Amber Archive Oct 2020: by subject

[AMBER] [GaMD-discuss] GaMD
- Neha Gandhi (Sun Oct 25 2020 - 17:11:36 PDT)
[AMBER] a metal bound Met
- Wu Xu (Wed Oct 28 2020 - 18:41:39 PDT)
- Vaibhav Dixit (Wed Oct 28 2020 - 18:31:06 PDT)
- Wu Xu (Wed Oct 28 2020 - 12:33:18 PDT)
[AMBER] A100 and RTX3090 Benchmarks
- Ross Walker (Tue Oct 06 2020 - 10:31:45 PDT)
- Ross Walker (Tue Oct 06 2020 - 10:13:48 PDT)
- David A Case (Tue Oct 06 2020 - 05:26:26 PDT)
- Filip Fratev (Tue Oct 06 2020 - 01:44:54 PDT)
[AMBER] about translation
- aishen (Sat Oct 03 2020 - 01:21:57 PDT)
[AMBER] Adding catalytic Magnesium ion
- Juraj Dobias (Mon Oct 19 2020 - 00:27:50 PDT)
- Abhilash J (Sat Oct 17 2020 - 14:41:57 PDT)
- Jisha B (Sat Oct 17 2020 - 03:22:48 PDT)
- Jisha B (Thu Oct 15 2020 - 15:10:17 PDT)
[AMBER] Adding Ions
- Gustaf Olsson (Thu Oct 22 2020 - 05:27:14 PDT)
- David A Case (Thu Oct 22 2020 - 05:21:51 PDT)
- Gustaf Olsson (Thu Oct 22 2020 - 01:01:09 PDT)
- Matias Machado (Wed Oct 21 2020 - 10:22:20 PDT)
- David A Case (Wed Oct 21 2020 - 05:40:45 PDT)
- Gustaf Olsson (Wed Oct 21 2020 - 05:26:56 PDT)
- Gustaf Olsson (Wed Oct 21 2020 - 00:04:40 PDT)
- Bill Ross (Tue Oct 20 2020 - 06:48:33 PDT)
- Gustaf Olsson (Tue Oct 20 2020 - 05:56:08 PDT)
[AMBER] Adding missing residues in a pdb file using tleap
- David A Case (Mon Oct 19 2020 - 04:39:14 PDT)
- SUNITA MUDULI (Sun Oct 18 2020 - 12:14:01 PDT)
[AMBER] Additional restraints in Umbrella sampling?
- Qing Lv (Thu Oct 01 2020 - 18:29:39 PDT)
[AMBER] AMBER 20 Benchmarks on NVIDIA RTX 3080/3090 and more
- Mike Mazanetz (Tue Oct 27 2020 - 03:40:10 PDT)
- Jason Hogrefe (Mon Oct 26 2020 - 15:26:13 PDT)
[AMBER] Amber 20 compilation with the intel 2019.1.1 compiler
- Scott Brozell (Fri Oct 30 2020 - 13:47:02 PDT)
- Vlad Cojocaru (Fri Oct 23 2020 - 01:28:11 PDT)
- Scott Brozell (Wed Oct 21 2020 - 16:04:20 PDT)
- Vlad Cojocaru (Wed Oct 21 2020 - 04:31:27 PDT)
- Scott Brozell (Tue Oct 20 2020 - 14:37:31 PDT)
- David A Case (Tue Oct 20 2020 - 10:50:49 PDT)
- Vlad Cojocaru (Tue Oct 20 2020 - 07:46:37 PDT)
- Vlad Cojocaru (Tue Oct 20 2020 - 04:37:59 PDT)
- Scott Brozell (Mon Oct 19 2020 - 19:10:10 PDT)
- Scott Brozell (Mon Oct 19 2020 - 18:44:09 PDT)
- Vlad Cojocaru (Mon Oct 19 2020 - 10:47:43 PDT)
[AMBER] Amber performance
- Ross Walker (Tue Oct 06 2020 - 16:19:45 PDT)
- Bill Ross (Tue Oct 06 2020 - 16:13:54 PDT)
- Jonathan Gabriel Canan Gomez (Tue Oct 06 2020 - 15:56:22 PDT)
[AMBER] Amber TI - crgmask
- Juraj Dobias (Fri Oct 30 2020 - 03:39:02 PDT)
- Delwakkada Liyanage, Senal Dinuka (Thu Oct 29 2020 - 08:16:23 PDT)
- Juraj Dobias (Thu Oct 29 2020 - 02:04:50 PDT)
- Delwakkada Liyanage, Senal Dinuka (Wed Oct 28 2020 - 09:02:42 PDT)
[AMBER] amber14 and amber16 are not working in new installation
- David A Case (Mon Oct 26 2020 - 06:23:20 PDT)
- Marcelo Andrade Chagas (Fri Oct 23 2020 - 19:31:47 PDT)
[AMBER] AMBER16 problem
- Seibold, Steve Allan (Wed Oct 21 2020 - 10:08:17 PDT)
- David A Case (Tue Oct 20 2020 - 10:59:46 PDT)
- Seibold, Steve Allan (Tue Oct 20 2020 - 07:56:20 PDT)
[AMBER] Amber20 and RNA simulations
- Piia Kokkonen (Wed Oct 28 2020 - 05:22:05 PDT)
- David A Case (Wed Oct 28 2020 - 04:58:52 PDT)
- Piia Kokkonen (Wed Oct 28 2020 - 03:31:13 PDT)
[AMBER] Amber20 compilation issue (related to boost?)
- Suman Chakrabarty (Fri Oct 09 2020 - 02:35:46 PDT)
- George M. Giambasu (Thu Oct 08 2020 - 20:25:18 PDT)
- Suman Chakrabarty (Wed Oct 07 2020 - 23:07:08 PDT)
[AMBER] Amber20 compiling warning
- David A Case (Mon Oct 19 2020 - 04:29:31 PDT)
- Tom Wang (Sun Oct 18 2020 - 05:40:44 PDT)
[AMBER] Amber20 installation for MPI, CUDA issues.
