBER 16 and 20?
- Michael Shokhen (Sun Mar 15 2020 - 10:56:00 PDT)
[AMBER] DBscan gives me errors in clustering
- Daniel Roe (Wed Mar 25 2020 - 12:18:53 PDT)
- Debarati DasGupta (Wed Mar 11 2020 - 08:40:34 PDT)
[AMBER] Differences in Lennard-Jones interactions in CPU vs GPU pmemd?
- Hanne Antila (Mon Mar 30 2020 - 09:26:43 PDT)
[AMBER] dvdl.dat file details AMBER18 TI
- Debarati DasGupta (Tue Mar 03 2020 - 07:48:35 PST)
[AMBER] error job.sh
- Gustaf Olsson (Thu Mar 05 2020 - 09:35:29 PST)
- MYRIAN TORRES RICO (Thu Mar 05 2020 - 09:05:40 PST)
[AMBER] Error while amber installation
- ankita mehta (Sat Mar 28 2020 - 23:26:38 PDT)
- mirzo (Sat Mar 28 2020 - 21:57:58 PDT)
- David A Case (Sat Mar 28 2020 - 16:47:06 PDT)
- ankita mehta (Sat Mar 28 2020 - 10:12:56 PDT)
[AMBER] Error: Could not find angle parameter
- David A Case (Sun Mar 29 2020 - 07:41:39 PDT)
- Rosellen, Martin (Sun Mar 29 2020 - 05:41:59 PDT)
[AMBER] EXTRACTING A PARTICULAR FRAME
- Daniel Roe (Thu Mar 12 2020 - 10:53:29 PDT)
- koushik kasavajhala (Thu Mar 12 2020 - 10:49:12 PDT)
- Daniel Roe (Thu Mar 12 2020 - 10:45:38 PDT)
- Sruthi Sudhakar (Thu Mar 12 2020 - 04:14:38 PDT)
- Gustaf Olsson (Thu Mar 12 2020 - 02:06:09 PDT)
- Sruthi Sudhakar (Thu Mar 12 2020 - 01:12:32 PDT)
- Gustaf Olsson (Thu Mar 12 2020 - 01:00:21 PDT)
- Sruthi Sudhakar (Thu Mar 12 2020 - 00:41:28 PDT)
[AMBER] FATAL Error: Atom does not have a type (Cation)
- David A Case (Wed Mar 25 2020 - 19:01:11 PDT)
- David A Case (Wed Mar 25 2020 - 18:51:25 PDT)
- Yoanes Vianney (Wed Mar 25 2020 - 14:56:43 PDT)
- Thomas Cheatham (Wed Mar 25 2020 - 14:09:54 PDT)
- Yoanes Vianney (Wed Mar 25 2020 - 13:28:33 PDT)
[AMBER] ff19SB + BSC1 + OPC + which ions ?
- Christina Bergonzo (Sun Mar 29 2020 - 14:28:35 PDT)
- Vlad Cojocaru (Sun Mar 29 2020 - 08:27:36 PDT)
- David A Case (Sun Mar 29 2020 - 07:36:29 PDT)
- Vlad Cojocaru (Sun Mar 29 2020 - 05:36:41 PDT)
[AMBER] Found an invalid periodicity in the prmtop file: ... CalcError: bin/mmpbsa_py_energy failed with prmtop .prmtop!
