Amber Archive Jan 2021: by subject

[AMBER] abfQMMM with Terachem
- Eugen Hruska (Tue Jan 12 2021 - 10:21:06 PST)
[AMBER] abmd ignores cv_min cv_max and resolution for colvar="TORSION"
- Feng Pan (Fri Jan 29 2021 - 12:39:46 PST)
- Luis Simon (Mon Jan 25 2021 - 13:03:43 PST)
[AMBER] Amber 16/cpptraj diffusion command
- Daniel Roe (Mon Jan 25 2021 - 06:11:36 PST)
- Pau Mayorga Delgado (Mon Jan 25 2021 - 00:37:48 PST)
[AMBER] Amber 20 installation, problems with the testing phase
- Beatriz Gomes Guimaraes (Thu Jan 07 2021 - 13:41:27 PST)
- David A Case (Thu Jan 07 2021 - 12:44:27 PST)
- Beatriz Gomes Guimaraes (Thu Jan 07 2021 - 05:21:44 PST)
- Beatriz Gomes Guimaraes (Wed Jan 06 2021 - 08:17:11 PST)
- David A Case (Tue Jan 05 2021 - 19:37:14 PST)
- Beatriz Gomes Guimaraes (Tue Jan 05 2021 - 06:31:46 PST)
- David A Case (Tue Jan 05 2021 - 05:26:19 PST)
- Beatriz Gomes Guimaraes (Mon Jan 04 2021 - 13:20:26 PST)
[AMBER] Amber GPU performance history
- David A Case (Sun Jan 10 2021 - 11:32:01 PST)
[AMBER] Amber20 with PLUMED running slow, with GPU utilisation ~40%
- Amanda Buyan (Tue Jan 12 2021 - 15:36:36 PST)
- Adrian Roitberg (Tue Jan 12 2021 - 09:55:56 PST)
- David A Case (Tue Jan 12 2021 - 09:51:06 PST)
- Amanda Buyan (Mon Jan 11 2021 - 19:24:58 PST)
[AMBER] antechamber assigns DU as atom type for nitrogen
- David A Case (Sat Jan 23 2021 - 14:23:53 PST)
- nguerin (Sat Jan 16 2021 - 19:47:04 PST)
[AMBER] backbone rmsd between mutant trajectories, comparing conformational space sampled
- Hector A. Baldoni (Tue Jan 12 2021 - 08:44:05 PST)
- Vaibhav Dixit (Mon Jan 11 2021 - 22:52:25 PST)
- David A Case (Mon Jan 11 2021 - 05:18:40 PST)
- Vaibhav Dixit (Sun Jan 10 2021 - 22:59:49 PST)
[AMBER] Bug in the Mol2 format: space converted into a new oxygen atom
- David A Case (Fri Jan 08 2021 - 07:01:31 PST)
- Mateusz Bieniek (Wed Jan 06 2021 - 06:40:28 PST)
[AMBER] Bug when using RESPA in REMD runs
- Charo del Genio (Sat Jan 30 2021 - 07:51:18 PST)
- Carlos Simmerling (Sat Jan 30 2021 - 07:08:30 PST)
- Brian Radak (Sat Jan 30 2021 - 07:01:45 PST)
- David A Case (Sat Jan 30 2021 - 07:01:26 PST)
- Charo del Genio (Sat Jan 30 2021 - 03:23:41 PST)
[AMBER] Can we perform combined clustering with multiple prmtop files and mdcrd files?