- Luka Bilić (Fri Oct 30 2020 - 03:30:45 PDT)
- Luka Bilić (Thu Oct 29 2020 - 12:38:15 PDT)
[AMBER] Amber20: Ampere microarchitecture support and Amber release in 2021
- Kraus, Sebastian (Tue Oct 27 2020 - 00:36:28 PDT)
[AMBER] Amber20: Ampere microarchitecture support and next Amber release
- David A Case (Mon Oct 26 2020 - 17:55:55 PDT)
- Kraus, Sebastian (Mon Oct 26 2020 - 12:18:42 PDT)
[AMBER] AmberMdPrep github cpptraj not sourced
- Vaibhav Dixit (Wed Oct 21 2020 - 04:37:06 PDT)
- Daniel Roe (Wed Oct 21 2020 - 03:38:33 PDT)
- Vaibhav Dixit (Fri Oct 09 2020 - 17:30:17 PDT)
[AMBER] assess which structures are similar between two MD-trajectories
- Vaibhav Dixit (Wed Oct 14 2020 - 20:51:04 PDT)
[AMBER] Bacteria cell membrane PDB
- Loo Kang (Mon Oct 19 2020 - 20:06:53 PDT)
[AMBER] Bond: Maximum coordination exceeded
- David A Case (Mon Oct 19 2020 - 04:37:02 PDT)
- Sarah Jane (Sun Oct 18 2020 - 11:21:45 PDT)
[AMBER] calculating differences in binding energy for enantiomers to amino acid based surfactants
- Billiot, Eugene (Tue Oct 20 2020 - 05:45:16 PDT)
[AMBER] Cannot access amber website
- Elvis Martis (Thu Oct 22 2020 - 08:44:27 PDT)
- Lang,Lijun (Thu Oct 22 2020 - 08:13:11 PDT)
[AMBER] Cannot run NPT
- mohamed marzouk (Mon Oct 12 2020 - 10:45:54 PDT)
- David A Case (Thu Oct 08 2020 - 05:04:46 PDT)
- Juraj Dobias (Thu Oct 08 2020 - 04:21:35 PDT)
- mohamed marzouk (Wed Oct 07 2020 - 19:41:01 PDT)
- David A Case (Wed Oct 07 2020 - 08:17:36 PDT)
- mohamed marzouk (Wed Oct 07 2020 - 07:05:56 PDT)
[AMBER] cellulose crystal structure ( cellulose bundles)
- Bill Ross (Thu Oct 29 2020 - 10:34:27 PDT)
- Pinky Mazumder (Thu Oct 29 2020 - 09:54:09 PDT)
- David A Case (Thu Oct 29 2020 - 05:05:03 PDT)
- Pinky Mazumder (Thu Oct 29 2020 - 00:59:00 PDT)
[AMBER] Changing lj_radius without changing lj_14_radius
- Matias Machado (Mon Oct 26 2020 - 14:43:38 PDT)
- Batuhan Kav (Mon Oct 26 2020 - 09:22:52 PDT)
- Matias Machado (Thu Oct 22 2020 - 07:43:42 PDT)
- Batuhan Kav (Thu Oct 22 2020 - 01:34:22 PDT)
- Matias Machado (Wed Oct 21 2020 - 11:25:38 PDT)
- Batuhan Kav (Mon Oct 19 2020 - 08:23:32 PDT)
[AMBER] CO2
- Raman Preet Singh (Wed Oct 28 2020 - 23:41:03 PDT)
- Carlos Simmerling (Wed Oct 28 2020 - 12:37:06 PDT)
- Michele Vanini (Wed Oct 28 2020 - 12:20:17 PDT)
- Raman Preet Singh (Wed Oct 28 2020 - 10:38:01 PDT)
- Michele Vanini (Wed Oct 28 2020 - 09:55:40 PDT)
[AMBER] Compiling CPPTRAJ from GitHub
- Gustaf Olsson (Thu Oct 08 2020 - 05:37:36 PDT)
- Daniel Roe (Wed Oct 07 2020 - 07:47:57 PDT)
- Gustaf Olsson (Tue Oct 06 2020 - 02:28:30 PDT)
- Gustaf Olsson (Tue Oct 06 2020 - 02:22:08 PDT)
- Gustaf Olsson (Tue Oct 06 2020 - 02:00:32 PDT)
- Daniel Roe (Mon Oct 05 2020 - 07:07:46 PDT)
- David A Case (Mon Oct 05 2020 - 06:58:23 PDT)
- Gustaf Olsson (Mon Oct 05 2020 - 00:09:07 PDT)
- Daniel Roe (Fri Oct 02 2020 - 08:41:39 PDT)
- David A Case (Fri Oct 02 2020 - 08:34:48 PDT)
- Gustaf Olsson (Fri Oct 02 2020 - 05:06:43 PDT)
- Gustaf Olsson (Fri Oct 02 2020 - 03:53:11 PDT)
[AMBER] Conda installation of AmberTools
- Hai Nguyen (Mon Oct 12 2020 - 09:54:35 PDT)
- mukesh raval (Sat Oct 10 2020 - 21:00:54 PDT)
[AMBER] Constant Force SMD simulation
- Vishal Singh (Thu Oct 29 2020 - 22:07:42 PDT)
- MR. RABINDRANATH PAUL (Thu Oct 29 2020 - 21:55:21 PDT)
