Amber Archive May 2020: by subject

[AMBER] 2 aminpurine parameter from Bryce reference?
- David A Case (Tue May 12 2020 - 18:47:22 PDT)
- Kenneth Huang (Tue May 12 2020 - 14:06:34 PDT)
- David A Case (Mon May 11 2020 - 18:12:43 PDT)
- Kenneth Huang (Mon May 11 2020 - 13:31:37 PDT)
- Kenneth Huang (Mon May 11 2020 - 13:15:55 PDT)
[AMBER] [EXTERNAL] addions
- Matias Machado (Wed May 06 2020 - 10:45:46 PDT)
- Smith, Micholas D. (Wed May 06 2020 - 10:18:27 PDT)
[AMBER] Abasic Site and Errant OH Group on Sugar
- David A Case (Mon May 04 2020 - 07:44:58 PDT)
- Christina Bergonzo (Mon May 04 2020 - 06:13:53 PDT)
- Robert Molt (Mon May 04 2020 - 05:40:40 PDT)
[AMBER] about charmmgen
- Francesco Pietra (Wed May 06 2020 - 09:28:01 PDT)
[AMBER] About having an auto-restart keyword for the amber/orca interface.
- Zhiyi Wu (Wed May 13 2020 - 14:41:11 PDT)
[AMBER] Absolute free energy calculation-GitHub
- Sadaf Rani (Sat May 16 2020 - 17:03:00 PDT)
[AMBER] adding hydrogen to pdbqt ligand files
- Eduardo Mayo (Thu May 28 2020 - 23:25:00 PDT)
[AMBER] addions
- James Kress (Sat May 09 2020 - 19:47:47 PDT)
- Robert Molt (Sat May 09 2020 - 17:20:10 PDT)
- Matias Machado (Sat May 09 2020 - 16:04:02 PDT)
- Robert Molt (Sat May 09 2020 - 15:13:44 PDT)
- James Kress (Sat May 09 2020 - 14:56:37 PDT)
- Robert Molt (Sat May 09 2020 - 14:35:24 PDT)
- Christina Bergonzo (Wed May 06 2020 - 09:17:48 PDT)
- Jisha B (Wed May 06 2020 - 08:55:28 PDT)
[AMBER] AMBER 16 NFE MULTI_RMSD Question on the Output of reaction variable
- Xiaoyong Zhang (Thu May 28 2020 - 08:39:38 PDT)
[AMBER] AMBER 18 GPU
- Liao (Thu May 14 2020 - 11:02:21 PDT)
- Renato Araujo (Thu May 14 2020 - 09:53:40 PDT)
[AMBER] AMBER Digest, Vol 3017, Issue 1
- David Cerutti (Sat May 30 2020 - 20:59:36 PDT)
- Gao J (Sat May 30 2020 - 19:18:36 PDT)
[AMBER] Amber for help
- 马海川 (Sat May 30 2020 - 06:04:02 PDT)
[AMBER] AMBER Tools 20: Bug in libraries of modified amino acids prevents force field load
- Kellon Belfon (Wed May 20 2020 - 14:13:51 PDT)
- Matias Machado (Wed May 20 2020 - 10:13:34 PDT)
[AMBER] Amber18 with AmberTools20 test.serial FAILURES and ERRORS
- Samanta M (Sat May 23 2020 - 11:07:50 PDT)
- David A Case (Sat May 23 2020 - 09:12:29 PDT)
- Josh Berryman (Sat May 23 2020 - 09:03:57 PDT)
- Samanta M (Sat May 23 2020 - 07:02:03 PDT)
[AMBER] Amber20 MPIC location problem
- Gerald Monard (Sun May 17 2020 - 07:26:29 PDT)
- David A Case (Sat May 16 2020 - 05:46:43 PDT)
- Filip Fratev (Fri May 15 2020 - 20:54:11 PDT)
[AMBER] Amber20 MPICH location problem
- David A Case (Sun May 17 2020 - 05:46:08 PDT)
- Filip Fratev (Sun May 17 2020 - 01:25:51 PDT)
- fratev.biomed.bas.bg (Sat May 16 2020 - 20:13:19 PDT)
- Filip Fratev (Sat May 16 2020 - 02:57:29 PDT)
[AMBER] amber20 output header
- David Cerutti (Sat May 30 2020 - 20:56:46 PDT)
- Baker, Joseph (Sat May 30 2020 - 19:18:49 PDT)