- David A Case (Tue Mar 10 2020 - 11:44:31 PDT)
- Harold Grosjean (Tue Mar 10 2020 - 10:47:02 PDT)
[AMBER] g09 genecp in QM/MM MD in amber
- Vaibhav Dixit (Mon Mar 02 2020 - 19:30:11 PST)
- James Kress (Mon Mar 02 2020 - 11:22:30 PST)
- Vaibhav Dixit (Sun Mar 01 2020 - 19:48:01 PST)
[AMBER] GAFF/AMBER peptide bond
- Petro (Sat Mar 14 2020 - 15:16:45 PDT)
- Carlos Simmerling (Sat Mar 14 2020 - 15:06:51 PDT)
- Song, Lin (Sat Mar 14 2020 - 14:56:15 PDT)
- Petro (Sat Mar 14 2020 - 14:43:35 PDT)
- Song, Lin (Sat Mar 14 2020 - 14:33:03 PDT)
- Petro (Sat Mar 14 2020 - 14:21:40 PDT)
[AMBER] GPU support information
- Serena Vittorio (Tue Mar 24 2020 - 03:12:26 PDT)
[AMBER] heme B parameter by mcpb
- Pengfei Li (Fri Mar 27 2020 - 13:54:42 PDT)
[AMBER] How to setup a QM/MM calculation in Amber
- Sadaf Rani (Fri Mar 27 2020 - 17:55:11 PDT)
- Goetz, Andreas (Fri Mar 27 2020 - 17:23:32 PDT)
- Sadaf Rani (Fri Mar 27 2020 - 16:39:12 PDT)
- James Kress (Fri Mar 27 2020 - 11:57:17 PDT)
- Sadaf Rani (Fri Mar 27 2020 - 02:36:32 PDT)
[AMBER] how to turned off C N terminal amino in tleap
- Petro (Sun Mar 15 2020 - 02:51:19 PDT)
- Yeng-Tseng Wang (Sun Mar 15 2020 - 00:21:06 PDT)
[AMBER] If a non-standard force field is used for proteins, how would you approach parameterization of lipids and ligands?
- Carlos Simmerling (Tue Mar 17 2020 - 03:18:53 PDT)
- Homeo Morphism (Tue Mar 17 2020 - 01:24:28 PDT)
[AMBER] Inconsistency in energy values between out files and cpptraj
- Daniel Roe (Tue Mar 10 2020 - 09:07:51 PDT)
- SHAUNAK BADANI (Sat Mar 07 2020 - 03:56:38 PST)
[AMBER] Incosistency in energy values from out files and cpptraj energy tools
- Daniel Roe (Tue Mar 10 2020 - 08:54:41 PDT)
- SHAUNAK BADANI (Tue Mar 10 2020 - 08:20:02 PDT)
[AMBER] information regarding space filling visualization
- Ahmed Elrashedy (Sat Mar 14 2020 - 06:04:43 PDT)
- Carlos Simmerling (Sat Mar 14 2020 - 02:50:36 PDT)
- Elvis Martis (Sat Mar 14 2020 - 02:49:08 PDT)
- Prasanth G, Research Scholar (Sat Mar 14 2020 - 02:18:55 PDT)
[AMBER] Installation problem for a parallel version of Amber18/AmberTools19
- Kosuke Tachibana (Wed Mar 25 2020 - 04:26:47 PDT)
- Kosuke Tachibana (Wed Mar 25 2020 - 02:57:54 PDT)
- Gustaf Olsson (Tue Mar 24 2020 - 23:46:19 PDT)
- Kosuke Tachibana (Tue Mar 24 2020 - 08:57:37 PDT)
- David A Case (Mon Mar 23 2020 - 06:38:48 PDT)
- Kosuke Tachibana (Sun Mar 22 2020 - 21:02:09 PDT)
[AMBER] Issue in drug parameter
- Carlos Simmerling (Sun Mar 01 2020 - 14:34:48 PST)
- David A Case (Sun Mar 01 2020 - 14:28:39 PST)
- SHAUNAK BADANI (Sun Mar 01 2020 - 10:13:45 PST)
- David A Case (Sun Mar 01 2020 - 05:32:04 PST)