- Vishal Singh (Thu Oct 29 2020 - 21:05:24 PDT)
[AMBER] controversy in PBSA and GBSA results
- Ray Luo (Tue Oct 20 2020 - 09:54:08 PDT)
- Carlos Simmerling (Tue Oct 20 2020 - 05:34:39 PDT)
- h_sahakyan.mb.sci.am (Tue Oct 20 2020 - 05:27:05 PDT)
- Ray Luo (Wed Oct 07 2020 - 10:35:08 PDT)
- Ray Luo (Wed Oct 07 2020 - 10:08:33 PDT)
- Ray Luo (Wed Oct 07 2020 - 10:06:39 PDT)
- h_sahakyan.mb.sci.am (Wed Oct 07 2020 - 06:19:19 PDT)
- h_sahakyan.mb.sci.am (Mon Oct 05 2020 - 09:04:26 PDT)
- Ray Luo (Mon Oct 05 2020 - 07:39:59 PDT)
- h_sahakyan.mb.sci.am (Sun Oct 04 2020 - 22:28:30 PDT)
- h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 23:32:19 PDT)
- h_sahakyan.mb.sci.am (Wed Sep 30 2020 - 21:16:05 PDT)
[AMBER] Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT
- Matias Machado (Thu Oct 01 2020 - 05:58:33 PDT)
[AMBER] correct md-input & prmtop for TI calculations
- Vaibhav Dixit (Mon Oct 26 2020 - 03:47:15 PDT)
- Vaibhav Dixit (Thu Oct 22 2020 - 02:27:55 PDT)
[AMBER] cpptraj unable to write pdb files using
- Vaibhav Dixit (Wed Oct 07 2020 - 16:43:25 PDT)
- Daniel Roe (Wed Oct 07 2020 - 08:35:37 PDT)
- David A Case (Wed Oct 07 2020 - 08:05:22 PDT)
- Elvis Martis (Wed Oct 07 2020 - 07:52:26 PDT)
- Daniel Roe (Wed Oct 07 2020 - 07:52:13 PDT)
- Daniel Roe (Wed Oct 07 2020 - 07:50:38 PDT)
- Vaibhav Dixit (Wed Oct 07 2020 - 06:47:17 PDT)
- Elvis Martis (Wed Oct 07 2020 - 05:40:39 PDT)
- Vaibhav Dixit (Wed Oct 07 2020 - 01:57:52 PDT)
- Vaibhav Dixit (Mon Oct 05 2020 - 21:16:18 PDT)
- Elvis Martis (Mon Oct 05 2020 - 21:06:15 PDT)
- Vaibhav Dixit (Mon Oct 05 2020 - 20:56:51 PDT)
- Elvis Martis (Sun Oct 04 2020 - 09:31:39 PDT)
- Vaibhav Dixit (Sun Oct 04 2020 - 09:15:12 PDT)
- Daniel Roe (Sun Oct 04 2020 - 06:46:05 PDT)
- Vaibhav Dixit (Sat Oct 03 2020 - 21:32:46 PDT)
[AMBER] cpptraj's hbond shows hbonds with carbon hydrogens
- German P. Barletta (Fri Oct 16 2020 - 13:03:50 PDT)
- Daniel Roe (Thu Oct 15 2020 - 15:48:27 PDT)
- German P. Barletta (Thu Oct 15 2020 - 12:53:21 PDT)
[AMBER] CPPTRAJ: Cluster structures keeping only one water, by position?
- Gustavo Seabra (Fri Oct 09 2020 - 15:10:23 PDT)
- Niel Henriksen (Fri Oct 09 2020 - 14:41:34 PDT)
- Gustavo Seabra (Fri Oct 09 2020 - 11:14:59 PDT)
[AMBER] Creating a coordinate bond in Leap
- Bill Ross (Sat Oct 17 2020 - 05:30:18 PDT)
- Bill Ross (Fri Oct 16 2020 - 22:13:13 PDT)
- Elvis Martis (Fri Oct 16 2020 - 22:10:59 PDT)
- Jenny 148 (Fri Oct 16 2020 - 21:53:54 PDT)
[AMBER] ddikick.x error during Fe3+ ion parameter derivation using Gamess
- Pengfei Li (Thu Oct 22 2020 - 14:14:09 PDT)
[AMBER] Different atomic partial charges on OD1/OD2
- Margareta Hellmann (Mon Oct 05 2020 - 07:59:37 PDT)
[AMBER] doubt charges
- MYRIAN TORRES RICO (Mon Oct 26 2020 - 02:15:27 PDT)
- MYRIAN TORRES RICO (Mon Oct 26 2020 - 02:11:53 PDT)
- gagandeep singh (Fri Oct 23 2020 - 06:27:09 PDT)
- Dr. Anselm Horn (Fri Oct 23 2020 - 08:28:58 PDT)
- MYRIAN TORRES RICO (Fri Oct 23 2020 - 07:10:55 PDT)
- David A Case (Fri Oct 23 2020 - 05:38:41 PDT)
- MYRIAN TORRES RICO (Fri Oct 23 2020 - 05:30:26 PDT)
- Dr. Anselm Horn (Fri Oct 23 2020 - 01:28:05 PDT)
- MYRIAN TORRES RICO (Fri Oct 23 2020 - 01:11:27 PDT)
[AMBER] drms comparison in sander during minimization?