[AMBER] Amber20 Performance on RTX (Turing): known problems, with a patch forthcoming
- David Cerutti (Thu May 28 2020 - 23:30:20 PDT)
[AMBER] Amber20 pmemd.cuda installation
- David A Case (Sun May 17 2020 - 17:34:56 PDT)
[AMBER] Amber20 pmemd.cuda installation and performance problems
- David Cerutti (Thu May 28 2020 - 15:51:16 PDT)
- David Cerutti (Wed May 27 2020 - 04:54:32 PDT)
- Filip Fratev (Wed May 27 2020 - 03:12:46 PDT)
- Filip Fratev (Wed May 27 2020 - 03:00:36 PDT)
- David Cerutti (Tue May 19 2020 - 12:39:50 PDT)
- viktor drobot (Sun May 17 2020 - 01:53:21 PDT)
- Filip Fratev (Sun May 17 2020 - 01:43:26 PDT)
[AMBER] Amber20 pmemd.cuda performance problems (especially on Turing-based GPUs)
- David Cerutti (Thu May 28 2020 - 08:34:25 PDT)
- Brent Krueger (Mon May 25 2020 - 06:04:28 PDT)
- David Cerutti (Mon May 25 2020 - 02:40:35 PDT)
- Thomas Zeiser (Mon May 25 2020 - 02:01:09 PDT)
[AMBER] Amber20 sander speed difference between cmake and old configure method
- David A Case (Tue May 12 2020 - 05:25:39 PDT)
- David A Case (Wed May 06 2020 - 09:22:33 PDT)
- Charo del Genio (Wed May 06 2020 - 05:07:51 PDT)
[AMBER] Amber20 sander speed difference between cmake and old configure method (addendum)
- Charo del Genio (Wed May 06 2020 - 06:35:18 PDT)
[AMBER] Amber20 serial make test FAILUREs on IBM Power9
- Cong Liu (Thu May 21 2020 - 14:03:33 PDT)
- David A Case (Thu May 21 2020 - 11:00:41 PDT)
- Cong Liu (Thu May 21 2020 - 07:08:05 PDT)
- Cong Liu (Thu May 21 2020 - 07:03:12 PDT)
[AMBER] Amber99SB force field
- Carlos Simmerling (Thu May 28 2020 - 07:12:52 PDT)
- Gustavo Seabra (Thu May 28 2020 - 06:56:08 PDT)
- Carlos Simmerling (Thu May 28 2020 - 06:16:02 PDT)
- Seketoulie Keretsu (Thu May 28 2020 - 05:51:12 PDT)
[AMBER] AmberTools20 comilation on macOS
- Gustaf Olsson (Wed May 06 2020 - 06:38:14 PDT)
- David A Case (Wed May 06 2020 - 05:31:52 PDT)
- Gustaf Olsson (Tue May 05 2020 - 22:33:59 PDT)
- David A Case (Tue May 05 2020 - 13:44:18 PDT)
- Gustaf Olsson (Tue May 05 2020 - 10:03:52 PDT)
- Gustaf Olsson (Tue May 05 2020 - 09:22:03 PDT)
- David A Case (Tue May 05 2020 - 05:58:58 PDT)
- Gustaf Olsson (Tue May 05 2020 - 02:33:42 PDT)
- Gustaf Olsson (Tue May 05 2020 - 01:38:13 PDT)
- Gustaf Olsson (Tue May 05 2020 - 01:22:42 PDT)
- Gustaf Olsson (Tue May 05 2020 - 01:07:11 PDT)
[AMBER] autoimage waters
- Hector A. Baldoni (Wed May 13 2020 - 16:40:35 PDT)
- Daniel Roe (Wed May 13 2020 - 15:07:25 PDT)
- Hector A. Baldoni (Wed May 13 2020 - 12:46:38 PDT)
[AMBER] C4 parameters for Au0 from INTERFACE FF
- sbojarowski.chem.uw.edu.pl (Tue May 05 2020 - 05:58:34 PDT)
[AMBER] can i analysis number of water molecules in protein by watershell
- Wesley Michael Botello-Smith (Wed May 20 2020 - 09:39:46 PDT)
- Daniel Roe (Wed May 20 2020 - 09:20:05 PDT)
- 石娜 (Wed May 06 2020 - 06:21:50 PDT)
[AMBER] cellulose chain