[AMBER] issue while installing AMBER tools on windows10 Linux subsystem
- Ana Ziad (Sat Mar 21 2020 - 08:50:07 PDT)
- Gustaf Olsson (Fri Mar 20 2020 - 15:49:39 PDT)
- Ana Ziad (Fri Mar 20 2020 - 10:29:33 PDT)
- David A Case (Fri Mar 20 2020 - 10:09:23 PDT)
- Ana Ziad (Fri Mar 20 2020 - 09:20:00 PDT)
- Gustaf Olsson (Wed Mar 18 2020 - 14:03:04 PDT)
- Ana Ziad (Tue Mar 17 2020 - 14:35:54 PDT)
[AMBER] KeyError: 'MG'
- Pengfei Li (Fri Mar 27 2020 - 14:26:40 PDT)
- Pengfei Li (Fri Mar 27 2020 - 14:21:21 PDT)
- Filipa Mendonça (Wed Mar 04 2020 - 09:00:33 PST)
[AMBER] linear interaction energy tool in AMBER
- Adrian Roitberg (Fri Mar 06 2020 - 08:47:52 PST)
- Akshay Prabhakant (Thu Mar 05 2020 - 21:24:01 PST)
[AMBER] Lone Pairs in AMBER FF
- 杨明俊 (Thu Mar 19 2020 - 03:57:52 PDT)
- David A Case (Sun Mar 15 2020 - 06:03:55 PDT)
- 杨明俊 (Sat Mar 14 2020 - 20:06:23 PDT)
- Carlos Simmerling (Sat Mar 14 2020 - 08:18:40 PDT)
- 杨明俊 (Sat Mar 14 2020 - 07:35:18 PDT)
[AMBER] MM-PB(GB)/SA error message
- Antonio Amber Carlesso (Tue Mar 24 2020 - 07:41:12 PDT)
[AMBER] mmpbsa_py_energy failed with prmtop dim_gas.prmtop
- Ray Luo (Fri Mar 27 2020 - 09:35:16 PDT)
- Azahara.Doncel.uv.es (Fri Mar 27 2020 - 09:11:29 PDT)
- Azahara.Doncel.uv.es (Thu Mar 12 2020 - 08:58:17 PDT)
[AMBER] Modified AA residue without NH2 end.
- Carlos Simmerling (Thu Mar 12 2020 - 03:51:55 PDT)
- Petro (Thu Mar 12 2020 - 03:41:16 PDT)
[AMBER] Modified force fields
- David A Case (Tue Mar 10 2020 - 11:38:36 PDT)
- Carlos Simmerling (Tue Mar 10 2020 - 10:53:10 PDT)
- Kellon Belfon (Tue Mar 10 2020 - 10:48:50 PDT)
- ankita mehta (Tue Mar 10 2020 - 10:26:47 PDT)
- Carlos Simmerling (Mon Mar 09 2020 - 09:45:00 PDT)
- ankita mehta (Mon Mar 09 2020 - 09:40:12 PDT)
- ankita mehta (Sun Mar 08 2020 - 20:52:39 PDT)
- Kellon Belfon (Sun Mar 08 2020 - 15:23:08 PDT)
- ankita mehta (Sun Mar 08 2020 - 10:59:09 PDT)
- David A Case (Fri Mar 06 2020 - 05:00:25 PST)
- ankita mehta (Thu Mar 05 2020 - 20:34:37 PST)
[AMBER] MPI+threads in Amber
- Daniel Roe (Tue Mar 31 2020 - 10:35:49 PDT)
- Rohit Zambre (Mon Mar 30 2020 - 10:01:21 PDT)
[AMBER] nastruct and modified base pairs
- Daniel Roe (Fri Mar 27 2020 - 06:00:00 PDT)
- Kenneth Huang (Thu Mar 26 2020 - 17:47:02 PDT)
- Daniel Roe (Thu Mar 26 2020 - 12:30:55 PDT)
- Kenneth Huang (Wed Mar 25 2020 - 14:10:44 PDT)
- Daniel Roe (Wed Mar 25 2020 - 12:42:00 PDT)
- Kenneth Huang (Wed Mar 25 2020 - 11:47:01 PDT)
[AMBER] Not recognising output file for N_OF_BONDS reaction coordinate
- Vishal Reddy (Fri Mar 13 2020 - 12:07:31 PDT)
[AMBER] NPT equilibration is crashing
- David Sáez (Sun Mar 29 2020 - 23:52:27 PDT)