- David A Case (Fri Oct 23 2020 - 05:31:32 PDT)
- Kenneth Huang (Thu Oct 22 2020 - 20:59:05 PDT)
- David A Case (Thu Oct 22 2020 - 05:42:27 PDT)
- Kenneth Huang (Wed Oct 21 2020 - 15:03:40 PDT)
[AMBER] error 403
- Ayesha Fatima (Thu Oct 22 2020 - 10:57:21 PDT)
[AMBER] Error building Amber
- Kazuo Ohta (Tue Oct 20 2020 - 19:08:05 PDT)
[AMBER] Error running small molecule simulation: "RESTARTED DUE TO LINMIN FAILURE" and "an illegal memory access was encountered launching kernel kClearForces" erros
- David A Case (Sun Oct 18 2020 - 05:37:19 PDT)
- Állan Ferrari (Thu Oct 15 2020 - 07:11:40 PDT)
- David A Case (Thu Oct 15 2020 - 06:43:25 PDT)
- Állan Ferrari (Thu Oct 15 2020 - 06:26:08 PDT)
- David A Case (Thu Oct 15 2020 - 05:10:07 PDT)
- Állan Ferrari (Wed Oct 14 2020 - 12:57:44 PDT)
- David A Case (Tue Oct 13 2020 - 08:05:30 PDT)
- Állan Ferrari (Tue Oct 13 2020 - 07:07:53 PDT)
[AMBER] Error: Failed to generate parameters
- David A Case (Fri Oct 02 2020 - 08:26:38 PDT)
- Jatin Kashyap (Thu Oct 01 2020 - 13:55:14 PDT)
- David A Case (Thu Oct 01 2020 - 13:45:02 PDT)
- Jatin Kashyap (Thu Oct 01 2020 - 09:57:17 PDT)
[AMBER] ERROR: The file contained 14 atoms not in residue templates
- Carlos Simmerling (Thu Oct 08 2020 - 12:48:34 PDT)
- Jatin Kashyap (Thu Oct 08 2020 - 12:28:14 PDT)
[AMBER] ff19SB and OPC, process_(min/md)out.perl and LEaP
- Gustaf Olsson (Mon Oct 26 2020 - 01:21:15 PDT)
- Gustaf Olsson (Mon Oct 26 2020 - 00:46:07 PDT)
- Carlos Simmerling (Sat Oct 24 2020 - 12:58:16 PDT)
- Gustaf Olsson (Sat Oct 24 2020 - 12:49:30 PDT)
- Carlos Simmerling (Fri Oct 23 2020 - 10:28:58 PDT)
- Gustaf Olsson (Fri Oct 23 2020 - 10:27:05 PDT)
- Gustaf Olsson (Fri Oct 23 2020 - 10:23:56 PDT)
- Daniel Roe (Fri Oct 23 2020 - 10:19:28 PDT)
- Carlos Simmerling (Fri Oct 23 2020 - 07:34:22 PDT)
- Daniel Roe (Fri Oct 23 2020 - 07:29:46 PDT)
- Carlos Simmerling (Fri Oct 23 2020 - 05:27:34 PDT)
- Daniel Roe (Fri Oct 23 2020 - 04:28:37 PDT)
- Gustaf Olsson (Fri Oct 23 2020 - 04:12:43 PDT)
- Daniel Roe (Fri Oct 23 2020 - 02:36:20 PDT)
- Gustaf Olsson (Fri Oct 23 2020 - 02:26:05 PDT)
- Carlos Simmerling (Thu Oct 22 2020 - 06:06:06 PDT)
- David A Case (Thu Oct 22 2020 - 05:47:51 PDT)
- Gustaf Olsson (Thu Oct 22 2020 - 02:27:13 PDT)
- Gustaf Olsson (Thu Oct 22 2020 - 01:53:17 PDT)
- Gustaf Olsson (Thu Oct 22 2020 - 00:10:34 PDT)
- Carlos Simmerling (Wed Oct 21 2020 - 06:32:50 PDT)
- Gustaf Olsson (Wed Oct 21 2020 - 05:36:30 PDT)
- Gustaf Olsson (Wed Oct 21 2020 - 01:10:10 PDT)
[AMBER] Force field for IDP
- David A Case (Fri Oct 30 2020 - 04:33:20 PDT)
- mohamed marzouk (Thu Oct 29 2020 - 08:31:29 PDT)
[AMBER] Fwd: AMBER Digest, Vol 3153, Issue 1
- David A Case (Fri Oct 16 2020 - 05:04:20 PDT)
- SATYAJIT KHATUA (Thu Oct 15 2020 - 21:59:05 PDT)
[AMBER] Fwd: Imaging issues with cpptraj
- Daniel Roe (Wed Oct 07 2020 - 07:53:32 PDT)
- Suchetana Gupta (Wed Oct 07 2020 - 00:12:36 PDT)
- Suchetana Gupta (Tue Oct 06 2020 - 23:56:51 PDT)
- Suchetana Gupta (Tue Oct 06 2020 - 21:43:51 PDT)
[AMBER] Fwd: MMGBSA Ligand Mask issues
- Suchetana Gupta (Wed Oct 14 2020 - 05:17:22 PDT)
[AMBER] Fwd: MMPBSA calculations with 1 explicit water molecule
- Ray Luo (Fri Oct 30 2020 - 08:02:45 PDT)
- divyabharathi korlepara (Thu Oct 22 2020 - 11:01:31 PDT)
[AMBER] GaMD
- Neha Gandhi (Thu Oct 22 2020 - 15:30:03 PDT)
[AMBER] Help with parameterization of non-standard amino acid
- Dr. Anselm Horn (Wed Oct 28 2020 - 07:57:34 PDT)
- Amit Sharma (Asstt. Prof., MCARS) (Wed Oct 28 2020 - 05:43:59 PDT)
[AMBER] Hitting the supercomputer wall limit before completion of minimization step
- Carlos Simmerling (Mon Oct 05 2020 - 11:52:19 PDT)
- Jatin Kashyap (Mon Oct 05 2020 - 09:25:13 PDT)
- Carlos Simmerling (Mon Oct 05 2020 - 08:38:43 PDT)
- Jatin Kashyap (Mon Oct 05 2020 - 08:28:44 PDT)
[AMBER] How does one build MMPBSA.py.MPI on a Centos 7 system?