- David A Case (Fri May 29 2020 - 09:32:06 PDT)
- Pinky Mazumder (Fri May 29 2020 - 07:46:58 PDT)
- Lachele Foley (Sat May 16 2020 - 02:33:03 PDT)
- Pinky Mazumder (Fri May 15 2020 - 20:53:27 PDT)
- Pinky Mazumder (Fri May 15 2020 - 20:51:30 PDT)
- Lachele Foley (Fri May 15 2020 - 20:09:26 PDT)
- Pinky Mazumder (Fri May 15 2020 - 10:00:57 PDT)
[AMBER] Changing hydrogen atom radius to optimize saltbridge in GB-OBC model
- Sunita Patel (Sun May 24 2020 - 06:07:07 PDT)
- Kellon Belfon (Sat May 23 2020 - 22:46:50 PDT)
- Sunita Patel (Sat May 23 2020 - 21:05:57 PDT)
- Carlos Simmerling (Sat May 23 2020 - 07:16:56 PDT)
- Sunita Patel (Sat May 23 2020 - 07:01:04 PDT)
[AMBER] clustering parameter files
- Daniel Roe (Tue May 26 2020 - 07:54:07 PDT)
- Ranim Maaieh (Mon May 25 2020 - 07:36:39 PDT)
[AMBER] CO atom type missing in PARMCHK.DAT
- Casalini Tommaso (Tue May 05 2020 - 11:53:42 PDT)
[AMBER] COM position
- Daniel Roe (Tue May 19 2020 - 04:30:22 PDT)
- mohamed marzouk (Tue May 19 2020 - 02:41:30 PDT)
[AMBER] Could not find control namelist error
- Carlos Simmerling (Sat May 16 2020 - 04:39:08 PDT)
- Jisha B (Sat May 16 2020 - 04:31:11 PDT)
[AMBER] cpptraj PCA PC-mode pseudo traj
- Schröder, David Christopher (Mon May 04 2020 - 13:52:47 PDT)
- Daniel Roe (Mon May 04 2020 - 13:46:52 PDT)
- Schröder, David Christopher (Mon May 04 2020 - 13:19:23 PDT)
[AMBER] CPPTRAJ: distance between atoms
- Daniel Roe (Mon May 04 2020 - 04:35:17 PDT)
- emanuele falbo (Mon May 04 2020 - 03:55:27 PDT)
[AMBER] creating parameters for a thioglycoside
- rosaester.forgione.unina.it (Mon May 11 2020 - 03:27:48 PDT)
- Karl Kirschner (Mon May 04 2020 - 11:28:22 PDT)
- rosaester.forgione.unina.it (Mon May 04 2020 - 09:59:39 PDT)
[AMBER] differences in EGB energies sander vs. pmemd
- David A Case (Thu May 14 2020 - 18:28:36 PDT)
- Niransha Kumarachchi (Thu May 14 2020 - 16:20:28 PDT)
[AMBER] Different LJ parameters in .dat file and 'atominfo' output
- Daniel Roe (Wed May 27 2020 - 07:59:41 PDT)
- José Daniel Martinez (Wed May 27 2020 - 01:25:01 PDT)
- Daniel Roe (Tue May 26 2020 - 08:23:36 PDT)
- José Daniel Martinez (Sat May 23 2020 - 05:17:50 PDT)
[AMBER] error MMPBSA
- Elvis Martis (Mon May 11 2020 - 05:53:01 PDT)
- David A Case (Mon May 11 2020 - 04:51:49 PDT)
- MYRIAN TORRES RICO (Mon May 11 2020 - 04:49:04 PDT)
- Elvis Martis (Mon May 11 2020 - 03:59:26 PDT)
- MYRIAN TORRES RICO (Mon May 11 2020 - 03:12:38 PDT)
[AMBER] Ewald grid size question
- David Cerutti (Sun May 10 2020 - 21:40:13 PDT)
- Yuliana Bosken (Sun May 10 2020 - 18:10:55 PDT)
- David A Case (Sun May 10 2020 - 18:05:03 PDT)
- Yuliana Bosken (Sun May 10 2020 - 16:10:01 PDT)
[AMBER] Flags to Turn off Charges in pmemd
- Sharif Nada (Wed May 06 2020 - 03:44:24 PDT)
[AMBER] FRCMOD FILE DATABASE
- Brent Krueger (Wed May 06 2020 - 05:17:17 PDT)
- Gustaf Olsson (Tue May 05 2020 - 22:43:24 PDT)