- Kenneth Huang (Fri Jan 29 2021 - 09:51:32 PST)
- Debarati DasGupta (Fri Jan 29 2021 - 06:36:40 PST)
[AMBER] Can't restart a RXSGLD run (possible bug)
- Charo del Genio (Sun Jan 31 2021 - 02:13:41 PST)
[AMBER] cif to pdb
- Daniel Roe (Wed Jan 06 2021 - 02:18:54 PST)
- Pinky Mazumder (Tue Jan 05 2021 - 23:07:49 PST)
- David A Case (Tue Jan 05 2021 - 05:30:30 PST)
- Pinky Mazumder (Mon Jan 04 2021 - 20:19:22 PST)
[AMBER] combining crashed trajectories
- Daniel Roe (Fri Jan 22 2021 - 10:46:45 PST)
- Dr. Anselm Horn (Wed Jan 20 2021 - 09:25:43 PST)
- Ayesha Fatima (Wed Jan 20 2021 - 05:58:19 PST)
[AMBER] Cpptraj
- Daniel Roe (Fri Jan 22 2021 - 09:23:30 PST)
- Daniel Roe (Thu Jan 21 2021 - 07:19:48 PST)
- Stejskal, Lenka (Thu Jan 21 2021 - 07:14:43 PST)
[AMBER] CPPTRAJ error while Clustering
- Daniel Roe (Fri Jan 08 2021 - 09:31:49 PST)
- Maghsoud, Yazdan (Fri Jan 08 2021 - 08:08:27 PST)
[AMBER] Cpptraj v13 command is not working fixatomorder
- Daniel Roe (Mon Jan 11 2021 - 09:43:55 PST)
- Ana Ziad (Sun Jan 10 2021 - 23:01:44 PST)
[AMBER] Creating input files using tleap
- Nicy yadav (Wed Jan 20 2021 - 06:26:08 PST)
- David A Case (Wed Jan 20 2021 - 05:30:06 PST)
- Nicy yadav (Tue Jan 19 2021 - 14:27:00 PST)
[AMBER] Distance of every c alpha in a protein to every other c alpha
- Daniel Roe (Tue Jan 19 2021 - 06:46:07 PST)
- Jenny 148 (Sun Jan 17 2021 - 21:50:28 PST)
[AMBER] DNA protein simulation protocol
- David A Case (Mon Jan 25 2021 - 19:11:46 PST)
- Airy Sanjeev (Mon Jan 25 2021 - 01:04:14 PST)
[AMBER] DNA-ligand simulation
- Thomas Cheatham (Thu Jan 14 2021 - 16:41:40 PST)
- Kehinde Idowu (Thu Jan 14 2021 - 16:33:20 PST)
[AMBER] do you know
- David A Case (Sun Jan 03 2021 - 06:16:11 PST)
- Gordon Richard Chalmers (Sun Jan 03 2021 - 04:57:50 PST)
[AMBER] Domain distances using cpptraj
- Athena N (Fri Jan 08 2021 - 23:19:12 PST)
[AMBER] doubt frames simulation
- MYRIAN TORRES RICO (Sat Jan 02 2021 - 06:01:08 PST)
- David A Case (Sat Jan 02 2021 - 05:55:59 PST)
- Carlos Simmerling (Sat Jan 02 2021 - 05:26:24 PST)
- MYRIAN TORRES RICO (Sat Jan 02 2021 - 05:00:50 PST)
[AMBER] Energy Evaluations
- Daniel Roe (Tue Jan 05 2021 - 08:14:15 PST)
- Carlos Simmerling (Tue Jan 05 2021 - 04:37:36 PST)
- Matthew Guberman-Pfeffer (Mon Jan 04 2021 - 20:51:42 PST)
[AMBER] Energy minimization script
- raissa.conceicao.bol.com.br (Fri Jan 22 2021 - 12:14:00 PST)