- David A Case (Mon Oct 05 2020 - 12:53:39 PDT)
- Hamed S. Hayatshahi (Mon Oct 05 2020 - 12:30:44 PDT)
[AMBER] how find Es from mdout to estimate vertical energy gap
- Adrian Roitberg (Sat Oct 31 2020 - 09:28:25 PDT)
- Vaibhav Dixit (Fri Oct 30 2020 - 13:56:58 PDT)
- Vaibhav Dixit (Fri Oct 30 2020 - 13:20:58 PDT)
- Adrian Roitberg (Fri Oct 30 2020 - 10:11:02 PDT)
- Vaibhav Dixit (Fri Oct 30 2020 - 10:05:07 PDT)
[AMBER] How to deal with oxygen atom on Fe=O of Compound I (heme enzyme, P450)
- Pengfei Li (Thu Oct 22 2020 - 14:36:01 PDT)
[AMBER] How to import (.pdb) files into xleap of AMBER generated by Cellulose builder
- Bill Ross (Thu Oct 29 2020 - 10:28:28 PDT)
- Pinky Mazumder (Thu Oct 29 2020 - 09:58:46 PDT)
- Dr. Anselm Horn (Thu Oct 29 2020 - 03:24:11 PDT)
- Pinky Mazumder (Wed Oct 28 2020 - 22:47:59 PDT)
[AMBER] how to use one prmtop for two trajectories with just one ion difference
- Thomas Cheatham (Thu Oct 08 2020 - 16:37:23 PDT)
- Vaibhav Dixit (Wed Oct 07 2020 - 17:03:46 PDT)
- Thomas Cheatham (Wed Oct 07 2020 - 16:17:10 PDT)
- Vaibhav Dixit (Sat Oct 03 2020 - 06:29:12 PDT)
- Carlos Simmerling (Sat Oct 03 2020 - 06:16:25 PDT)
- Vaibhav Dixit (Fri Oct 02 2020 - 14:12:32 PDT)
- Carlos Simmerling (Fri Oct 02 2020 - 09:30:26 PDT)
- Vaibhav Dixit (Fri Oct 02 2020 - 08:42:28 PDT)
- Carlos Simmerling (Fri Oct 02 2020 - 08:06:47 PDT)
- Vaibhav Dixit (Fri Oct 02 2020 - 07:55:35 PDT)
[AMBER] image protein complex iwrap=1
- Daniel Roe (Sun Oct 04 2020 - 06:51:56 PDT)
- David A Case (Fri Oct 02 2020 - 08:43:53 PDT)
- Ari Zeida (Fri Oct 02 2020 - 07:21:41 PDT)
[AMBER] Imaging issues with cpptraj
- Suchetana Gupta (Tue Oct 06 2020 - 00:09:41 PDT)
[AMBER] Installation of AMBER20 on CentOS 7
- David A Case (Wed Oct 14 2020 - 12:20:55 PDT)
- Pandey Anwesh (Wed Oct 14 2020 - 06:53:31 PDT)
[AMBER] installing Amber18 and AmberTools20
- David A Case (Thu Oct 22 2020 - 05:37:10 PDT)
- Seibold, Steve Allan (Wed Oct 21 2020 - 10:40:43 PDT)
[AMBER] Is the amber website down? 9am EST
- David A Case (Thu Oct 22 2020 - 12:42:47 PDT)
- Debarati DasGupta (Thu Oct 22 2020 - 06:13:12 PDT)
[AMBER] Is there a way to analyze contact maps of mixtures of more than 2 components?
- Naxhije Berisha (Fri Oct 23 2020 - 10:44:52 PDT)
[AMBER] KeyError: 'H262'
- Wu Xu (Fri Oct 23 2020 - 18:57:32 PDT)
- Wu Xu (Thu Oct 22 2020 - 20:09:03 PDT)
- Pengfei Li (Thu Oct 22 2020 - 15:32:52 PDT)
- Wu Xu (Thu Oct 15 2020 - 20:25:27 PDT)
[AMBER] Loading R.E.D server parameters into xleap
- Emmett Leddin (Fri Oct 16 2020 - 10:11:59 PDT)
- Sruthi Sudhakar (Fri Oct 16 2020 - 06:12:44 PDT)
- Emmett Leddin (Fri Oct 16 2020 - 05:05:09 PDT)
- Sruthi Sudhakar (Fri Oct 16 2020 - 02:50:13 PDT)
[AMBER] MCPB with OPC water?