- Jenny 148 (Tue May 05 2020 - 22:33:20 PDT)
[AMBER] Free energy calculation and system crash
- Carlos Simmerling (Mon May 04 2020 - 06:11:04 PDT)
- Sadaf Rani (Mon May 04 2020 - 06:08:01 PDT)
- Sadaf Rani (Sat May 02 2020 - 17:29:43 PDT)
- Carlos Simmerling (Sat May 02 2020 - 16:44:52 PDT)
- Sadaf Rani (Sat May 02 2020 - 15:54:14 PDT)
[AMBER] Free energy of solvation using polarizable force fields
- David A Case (Sat May 23 2020 - 09:31:35 PDT)
- Carl Heroneme (Thu May 21 2020 - 14:11:06 PDT)
[AMBER] Galactosylation of 5-Hydroxylysine
- Lachele Foley (Tue May 19 2020 - 13:21:50 PDT)
- Harald Lanig (Thu May 14 2020 - 09:05:08 PDT)
[AMBER] GPU based TI runs
- Debarati DasGupta (Sat May 09 2020 - 10:40:39 PDT)
- Song, Lin (Sat May 09 2020 - 10:28:51 PDT)
- Debarati DasGupta (Sat May 09 2020 - 08:57:13 PDT)
- Song, Lin (Sat May 09 2020 - 08:41:54 PDT)
- Debarati DasGupta (Sat May 09 2020 - 07:00:52 PDT)
- David A Case (Sat May 09 2020 - 06:10:19 PDT)
- Debarati DasGupta (Sat May 09 2020 - 04:56:04 PDT)
[AMBER] help
- MYRIAN TORRES RICO (Fri May 15 2020 - 01:58:37 PDT)
- David A Case (Thu May 14 2020 - 18:31:31 PDT)
- MYRIAN TORRES RICO (Wed May 13 2020 - 10:27:53 PDT)
- David A Case (Tue May 12 2020 - 18:34:27 PDT)
- MYRIAN TORRES RICO (Tue May 12 2020 - 09:21:29 PDT)
[AMBER] Help with Acpype in AmberTools19
- Prapasiri Pongprayoon (Sun May 24 2020 - 23:07:32 PDT)
[AMBER] Help with Acpype on AMberTools19
- Prapasiri Pongprayoon (Sun May 24 2020 - 23:02:50 PDT)
[AMBER] how to compute the protein interaction surface with the ligand
- Thomas Evangelidis (Sat May 23 2020 - 17:11:51 PDT)
- Carlos Simmerling (Sat May 23 2020 - 16:45:00 PDT)
- Thomas Evangelidis (Sat May 23 2020 - 16:32:54 PDT)
- Carlos Simmerling (Wed May 20 2020 - 12:43:24 PDT)
- Thomas Evangelidis (Wed May 20 2020 - 11:26:48 PDT)
- David A Case (Wed May 20 2020 - 10:31:03 PDT)
- Daniel Roe (Wed May 20 2020 - 09:00:42 PDT)
- Thomas Evangelidis (Mon May 18 2020 - 13:56:33 PDT)
- Thomas Evangelidis (Fri May 08 2020 - 15:57:39 PDT)
[AMBER] how to identify lipids around a protein
- Prajwal Nandekar (Fri May 29 2020 - 18:22:43 PDT)
- Sally Pias (Fri May 29 2020 - 17:53:48 PDT)
[AMBER] How to merge GLYCAM06 and lipid17 to generate force field for simple g; ycolipids?
- Lachele Foley (Sun May 10 2020 - 11:31:33 PDT)
- Vijay Achari (Thu May 07 2020 - 01:30:37 PDT)
[AMBER] How to perameterize peptide like compound
- Liao (Wed May 13 2020 - 00:00:47 PDT)
- David Cerutti (Tue May 12 2020 - 08:39:01 PDT)
- Rana Rehan Khalid (Tue May 12 2020 - 05:38:00 PDT)
[AMBER] How to use set pert=true
- Dawid das (Fri May 22 2020 - 07:34:35 PDT)
- David A Case (Wed May 20 2020 - 18:15:53 PDT)
- Dawid das (Wed May 20 2020 - 12:07:10 PDT)
- David A Case (Wed May 20 2020 - 10:43:27 PDT)
- Dawid das (Wed May 20 2020 - 09:32:27 PDT)
[AMBER] igb for non-aqueous solvent?