- Sunita Patel (Sun Mar 29 2020 - 03:37:43 PDT)
- Carlos Simmerling (Sun Mar 29 2020 - 03:19:23 PDT)
- David Sáez (Sat Mar 28 2020 - 22:01:24 PDT)
- Sunita Patel (Sat Mar 28 2020 - 21:11:36 PDT)
[AMBER] parameterization with crystal water
- David A Case (Wed Mar 25 2020 - 18:41:55 PDT)
- Hira Jabeen (Wed Mar 25 2020 - 10:53:52 PDT)
[AMBER] parameters for Si3N4
- Akshay Prabhakant (Mon Mar 16 2020 - 21:11:06 PDT)
[AMBER] PDB Modification
- Osman, Roman (Mon Mar 30 2020 - 09:08:00 PDT)
- ankita mehta (Mon Mar 30 2020 - 08:55:23 PDT)
- Osman, Roman (Mon Mar 30 2020 - 08:30:39 PDT)
- ankita mehta (Mon Mar 30 2020 - 06:43:50 PDT)
[AMBER] problem adding MG.off file
- Nicolas Feldman (Mon Mar 02 2020 - 04:31:19 PST)
[AMBER] problem in MCPB.py
- Pengfei Li (Fri Mar 27 2020 - 14:05:29 PDT)
- wujue (Wed Mar 04 2020 - 19:41:49 PST)
[AMBER] problems implementing tiMerge for base pair mutation
- Gabriel Jara (Thu Mar 12 2020 - 10:18:00 PDT)
[AMBER] Problems with Nvidia Drivers
- Andrea H. Kasun (Sun Mar 29 2020 - 04:14:24 PDT)
- Ross Walker (Sat Mar 28 2020 - 07:32:07 PDT)
- Andrea H. Kasun (Sat Mar 28 2020 - 03:21:02 PDT)
- Ross Walker (Thu Mar 26 2020 - 12:49:14 PDT)
- Andrea H. Kasun (Thu Mar 26 2020 - 10:25:16 PDT)
[AMBER] QM/MM Convergence questions
- 辛志宏 (Mon Mar 09 2020 - 20:02:03 PDT)
- Goetz, Andreas (Mon Mar 09 2020 - 12:17:48 PDT)
- 辛志宏 (Mon Mar 09 2020 - 02:55:21 PDT)
- David A Case (Fri Mar 06 2020 - 04:51:58 PST)
- 辛志宏 (Thu Mar 05 2020 - 18:22:32 PST)
- Busra Demir (Thu Mar 05 2020 - 03:41:27 PST)
- 辛志宏 (Thu Mar 05 2020 - 01:07:44 PST)
[AMBER] Query regarding 3DRISM in Amber with CHARMM force field
- Rakesh Srivastava (Fri Mar 06 2020 - 22:20:51 PST)
[AMBER] Question about MMPBSA calculation
- Rinsha Chk (Mon Mar 09 2020 - 06:31:50 PDT)
- Elvis Martis (Mon Mar 09 2020 - 03:41:42 PDT)
- Rinsha Chk (Mon Mar 09 2020 - 03:06:13 PDT)
[AMBER] Question of units
- James Kress (Mon Mar 02 2020 - 18:47:26 PST)
- David A Case (Mon Mar 02 2020 - 18:36:25 PST)
- James Kress (Mon Mar 02 2020 - 14:19:12 PST)
[AMBER] questions about paramfit and frcmod file
- ttz (Mon Mar 23 2020 - 21:00:34 PDT)
- David Cerutti (Sun Mar 22 2020 - 23:36:44 PDT)
- ttz (Sun Mar 22 2020 - 15:11:30 PDT)
[AMBER] Questions on force field
- David A Case (Fri Mar 13 2020 - 04:28:59 PDT)
- Sasthi Mandal (Fri Mar 13 2020 - 00:03:28 PDT)
[AMBER] Reg: MMGBSA for NAMD trajectory
- David A Case (Wed Mar 11 2020 - 11:20:43 PDT)
- Lara rajam (Wed Mar 11 2020 - 10:25:51 PDT)
[AMBER] REMD hybrid solvent model
- koushik (Wed Mar 11 2020 - 10:35:51 PDT)
- Carlos Simmerling (Wed Mar 11 2020 - 10:32:33 PDT)
- Hosein Geraili Daronkola (Wed Mar 11 2020 - 10:13:35 PDT)