- Gustavo Seabra (Thu Oct 22 2020 - 17:11:19 PDT)
- Pengfei Li (Thu Oct 22 2020 - 13:59:34 PDT)
[AMBER] MD error
- Kehinde Idowu (Mon Oct 19 2020 - 07:58:48 PDT)
- David A Case (Mon Oct 19 2020 - 04:42:58 PDT)
- Kehinde Idowu (Sun Oct 18 2020 - 14:24:14 PDT)
[AMBER] mdout error
- Alejandro Cagnoni (Tue Oct 20 2020 - 04:54:13 PDT)
[AMBER] mdout issue
- Alejandro Cagnoni (Thu Oct 15 2020 - 07:01:53 PDT)
[AMBER] Metalloprotein-ligand complex modelling for MMPBSA.py
- SATYAJIT KHATUA (Mon Oct 19 2020 - 00:59:36 PDT)
[AMBER] mm-pbsa calculation
- Suchetana Gupta (Sun Oct 18 2020 - 00:13:36 PDT)
- Serena Vittorio (Fri Oct 16 2020 - 09:21:24 PDT)
[AMBER] mm-pbsa calculation: SA Bomb in circle(): Stored surface arcs over limit
- David A Case (Mon Oct 19 2020 - 04:47:09 PDT)
- Serena Vittorio (Mon Oct 19 2020 - 01:27:56 PDT)
[AMBER] MM/PBSA after minimization
- David A Case (Fri Oct 30 2020 - 04:38:53 PDT)
- h_sahakyan.mb.sci.am (Thu Oct 29 2020 - 12:56:21 PDT)
[AMBER] MMGBSA Ligand Mask issues
- Suchetana Gupta (Tue Oct 13 2020 - 03:03:31 PDT)
[AMBER] MMGBSA/MMPBSA Help
- Ray Luo (Fri Oct 30 2020 - 07:42:37 PDT)
- Abdul-Rashid III Sampaco (Sat Oct 03 2020 - 04:33:44 PDT)
[AMBER] MMPBS decomposition error
- MYRIAN TORRES RICO (Wed Oct 21 2020 - 02:05:27 PDT)
[AMBER] mmpbsa error
- MYRIAN TORRES RICO (Tue Oct 27 2020 - 01:37:12 PDT)
- David A Case (Mon Oct 26 2020 - 17:48:53 PDT)
- MYRIAN TORRES RICO (Mon Oct 26 2020 - 10:30:43 PDT)
- David A Case (Mon Oct 26 2020 - 06:26:32 PDT)
- MYRIAN TORRES RICO (Mon Oct 26 2020 - 05:53:47 PDT)
[AMBER] MMPBSA.py TypeError: a bytes-like object is required, not 'str'
- Hamed S. Hayatshahi (Mon Oct 05 2020 - 11:15:06 PDT)
- Ray Luo (Thu Oct 01 2020 - 20:16:16 PDT)
- سید حامد سادات حیاتشاهی (Thu Oct 01 2020 - 13:52:28 PDT)
[AMBER] Modification of dihedral torsion potential
- David A Case (Thu Oct 01 2020 - 05:03:36 PDT)
[AMBER] NAMD trajectory analysis with cpptraj
- sangita kachhap (Sat Oct 17 2020 - 02:53:29 PDT)
- Daniel Roe (Sat Oct 17 2020 - 00:05:42 PDT)
- sangita kachhap (Fri Oct 16 2020 - 12:35:39 PDT)
[AMBER] NMR restraints
- Debarati DasGupta (Sat Oct 31 2020 - 07:46:15 PDT)
- Debarati DasGupta (Sat Oct 31 2020 - 05:54:14 PDT)
- Carlos Simmerling (Sat Oct 31 2020 - 05:42:30 PDT)
- Debarati DasGupta (Sat Oct 31 2020 - 05:40:45 PDT)
- David A Case (Fri Oct 30 2020 - 18:21:41 PDT)
- Carlos Simmerling (Fri Oct 30 2020 - 14:11:50 PDT)
- Debarati DasGupta (Fri Oct 30 2020 - 12:37:48 PDT)
[AMBER] NOE analysis with cpptraj
- Pavlína Pokorná (Mon Oct 19 2020 - 06:17:47 PDT)
[AMBER] Normalized eigen values
- DHEERAJ CHITARA (Thu Oct 29 2020 - 09:51:27 PDT)
[AMBER] not writing restart file
- Erik Zuiderweg (Fri Oct 09 2020 - 03:57:55 PDT)
- Qinghua Liao (Thu Oct 08 2020 - 09:20:35 PDT)
- Erik Zuiderweg (Thu Oct 08 2020 - 09:17:41 PDT)
[AMBER] NVIDIA GeForce RTX 3080 GPUs
- German P. Barletta (Sun Oct 11 2020 - 13:10:54 PDT)
- Mike Mazanetz (Sat Oct 10 2020 - 13:26:06 PDT)
- Ross Walker (Sat Oct 10 2020 - 06:58:21 PDT)
- Mike Mazanetz (Fri Oct 09 2020 - 10:23:33 PDT)
- Adrian Roitberg (Fri Oct 09 2020 - 09:44:49 PDT)
- David Cerutti (Fri Oct 09 2020 - 09:41:08 PDT)
- Mike Mazanetz (Fri Oct 09 2020 - 08:36:46 PDT)
[AMBER] NVIDIA GeForce RTX 3080 GPUs (Ross Walker)
- Ross Walker (Sat Oct 10 2020 - 14:21:47 PDT)
- German P. Barletta (Sat Oct 10 2020 - 12:48:39 PDT)
[AMBER] NVIDIA GeForce RTX 3090 GPUs
- Mike Mazanetz (Thu Oct 22 2020 - 05:11:35 PDT)
[AMBER] partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule
- BLUNTZER Marie (Tue Oct 13 2020 - 07:45:22 PDT)
- James Kress (Mon Oct 12 2020 - 15:52:51 PDT)
- BLUNTZER Marie (Mon Oct 12 2020 - 05:42:34 PDT)
- David A Case (Mon Oct 12 2020 - 05:06:31 PDT)
- BLUNTZER Marie (Mon Oct 12 2020 - 04:09:32 PDT)
[AMBER] partial charges for modified nucleotide
- Kenneth Huang (Fri Oct 02 2020 - 17:36:31 PDT)
- David A Case (Fri Oct 02 2020 - 08:31:00 PDT)
- Farkhad Maksudov (Thu Oct 01 2020 - 18:28:28 PDT)
[AMBER] Permute dihedrals
- Daniel Roe (Fri Oct 09 2020 - 06:02:22 PDT)
- David Poole (Fri Oct 09 2020 - 04:40:53 PDT)
[AMBER] pmemd
- Dr. Anselm Horn (Fri Oct 02 2020 - 03:20:42 PDT)
- aishen (Thu Oct 01 2020 - 13:50:45 PDT)
- David A Case (Thu Oct 01 2020 - 13:40:41 PDT)
- Elvis Martis (Thu Oct 01 2020 - 09:49:36 PDT)
- aishen (Thu Oct 01 2020 - 09:44:55 PDT)
[AMBER] pmemd with hybrid mpi/mp
- Bill Abbott (Tue Oct 27 2020 - 13:13:32 PDT)
- David A Case (Tue Oct 27 2020 - 13:04:24 PDT)
- Bill Abbott (Tue Oct 27 2020 - 12:28:53 PDT)
[AMBER] pmemd.cuda and CPU cores
- David A Case (Wed Oct 28 2020 - 04:41:22 PDT)
- Abdul Basit (Tue Oct 27 2020 - 20:13:46 PDT)
[AMBER] PMF calculation
- somdev pahari (Thu Oct 15 2020 - 10:11:28 PDT)
[AMBER] Prmtop for protein + 2 identical ligands has wrong dihedral parameters for the second ligand. LEaP bug?