- Timothy Schutt (Fri May 29 2020 - 06:40:59 PDT)
[AMBER] Installation error
- Hrishikesh Dhondge (Sat May 16 2020 - 03:14:40 PDT)
- David A Case (Fri May 15 2020 - 07:38:38 PDT)
- Hrishikesh Dhondge (Fri May 15 2020 - 03:09:44 PDT)
[AMBER] Installation Error while linking C executable xaLeap
- Hrishikesh Dhondge (Fri May 15 2020 - 06:33:14 PDT)
[AMBER] installation failed libsanderles.dir amd plumed
- Andrew Waight (Wed May 27 2020 - 07:11:45 PDT)
- David A Case (Wed May 27 2020 - 05:25:20 PDT)
- Andrew Waight (Tue May 26 2020 - 21:07:59 PDT)
[AMBER] installation problem
- David A Case (Thu May 14 2020 - 03:56:51 PDT)
- Arthur Glasfeld (Wed May 13 2020 - 16:05:06 PDT)
[AMBER] Installing latest ambertools (2020) with conda
- David A Case (Thu May 28 2020 - 08:34:10 PDT)
- Alan (Thu May 28 2020 - 06:04:48 PDT)
- David A Case (Thu May 28 2020 - 05:59:13 PDT)
- Alan (Thu May 28 2020 - 02:41:50 PDT)
[AMBER] Leaprc error
- janardhanan c (Sun May 03 2020 - 02:58:54 PDT)
- Daniel Roe (Sat May 02 2020 - 04:33:32 PDT)
- janardhanan c (Sat May 02 2020 - 03:11:07 PDT)
[AMBER] Mass-weighted RMSD one-liner with cpptraj - possible?
- Martin Mielke (Fri May 08 2020 - 03:06:43 PDT)
- Daniel Roe (Thu May 07 2020 - 12:47:11 PDT)
- Daniel Roe (Wed May 06 2020 - 06:52:58 PDT)
- Martin Mielke (Wed May 06 2020 - 06:28:27 PDT)
- Martin Mielke (Tue May 05 2020 - 14:26:57 PDT)
- Daniel Roe (Tue May 05 2020 - 06:08:34 PDT)
- Martin Mielke (Mon May 04 2020 - 06:23:09 PDT)
[AMBER] MD and MD-tar restrictions
- MYRIAN TORRES RICO (Fri May 08 2020 - 03:53:54 PDT)
[AMBER] Minimum recommended hardware specs for AmberTools20 and Amber20
- Martin Mielke (Thu May 07 2020 - 00:41:16 PDT)
- Adrianne Lee (Wed May 06 2020 - 14:57:49 PDT)
[AMBER] Missing bond parameters after MCPB.py
- Oleksandr Kravchenko (Wed May 27 2020 - 03:29:31 PDT)
[AMBER] MM-PBSA calculation error
- David A Case (Wed May 06 2020 - 05:36:48 PDT)
- Serena Vittorio (Wed May 06 2020 - 02:01:38 PDT)
[AMBER] MMGBSA-DECOM calculation
- Elvis Martis (Wed May 06 2020 - 06:32:28 PDT)
- Renato Araujo (Wed May 06 2020 - 06:27:05 PDT)
- Renato Araujo (Wed May 06 2020 - 06:15:39 PDT)
- Elvis Martis (Wed May 06 2020 - 05:25:52 PDT)
- Renato Araujo (Wed May 06 2020 - 04:17:46 PDT)
[AMBER] MMPBSA - per residue decomposition
- Prasanth G, Research Scholar (Fri May 22 2020 - 23:50:47 PDT)
- Prasanth G, Research Scholar (Thu May 21 2020 - 01:09:47 PDT)
[AMBER] MMPBSA - Ternary System = protein-ligand-1-ligand-2
- David A Case (Mon May 11 2020 - 04:55:47 PDT)
- Marcelo Andrade Chagas (Mon May 11 2020 - 04:17:38 PDT)