- David A Case (Fri Jan 22 2021 - 07:22:15 PST)
- raissa.conceicao.bol.com.br (Fri Jan 22 2021 - 05:45:00 PST)
[AMBER] Error in minimization
- Carlos Simmerling (Thu Jan 28 2021 - 13:51:06 PST)
- Kehinde Idowu (Thu Jan 28 2021 - 13:06:05 PST)
[AMBER] Error in the apr.py code - steered MD simulation
- Eduardo R. Almeida (Mon Jan 04 2021 - 19:29:23 PST)
[AMBER] Error in xleap: water molecules
- Eduardo R. Almeida (Sun Jan 10 2021 - 11:13:36 PST)
- David A Case (Sun Jan 10 2021 - 07:45:24 PST)
- Eduardo R. Almeida (Sat Jan 09 2021 - 19:02:21 PST)
- Bill Ross (Sat Jan 09 2021 - 18:31:13 PST)
- David A Case (Sat Jan 09 2021 - 18:25:13 PST)
- Bill Ross (Sat Jan 09 2021 - 15:52:54 PST)
- Eduardo R. Almeida (Sat Jan 09 2021 - 15:44:17 PST)
- Bill Ross (Sat Jan 09 2021 - 15:31:41 PST)
- Eduardo R. Almeida (Sat Jan 09 2021 - 15:29:40 PST)
- Bill Ross (Sat Jan 09 2021 - 13:37:22 PST)
- David A Case (Sat Jan 09 2021 - 13:10:50 PST)
- Bill Ross (Sat Jan 09 2021 - 09:30:56 PST)
- Eduardo R. Almeida (Sat Jan 09 2021 - 06:42:19 PST)
- David A Case (Sat Jan 09 2021 - 05:51:19 PST)
- Bill Ross (Fri Jan 08 2021 - 20:43:00 PST)
- Eduardo R. Almeida (Fri Jan 08 2021 - 15:39:20 PST)
[AMBER] error job
- MYRIAN TORRES RICO (Thu Jan 14 2021 - 00:36:31 PST)
- Carlos Simmerling (Wed Jan 13 2021 - 04:40:21 PST)
- MYRIAN TORRES RICO (Tue Jan 12 2021 - 09:20:44 PST)
- Carlos Simmerling (Tue Jan 12 2021 - 07:41:44 PST)
- MYRIAN TORRES RICO (Tue Jan 12 2021 - 07:10:57 PST)
- Carlos Simmerling (Tue Jan 12 2021 - 06:51:34 PST)
- MYRIAN TORRES RICO (Tue Jan 12 2021 - 06:38:11 PST)
- David A Case (Tue Jan 12 2021 - 05:25:58 PST)
- MYRIAN TORRES RICO (Tue Jan 12 2021 - 01:02:25 PST)
- David A Case (Mon Jan 11 2021 - 05:26:09 PST)
- MYRIAN TORRES RICO (Mon Jan 11 2021 - 03:09:58 PST)
[AMBER] Error searching for compatible GPU
- Hongwei Tan (Sun Jan 10 2021 - 16:50:33 PST)
- David A Case (Sun Jan 10 2021 - 07:35:50 PST)
- Hongwei Tan (Sun Jan 10 2021 - 00:29:22 PST)
[AMBER] Error while clustering on CPPTRAJ
- Daniel Roe (Tue Jan 19 2021 - 10:03:31 PST)
- Daniel Fernández Remacha (Tue Jan 19 2021 - 09:50:24 PST)
- Daniel Roe (Tue Jan 19 2021 - 09:39:31 PST)
- dnlfr1994.gmail.com (Tue Jan 19 2021 - 09:20:52 PST)
- Daniel Roe (Thu Jan 14 2021 - 15:58:44 PST)
- dnlfr1994.gmail.com (Thu Jan 14 2021 - 09:50:22 PST)
- Daniel Roe (Thu Jan 14 2021 - 07:51:32 PST)
- dnlfr1994.gmail.com (Thu Jan 14 2021 - 05:03:45 PST)
[AMBER] error...