- Carlos Simmerling (Wed Mar 11 2020 - 08:39:32 PDT)
- Hosein Geraili Daronkola (Wed Mar 11 2020 - 08:35:21 PDT)
- Carlos Simmerling (Tue Mar 10 2020 - 19:09:09 PDT)
- koushik kasavajhala (Tue Mar 10 2020 - 13:24:06 PDT)
- Hosein Geraili Daronkola (Tue Mar 10 2020 - 13:09:00 PDT)
[AMBER] replica exchange with GPU
- Cruzeiro,Vinicius Wilian D (Mon Mar 02 2020 - 08:45:44 PST)
- Alessandro Contini (Mon Mar 02 2020 - 02:43:16 PST)
- bbalta.itu.edu.tr (Mon Mar 02 2020 - 01:21:20 PST)
[AMBER] residue library for na_link AmberTools19
- Gül Zerze (Thu Mar 26 2020 - 10:33:34 PDT)
- David A Case (Thu Mar 26 2020 - 05:10:41 PDT)
- Gül Zerze (Wed Mar 25 2020 - 18:38:27 PDT)
[AMBER] RTX 2020 Super GPU Random Memorry Errors
- Giorgos Lambrinidis (Sat Mar 21 2020 - 12:36:07 PDT)
[AMBER] RTX 2020 Super GPU Random Memory Errors
- Giorgos Lambrinidis (Sun Mar 22 2020 - 02:56:10 PDT)
- Stephan Schott (Sat Mar 21 2020 - 16:44:27 PDT)
- David Cerutti (Sat Mar 21 2020 - 15:54:50 PDT)
- Giorgos Lambrinidis (Sat Mar 21 2020 - 12:43:43 PDT)
[AMBER] setting pdb file
- Nicolas Feldman (Sat Mar 21 2020 - 10:03:59 PDT)
- Carlos Simmerling (Fri Mar 20 2020 - 16:55:37 PDT)
- Nicolas Feldman (Fri Mar 20 2020 - 15:57:24 PDT)
- Gustaf Olsson (Fri Mar 20 2020 - 15:52:25 PDT)
- Nicolas Feldman (Fri Mar 20 2020 - 15:44:02 PDT)
- Gustaf Olsson (Fri Mar 20 2020 - 15:31:17 PDT)
- Nicolas Feldman (Fri Mar 20 2020 - 13:01:15 PDT)
- Carlos Simmerling (Fri Mar 20 2020 - 12:55:57 PDT)
- Nicolas Feldman (Fri Mar 20 2020 - 12:41:57 PDT)
- Daniel Roe (Fri Mar 20 2020 - 12:29:27 PDT)
- Nicolas Feldman (Fri Mar 20 2020 - 11:49:46 PDT)
[AMBER] sieve keyword in cpptraj clustering
- Daniel Roe (Wed Mar 25 2020 - 12:16:43 PDT)
- Debarati DasGupta (Tue Mar 10 2020 - 06:36:59 PDT)
[AMBER] SImulation prepared using CHARMM GUI terminates with no error at the NTP step
- Gustaf Olsson (Wed Mar 25 2020 - 23:58:56 PDT)
- Lenka (Wed Mar 25 2020 - 16:16:37 PDT)
[AMBER] simulations of proteins with 2 domains connected by a linker
- Vlad Cojocaru (Thu Mar 12 2020 - 11:03:40 PDT)
- Carlos Simmerling (Thu Mar 12 2020 - 06:58:25 PDT)
- Vlad Cojocaru (Thu Mar 12 2020 - 02:57:47 PDT)
[AMBER] Simulations Without Network
- Garcia, Mauro (Fri Mar 27 2020 - 15:31:29 PDT)
- Gustaf Olsson (Fri Mar 27 2020 - 13:21:09 PDT)
- David Cerutti (Fri Mar 27 2020 - 09:56:55 PDT)
- Garcia, Mauro (Fri Mar 27 2020 - 09:34:57 PDT)
[AMBER] sum of charges from parm file
- Clorice Reinhardt (Tue Mar 31 2020 - 15:40:38 PDT)
[AMBER] tar-MD with custom J-coupling relation
- Christina Bergonzo (Tue Mar 03 2020 - 06:02:34 PST)
- Dieter Buyst (Tue Mar 03 2020 - 05:37:30 PST)