[AMBER] Mol2 to generatee prepc and frcmod fo using Antechamer
- David A Case (Tue May 19 2020 - 18:25:15 PDT)
- Lod King (Tue May 19 2020 - 10:53:07 PDT)
- David A Case (Tue May 19 2020 - 05:02:32 PDT)
- Renato Araujo (Sun May 17 2020 - 07:31:37 PDT)
- Lod King (Sun May 17 2020 - 06:40:47 PDT)
- Renato Araujo (Sun May 17 2020 - 06:12:50 PDT)
- Lod King (Sat May 16 2020 - 19:00:01 PDT)
- David A Case (Sat May 16 2020 - 18:48:47 PDT)
- Lod King (Sat May 16 2020 - 13:16:25 PDT)
- David A Case (Sat May 16 2020 - 05:05:07 PDT)
- Lod King (Fri May 15 2020 - 21:09:20 PDT)
- Renato Araujo (Fri May 15 2020 - 16:01:40 PDT)
- Lod King (Fri May 15 2020 - 08:36:08 PDT)
[AMBER] Neutralizing a system
- David A Case (Sun May 10 2020 - 11:17:53 PDT)
- Jenny 148 (Sun May 10 2020 - 05:56:45 PDT)
[AMBER] NPT 2 ns of equilibration
- Carlos Simmerling (Sat May 02 2020 - 12:44:56 PDT)
- Debarati DasGupta (Sat May 02 2020 - 11:27:21 PDT)
[AMBER] OHE residue and crashing
- David A Case (Wed May 13 2020 - 13:18:59 PDT)
- Piia Kokkonen (Wed May 13 2020 - 05:46:18 PDT)
- David A Case (Tue May 12 2020 - 05:21:38 PDT)
- Piia Kokkonen (Mon May 11 2020 - 23:04:31 PDT)
- Christina Bergonzo (Mon May 11 2020 - 05:48:28 PDT)
- David A Case (Sun May 10 2020 - 11:28:15 PDT)
- Piia Kokkonen (Fri May 08 2020 - 06:49:50 PDT)
[AMBER] Open a hole into an equilibrated lipid bilayer
- Eduardo R. Almeida (Tue May 12 2020 - 19:44:54 PDT)
[AMBER] parameter for modified residue
- sangita kachhap (Tue May 19 2020 - 12:56:35 PDT)
- David A Case (Tue May 19 2020 - 04:43:40 PDT)
- sangita kachhap (Mon May 18 2020 - 09:32:01 PDT)
[AMBER] paramfit - negative energy for 1 of the 2 term
- Erdem Yeler (Sat May 23 2020 - 08:17:55 PDT)
- Robin Betz (Thu May 21 2020 - 14:51:02 PDT)
- Erdem Yeler (Thu May 21 2020 - 05:26:07 PDT)
[AMBER] pmemd simulation
- David Cerutti (Tue May 12 2020 - 23:52:06 PDT)
- Sofia Vasilakaki (Tue May 12 2020 - 23:01:28 PDT)
[AMBER] QM/MM MD: Error reading box
- emanuele falbo (Mon May 25 2020 - 02:39:39 PDT)
- David A Case (Sun May 24 2020 - 06:26:43 PDT)
- emanuele falbo (Sun May 24 2020 - 02:37:03 PDT)
- Daniel Roe (Fri May 22 2020 - 08:55:51 PDT)
- Daniel Roe (Fri May 22 2020 - 08:05:03 PDT)
- emanuele falbo (Fri May 22 2020 - 06:58:27 PDT)
- David A Case (Fri May 22 2020 - 05:32:37 PDT)
- Daniel Roe (Fri May 22 2020 - 04:44:34 PDT)
- emanuele falbo (Fri May 22 2020 - 01:23:23 PDT)
- David A Case (Thu May 21 2020 - 11:05:06 PDT)
- emanuele falbo (Thu May 21 2020 - 07:42:33 PDT)
[AMBER] QM/MM with finite temperature string
- Pratul Agarwal (Fri May 01 2020 - 11:17:57 PDT)
[AMBER] Query regarding calculating RMSF.