- Mariano Curti (Mon Oct 26 2020 - 02:18:33 PDT)
- Pengfei Li (Thu Oct 22 2020 - 14:19:21 PDT)
[AMBER] Problem in AMBER18 Installation
- Mariangela Dametto (Thu Oct 01 2020 - 09:58:09 PDT)
[AMBER] Problem with acpype
- Michele Vanini (Sat Oct 31 2020 - 02:08:54 PDT)
[AMBER] Problems with using pdb4amber (and possibly other programs) on Ubuntu 20.04
- bgostyns.cbmm.lodz.pl (Thu Oct 08 2020 - 04:11:20 PDT)
- Hai Nguyen (Wed Oct 07 2020 - 14:36:38 PDT)
- David A Case (Wed Oct 07 2020 - 08:15:35 PDT)
- bgostyns.cbmm.lodz.pl (Wed Oct 07 2020 - 06:52:03 PDT)
[AMBER] process_mdout.perl for pmemd
- Jorge Iulek (Sun Oct 18 2020 - 10:50:59 PDT)
- Rodrigo Galindo-Murillo (Sat Oct 17 2020 - 14:45:44 PDT)
- Jorge Iulek (Sat Oct 17 2020 - 14:31:07 PDT)
[AMBER] QMMM SCC-DFTB: Convergence could not be achieved
- Sarah Jane (Wed Oct 07 2020 - 10:22:46 PDT)
[AMBER] Query about using MMPBSA.py to calculate the binding free energy for a ligand bound enzyme
- David A Case (Thu Oct 15 2020 - 11:29:26 PDT)
- SATYAJIT KHATUA (Thu Oct 15 2020 - 09:41:54 PDT)
[AMBER] Query regarding Dialanine peptide 2d ABMD tutorial in the NFE category
- David A Case (Fri Oct 02 2020 - 08:19:45 PDT)
- SHAUNAK BADANI (Thu Oct 01 2020 - 13:26:28 PDT)
[AMBER] Query regarding ion constraint in MD simulations
- Nisha Amarnath Jonniya (Sat Oct 03 2020 - 19:33:58 PDT)
[AMBER] Question about force field for proteins
- Asaf Farhi (Fri Oct 16 2020 - 15:04:49 PDT)
- Carlos Simmerling (Sun Oct 11 2020 - 04:27:02 PDT)
- Asaf Farhi (Sat Oct 10 2020 - 11:49:32 PDT)
- Asaf Farhi (Mon Oct 05 2020 - 08:42:33 PDT)
- Carlos Simmerling (Mon Oct 05 2020 - 08:36:49 PDT)
- Asaf Farhi (Mon Oct 05 2020 - 08:31:10 PDT)
[AMBER] R: mm-pbsa calculation
- Giulio Poli (Wed Oct 28 2020 - 01:47:20 PDT)
- Suchetana Gupta (Tue Oct 27 2020 - 22:21:26 PDT)
- Serena Vittorio (Mon Oct 19 2020 - 02:36:36 PDT)
[AMBER] REST2 in Amber
- Qinghua Liao (Mon Oct 05 2020 - 08:30:05 PDT)
[AMBER] rms(d) or (f) per residue
- Seibold, Steve Allan (Sat Oct 17 2020 - 05:01:36 PDT)
- Daniel Roe (Fri Oct 16 2020 - 10:32:11 PDT)
- Seibold, Steve Allan (Fri Oct 16 2020 - 10:21:58 PDT)
- Daniel Roe (Fri Oct 16 2020 - 10:06:25 PDT)
- Seibold, Steve Allan (Fri Oct 16 2020 - 09:51:09 PDT)
[AMBER] RMSD (non mass-weighted) as collective variable in Amber-18
- Madhur Aggarwal (Sun Oct 18 2020 - 14:20:09 PDT)
[AMBER] RMSD of ligand in pocket
- Debarati DasGupta (Sun Oct 18 2020 - 08:05:42 PDT)
- Debarati DasGupta (Wed Oct 07 2020 - 16:03:08 PDT)
- Daniel Roe (Wed Oct 07 2020 - 08:02:28 PDT)
- Juraj Dobias (Mon Oct 05 2020 - 05:32:31 PDT)
- Debarati DasGupta (Mon Oct 05 2020 - 05:16:53 PDT)
- David A Case (Sun Oct 04 2020 - 17:54:09 PDT)
- Debarati DasGupta (Sun Oct 04 2020 - 06:55:41 PDT)
- Daniel Roe (Sun Oct 04 2020 - 06:48:10 PDT)
- Debarati DasGupta (Sat Oct 03 2020 - 08:08:20 PDT)
[AMBER] RMSD, Rg density map
- mohamed marzouk (Tue Oct 20 2020 - 20:17:58 PDT)
- mohamed marzouk (Tue Oct 20 2020 - 11:06:36 PDT)
- mohamed marzouk (Fri Oct 16 2020 - 09:57:45 PDT)
- Daniel Roe (Wed Oct 14 2020 - 11:48:51 PDT)
- mohamed marzouk (Mon Oct 12 2020 - 11:00:45 PDT)
[AMBER] server issues 403 on ambermd.org
- Gustaf Olsson (Thu Oct 22 2020 - 23:51:35 PDT)
- Mike Mazanetz (Thu Oct 22 2020 - 06:49:11 PDT)
[AMBER] Steered MD at constant force
- Vishal Singh (Mon Oct 26 2020 - 05:15:01 PDT)