[AMBER] Texas red force field
- Tiejun Wei (Mon Mar 16 2020 - 08:27:20 PDT)
[AMBER] TI production error in nstep =1
- Debarati DasGupta (Fri Mar 06 2020 - 06:46:40 PST)
- David A Case (Fri Mar 06 2020 - 04:48:17 PST)
- Debarati DasGupta (Thu Mar 05 2020 - 13:38:21 PST)
[AMBER] TI runs on GPU
- Debarati DasGupta (Sun Mar 15 2020 - 06:56:06 PDT)
- David A Case (Fri Mar 13 2020 - 04:24:39 PDT)
- Debarati DasGupta (Thu Mar 12 2020 - 13:48:29 PDT)
[AMBER] tleap for Mg2+ data type
- Sunita Patel (Thu Mar 26 2020 - 20:26:25 PDT)
- Sunita Patel (Thu Mar 26 2020 - 20:19:21 PDT)
- David A Case (Wed Mar 25 2020 - 19:09:01 PDT)
- Sunita Patel (Wed Mar 25 2020 - 17:32:05 PDT)
- Stephan Schott (Wed Mar 25 2020 - 07:36:52 PDT)
- Sunita Patel (Wed Mar 25 2020 - 07:15:44 PDT)
[AMBER] tleap/xleap performance enhancement
- Himanshu Joshi (Wed Mar 04 2020 - 10:13:11 PST)
[AMBER] Unavailability of the file related to -cprestrt flag in equilibration (NPT) step of constant pH MD in Amber14 with AmberTools15
- SATYAJIT KHATUA (Fri Mar 06 2020 - 23:14:32 PST)
[AMBER] units of the calculated diffusion coefficient
- Daniel Roe (Thu Mar 12 2020 - 10:48:55 PDT)
- Chetna Tyagi (Wed Mar 11 2020 - 10:54:27 PDT)
[AMBER] unusual planarity change during md.
- Adrian Roitberg (Thu Mar 12 2020 - 08:38:14 PDT)
- Sruthi Sudhakar (Thu Mar 12 2020 - 08:25:40 PDT)
[AMBER] Weird error with antechamber for metal ion / MCPB tutorial
- Gustavo Seabra (Fri Mar 27 2020 - 21:31:38 PDT)
- Pengfei Li (Fri Mar 27 2020 - 13:57:51 PDT)
[AMBER] What is the default pH when loading a protein in Amber environment
- Carlos Simmerling (Wed Mar 11 2020 - 04:48:30 PDT)
- Siavoush Dastmalchi (Wed Mar 11 2020 - 04:20:41 PDT)
[AMBER] What's the least biased way to stop a molecule from crossing a periodic boundary?
- Carlos Simmerling (Thu Mar 12 2020 - 04:48:44 PDT)
- Carlos Simmerling (Thu Mar 12 2020 - 04:21:40 PDT)
- Homeo Morphism (Thu Mar 12 2020 - 04:16:23 PDT)
[AMBER] When I use fitted parameters as initial parameters in paramfit, I am getting different results?
- Erdem Yeler (Thu Mar 12 2020 - 00:33:01 PDT)
- David Cerutti (Mon Mar 09 2020 - 10:36:58 PDT)
- Erdem Yeler (Mon Mar 09 2020 - 05:34:01 PDT)
- Erdem Yeler (Mon Mar 09 2020 - 02:10:48 PDT)
- Robin Betz (Fri Mar 06 2020 - 13:08:21 PST)
- David Cerutti (Fri Mar 06 2020 - 11:10:49 PST)
- Erdem Yeler (Fri Mar 06 2020 - 04:11:20 PST)
[AMBER] Writing Trajectories as netcdf files
- Hunter Wilson (Wed Mar 25 2020 - 12:19:46 PDT)
- Stephan Schott (Wed Mar 25 2020 - 10:22:26 PDT)
- emanuele falbo (Wed Mar 25 2020 - 10:16:46 PDT)
- Hunter Wilson (Wed Mar 25 2020 - 10:11:08 PDT)

Amber Archive Mar 2020 by subject