- Daniel Roe (Mon May 18 2020 - 09:03:46 PDT)
- Md Fulbabu Sk (Fri May 15 2020 - 04:57:32 PDT)
- DHEERAJ CHITARA (Thu May 14 2020 - 23:51:19 PDT)
[AMBER] Query regarding force fields
- Carlos Simmerling (Fri May 15 2020 - 11:25:18 PDT)
- SHAUNAK BADANI (Fri May 15 2020 - 11:10:15 PDT)
[AMBER] Questions about PCA
- Daniel Roe (Wed May 20 2020 - 09:16:42 PDT)
- Kat G (Thu May 14 2020 - 21:27:24 PDT)
[AMBER] Questions about QM
- Ignjat Filipović (Mon May 25 2020 - 07:23:45 PDT)
[AMBER] questions for mdgx-virtual site
- David Cerutti (Fri May 29 2020 - 02:49:46 PDT)
- David Cerutti (Fri May 29 2020 - 02:42:42 PDT)
- Gao J (Fri May 29 2020 - 01:29:44 PDT)
[AMBER] Release of Amber20 and AmberTools20
- David A Case (Mon May 04 2020 - 07:40:01 PDT)
- Robert Molt (Mon May 04 2020 - 05:42:25 PDT)
- David A Case (Mon May 04 2020 - 05:34:13 PDT)
[AMBER] RMSD discontinuity between NPT and NVT with restraints
- Thomas Gaillard (Wed May 06 2020 - 08:57:00 PDT)
[AMBER] SHAKE ALgorithm and frcmod file
- Elif Çiğdem Calvin (Fri May 01 2020 - 05:52:30 PDT)
- David A Case (Fri May 01 2020 - 05:34:04 PDT)
- Elif Çiğdem Calvin (Fri May 01 2020 - 05:27:35 PDT)
- Carlos Simmerling (Fri May 01 2020 - 05:25:48 PDT)
- Elif Çiğdem Calvin (Fri May 01 2020 - 05:22:51 PDT)
- Elif Çiğdem Calvin (Thu Apr 30 2020 - 14:14:10 PDT)
[AMBER] Similar RESP1 and RESP2 fitting outputs
- Kodituwakku,Dimuthu Nirmani (Fri May 15 2020 - 07:16:21 PDT)
[AMBER] Simulating pyridine in water TIP3P
- David A Case (Thu May 28 2020 - 18:33:01 PDT)
- Debarati DasGupta (Thu May 28 2020 - 09:22:57 PDT)
[AMBER] Simulation stops during NPT
- David A Case (Mon May 04 2020 - 05:38:24 PDT)
- Sunita Patel (Sun May 03 2020 - 18:45:07 PDT)
- Sunita Patel (Sun May 03 2020 - 11:52:50 PDT)
- Carlos Simmerling (Sun May 03 2020 - 05:07:25 PDT)
- Sunita Patel (Sat May 02 2020 - 23:11:09 PDT)
- Carlos Simmerling (Sat May 02 2020 - 03:30:55 PDT)
- Sunita Patel (Sat May 02 2020 - 03:18:09 PDT)
[AMBER] Small molecules paramters
- Gustavo Seabra (Fri May 29 2020 - 09:20:56 PDT)
- Gustaf Olsson (Thu May 28 2020 - 22:53:03 PDT)
- Athena N (Thu May 28 2020 - 05:47:24 PDT)
[AMBER] Steered MD with COM_ANGLE
- Feng Pan (Mon May 18 2020 - 06:35:27 PDT)
- Amanda Buyan (Thu May 14 2020 - 19:20:28 PDT)
- Kellon Belfon (Thu May 14 2020 - 12:04:04 PDT)
- Amanda Buyan (Wed May 13 2020 - 23:18:43 PDT)
- Kellon Belfon (Wed May 13 2020 - 19:34:31 PDT)
- Amanda Buyan (Wed May 13 2020 - 16:43:06 PDT)
- Adrian Roitberg (Wed May 13 2020 - 16:36:49 PDT)
- Amanda Buyan (Wed May 13 2020 - 16:32:22 PDT)
[AMBER] Temperature and total energy keeps dropping with NVE ensemble
- David Cerutti (Sun May 10 2020 - 22:23:53 PDT)
- Adrian Roitberg (Sat May 09 2020 - 08:52:55 PDT)
- David A Case (Sat May 09 2020 - 06:03:05 PDT)
- Liao (Fri May 08 2020 - 21:38:15 PDT)
[AMBER] the error from make test.serial