- Carlos Simmerling (Mon Jan 04 2021 - 05:38:24 PST)
- MYRIAN TORRES RICO (Mon Jan 04 2021 - 02:09:35 PST)
- Carlos Simmerling (Sun Jan 03 2021 - 13:29:47 PST)
- Bill Ross (Sun Jan 03 2021 - 13:14:18 PST)
- MYRIAN TORRES RICO (Sun Jan 03 2021 - 11:43:56 PST)
- Bill Ross (Sun Jan 03 2021 - 11:07:33 PST)
- MYRIAN TORRES RICO (Sun Jan 03 2021 - 09:19:00 PST)
[AMBER] Errors whilst installing GPU Amber20
- Victoria E Hill (Wed Jan 13 2021 - 09:41:58 PST)
- tluchko (Wed Jan 13 2021 - 09:06:03 PST)
- Victoria E Hill (Wed Jan 13 2021 - 09:05:35 PST)
- David A Case (Wed Jan 13 2021 - 05:37:13 PST)
- Victoria E Hill (Wed Jan 13 2021 - 03:58:43 PST)
[AMBER] Extending DNA structure
- Airy Sanjeev (Tue Jan 19 2021 - 02:00:55 PST)
- Vlad Cojocaru (Tue Jan 19 2021 - 01:39:58 PST)
- Airy Sanjeev (Mon Jan 18 2021 - 19:57:16 PST)
[AMBER] ff15ipq-m force field for protein mimetics
- Lillian Chong (Tue Jan 12 2021 - 05:46:41 PST)
[AMBER] Fixed the problem of AMBER20 run with pmemd.cuda with CUDA11.1 and 3080 GPU card
- Setyanto Md (Sun Jan 03 2021 - 23:47:14 PST)
- liu kai (Sat Jan 02 2021 - 18:35:20 PST)
- Mohd Farid Ismail (Fri Jan 01 2021 - 16:54:56 PST)
[AMBER] Found bug in sander in restarting SGLD replica exchange runs
- Charo del Genio (Sun Jan 31 2021 - 04:35:28 PST)
[AMBER] Fwd: copper RISM
- angad sharma (Wed Jan 06 2021 - 06:13:38 PST)
[AMBER] Fwd: Creating a bond in leap
- Kenneth Huang (Mon Jan 11 2021 - 14:03:23 PST)
- Victoria E Hill (Mon Jan 11 2021 - 13:37:33 PST)
[AMBER] Fwd: Distance of every c alpha in a protein to every other c alpha
- Daniel Roe (Mon Jan 25 2021 - 06:16:32 PST)
- Jenny 148 (Mon Jan 25 2021 - 02:11:00 PST)
[AMBER] Fwd: Domain distances using cpptraj
- David A Case (Sun Jan 10 2021 - 05:23:03 PST)
- Athena N (Sat Jan 09 2021 - 20:15:28 PST)
[AMBER] Fwd: Error during amber16 installation
- David A Case (Fri Jan 22 2021 - 07:17:02 PST)
- spss4.iacs.res.in (Thu Jan 21 2021 - 20:59:09 PST)
- David A Case (Thu Jan 21 2021 - 05:16:12 PST)
- spss4.iacs.res.in (Thu Jan 21 2021 - 02:29:46 PST)
[AMBER] gaff/parm
- MYRIAN TORRES RICO (Thu Jan 14 2021 - 05:50:01 PST)
- David A Case (Thu Jan 14 2021 - 05:34:07 PST)
- MYRIAN TORRES RICO (Thu Jan 14 2021 - 01:36:10 PST)
[AMBER] GB pairwise decomposition - Salt Bridge
- Carlos Simmerling (Wed Jan 06 2021 - 06:49:36 PST)
- Tarsis (Wed Jan 06 2021 - 06:28:57 PST)
[AMBER] Generating LJ paramters of divalent copper ions
- David A Case (Sun Jan 03 2021 - 06:09:27 PST)
- angad sharma (Sat Jan 02 2021 - 10:15:43 PST)
[AMBER] Help to generate prmtop and .crd files from a PDB trajectory
- Daniel Roe (Thu Jan 28 2021 - 07:03:28 PST)
- Kenneth Huang (Tue Jan 26 2021 - 11:55:43 PST)
- Devlina Chakravarty (Mon Jan 25 2021 - 17:46:03 PST)
[AMBER] How does the xleap/teap recognize the H3O+ (hydronium) ions?