- Vishal Singh (Mon Oct 19 2020 - 05:28:49 PDT)
[AMBER] System preparation for MMPBSA.py
- Ray Luo (Fri Oct 30 2020 - 08:07:32 PDT)
- SATYAJIT KHATUA (Mon Oct 26 2020 - 21:29:12 PDT)
[AMBER] TI calculation input clarification
- Delwakkada Liyanage, Senal Dinuka (Tue Oct 27 2020 - 10:00:51 PDT)
[AMBER] TI not compatible with GB on GPU
- Vaibhav Dixit (Thu Oct 22 2020 - 02:29:55 PDT)
- David A Case (Thu Oct 22 2020 - 05:04:32 PDT)
- Vaibhav Dixit (Wed Oct 21 2020 - 23:52:56 PDT)
- Debarati DasGupta (Wed Oct 21 2020 - 07:46:07 PDT)
- Debarati DasGupta (Wed Oct 21 2020 - 07:45:14 PDT)
- Vaibhav Dixit (Wed Oct 21 2020 - 05:59:26 PDT)
- Debarati DasGupta (Wed Oct 21 2020 - 05:21:46 PDT)
- Vaibhav Dixit (Tue Oct 20 2020 - 02:27:07 PDT)
[AMBER] Tri-coordination environment in zinc
- Bill Ross (Thu Oct 29 2020 - 23:59:57 PDT)
- SATYAJIT KHATUA (Thu Oct 29 2020 - 22:39:20 PDT)
- Pengfei Li (Thu Oct 22 2020 - 14:22:53 PDT)
[AMBER] Trouble installing pbsa cuda code
- David A Case (Sat Oct 24 2020 - 10:18:29 PDT)
- Wesley Michael Botello-Smith (Fri Oct 23 2020 - 20:32:39 PDT)
- Tru Huynh (Thu Oct 22 2020 - 14:09:32 PDT)
- David A Case (Thu Oct 22 2020 - 12:59:18 PDT)
- Wesley Michael Botello-Smith (Thu Oct 22 2020 - 11:47:41 PDT)
[AMBER] usage of nmr (between COMs) restraints with pmem.cuda
- Dmitry Karlov (Sun Oct 04 2020 - 06:57:55 PDT)
[AMBER] Using parmchk2 with GLYCAM_06j.dat
- Delwakkada Liyanage, Senal Dinuka (Tue Oct 13 2020 - 12:44:58 PDT)
[AMBER] Verbose - Output File Information Not Changing
- David A Case (Fri Oct 09 2020 - 05:01:19 PDT)
- An Ta (Wed Oct 07 2020 - 17:09:14 PDT)
- An Ta (Wed Oct 07 2020 - 16:17:29 PDT)
- An Ta (Wed Oct 07 2020 - 11:55:43 PDT)
[AMBER] vlimit=10 compromise for Amber 20 error: "an illegal memory access was encountered launching kernel kClearForces"?
- Elvis Martis (Fri Oct 16 2020 - 19:24:00 PDT)
- Liao (Fri Oct 16 2020 - 14:30:45 PDT)
- David A Case (Thu Oct 15 2020 - 11:32:41 PDT)
- Liao (Thu Oct 15 2020 - 07:54:31 PDT)
- David A Case (Thu Oct 15 2020 - 05:13:28 PDT)
- Liao (Tue Oct 13 2020 - 11:29:23 PDT)
[AMBER] VMD 1.9.4 could not read AMBER16 .mdcrd
- Wu Xu (Fri Oct 16 2020 - 19:36:23 PDT)
- Daniel Roe (Fri Oct 16 2020 - 12:21:42 PDT)
- Grant Keller (Fri Oct 16 2020 - 10:40:46 PDT)
- aishen.free.fr (Fri Oct 16 2020 - 06:16:44 PDT)
- Wu Xu (Fri Oct 16 2020 - 05:46:11 PDT)
- viktor (Fri Oct 16 2020 - 04:27:32 PDT)
- Mariano Curti (Fri Oct 16 2020 - 00:01:56 PDT)
- aishen (Thu Oct 15 2020 - 23:45:47 PDT)
- Vaibhav Dixit (Thu Oct 15 2020 - 22:50:00 PDT)
- Elvis Martis (Thu Oct 15 2020 - 22:31:45 PDT)
- Bill Ross (Thu Oct 15 2020 - 21:41:27 PDT)
- Wu Xu (Thu Oct 15 2020 - 21:23:17 PDT)
[AMBER] Which OS/Amber combinations are supported?
- Gerald Monard (Mon Oct 05 2020 - 23:41:35 PDT)
- Kevin Keane (Mon Oct 05 2020 - 13:06:37 PDT)
[AMBER] Xleap error
- Elvis Martis (Thu Oct 29 2020 - 03:26:34 PDT)
- Jisha B (Thu Oct 29 2020 - 02:17:22 PDT)
Conversion of Gromacs [atomtypes] and [nonbond_params] to Amber NONBON and LJEDIT
- Matias Machado (Sat Oct 03 2020 - 09:00:54 PDT)
- Nick Palmer (Thu Oct 01 2020 - 16:16:21 PDT)
partial charge calculation (RESP) using gaussian09/antechamber (ambertools17) on a symmetrical molecule
- BLUNTZER Marie (Mon Oct 12 2020 - 04:16:01 PDT)

Amber Archive Oct 2020 by subject