- David A Case (Sun May 10 2020 - 11:17:28 PDT)
- 谢信锐 (Sun May 10 2020 - 07:00:09 PDT)
- David A Case (Sun May 10 2020 - 06:19:42 PDT)
- 谢信锐 (Sun May 10 2020 - 05:28:34 PDT)
[AMBER] The lipid section in the 2020 manual require updating
- Stephan Schott (Tue May 05 2020 - 07:39:53 PDT)
- Ross Walker (Tue May 05 2020 - 07:30:23 PDT)
- Gould, Ian R (Tue May 05 2020 - 07:19:50 PDT)
- Stephan Schott (Tue May 05 2020 - 06:45:59 PDT)
- David A Case (Tue May 05 2020 - 06:09:05 PDT)
- Zhiyi Wu (Tue May 05 2020 - 03:38:05 PDT)
[AMBER] Thermodynamic integration by parameter interpolation (PI-TI)
- Veenis, Andrew Jay (Thu May 07 2020 - 07:01:05 PDT)
[AMBER] TI production runs(20ns) NVT query
- Debarati DasGupta (Thu May 21 2020 - 07:05:42 PDT)
[AMBER] TI simulations
- Debarati DasGupta (Fri May 01 2020 - 05:27:21 PDT)
- Song, Lin (Thu Apr 30 2020 - 17:18:02 PDT)
[AMBER] timestep dt for higher temperatures
- David A Case (Fri May 01 2020 - 05:36:33 PDT)
- Liao (Fri May 01 2020 - 00:41:54 PDT)
[AMBER] tlea
- David Cerutti (Sun May 10 2020 - 12:19:38 PDT)
- Lachele Foley (Sun May 10 2020 - 11:14:40 PDT)
[AMBER] Tool to calculate CSP and NOE for DNA trajectory?
- Kenneth Huang (Thu May 28 2020 - 20:57:59 PDT)
- Christina Bergonzo (Thu May 28 2020 - 05:42:20 PDT)
- Kenneth Huang (Wed May 27 2020 - 16:47:41 PDT)
[AMBER] Topology and parameters for the T4 - Thyroxine
- David A Case (Tue May 12 2020 - 18:51:17 PDT)
- Marcelo Andrade Chagas (Tue May 12 2020 - 15:08:35 PDT)
[AMBER] updating to ambertools 20 from version 19
- David A Case (Fri May 15 2020 - 07:42:04 PDT)
- Homeo Morphism (Fri May 15 2020 - 03:57:48 PDT)
[AMBER] upgrade to 19
- David A Case (Sat May 16 2020 - 05:29:36 PDT)
- Scott Brozell (Fri May 15 2020 - 15:01:29 PDT)
[AMBER] Using pytraj with jupyter notebook
- Hai Nguyen (Sun May 31 2020 - 16:43:39 PDT)
- Rangarajan, Amith (Sun May 31 2020 - 12:44:17 PDT)
[AMBER] What would you like to see in visualization of chemical data?
- Jan Mičan (Tue May 26 2020 - 09:59:39 PDT)
[AMBER] wrong geometry amide nitrogen
- Arnaud Bondon (Sat May 02 2020 - 05:30:27 PDT)
- Junmei Wang (Fri May 01 2020 - 12:50:30 PDT)
- Arnaud Bondon (Fri May 01 2020 - 03:54:42 PDT)
[AMBER] Xmin minimisation
- David A Case (Sat May 09 2020 - 05:59:17 PDT)
- Scott Brozell (Fri May 08 2020 - 17:41:26 PDT)
- Athena N (Fri May 08 2020 - 10:18:41 PDT)
Amber18 - MPI version error on HPC Cluster
- David A Case (Fri May 15 2020 - 07:46:18 PDT)
- Gustaf Olsson (Thu May 14 2020 - 22:34:46 PDT)
- Sivanandam Magudeeswaran (Thu May 14 2020 - 21:04:53 PDT)
Amber99SB force field
- Smith, Micholas D. (Thu May 28 2020 - 11:54:46 PDT)
MM-PBSA calculation error
- Serena Vittorio (Thu May 07 2020 - 02:26:12 PDT)
- David A Case (Wed May 06 2020 - 09:32:42 PDT)
- Serena Vittorio (Wed May 06 2020 - 08:38:01 PDT)

Amber Archive May 2020 by subject