- Hector A. Baldoni (Wed Jan 06 2021 - 19:11:18 PST)
- Eduardo R. Almeida (Wed Jan 06 2021 - 19:05:49 PST)
- Bill Ross (Wed Jan 06 2021 - 18:59:35 PST)
- Bill Ross (Wed Jan 06 2021 - 18:56:01 PST)
- Eduardo R. Almeida (Wed Jan 06 2021 - 18:37:00 PST)
- Bill Ross (Wed Jan 06 2021 - 18:24:57 PST)
- Eduardo R. Almeida (Wed Jan 06 2021 - 18:18:58 PST)
- Bill Ross (Wed Jan 06 2021 - 18:03:59 PST)
- Eduardo R. Almeida (Wed Jan 06 2021 - 17:33:46 PST)
- Eduardo R. Almeida (Wed Jan 06 2021 - 17:28:27 PST)
- Bill Ross (Wed Jan 06 2021 - 17:08:11 PST)
- Bill Ross (Wed Jan 06 2021 - 17:06:34 PST)
- Eduardo R. Almeida (Wed Jan 06 2021 - 15:15:55 PST)
[AMBER] How to apply Compressive loading on wood
- Pinky Mazumder (Sat Jan 16 2021 - 18:55:54 PST)
[AMBER] How to apply GLYCAM Parameters
- Matthew Guberman-Pfeffer (Sun Jan 03 2021 - 12:45:07 PST)
[AMBER] How to apply shear loading on carbohydrates
- Pinky Mazumder (Fri Jan 08 2021 - 21:11:18 PST)
[AMBER] How to extract restart file with velocity from a trajectory file?
- Carlos Simmerling (Fri Jan 22 2021 - 09:32:11 PST)
- 辛志宏 (Fri Jan 22 2021 - 06:19:42 PST)
[AMBER] How to fix the issue of generating restart file from a trajectory?
- Daniel Roe (Thu Jan 28 2021 - 07:10:41 PST)
- 辛志宏 (Wed Jan 27 2021 - 20:00:04 PST)
[AMBER] how to get amber 18 tools
- David A Case (Wed Jan 27 2021 - 12:09:44 PST)
- Sadaf Rani (Wed Jan 27 2021 - 06:44:55 PST)
- Carlos Simmerling (Wed Jan 27 2021 - 06:10:59 PST)
- Sadaf Rani (Wed Jan 27 2021 - 04:25:11 PST)
[AMBER] how to pull group of atoms towards a fixed molecule using Steered molecular dynamics simulation
- Pinky Mazumder (Fri Jan 08 2021 - 17:11:43 PST)
[AMBER] How to pull two group of atoms in two different direction?
- Pinky Mazumder (Sun Jan 24 2021 - 16:23:33 PST)
[AMBER] How to pull/push group of atoms
- Pinky Mazumder (Sat Jan 09 2021 - 21:06:06 PST)
[AMBER] How to use AM1 for Ti atom in Amber?
- David A Case (Mon Jan 11 2021 - 05:32:54 PST)
- 孙天宇 (Sun Jan 10 2021 - 21:28:23 PST)
[AMBER] How to use GLYCAM_06j-1 in LAMMPS
- Pinky Mazumder (Sat Jan 16 2021 - 13:35:18 PST)
- David A Case (Sat Jan 16 2021 - 06:44:04 PST)
- Pinky Mazumder (Fri Jan 15 2021 - 15:43:05 PST)
[AMBER] in chimera, which one should I use for carbohydrates
- David A Case (Fri Jan 29 2021 - 09:32:23 PST)
- Pinky Mazumder (Fri Jan 29 2021 - 07:38:28 PST)
[AMBER] Issue about the generaton of rst files
- Daniel Roe (Tue Jan 12 2021 - 06:28:48 PST)
- 辛志宏 (Tue Jan 12 2021 - 04:33:44 PST)
- Daniel Roe (Mon Jan 11 2021 - 09:42:02 PST)
- 辛志宏 (Sun Jan 10 2021 - 06:41:11 PST)
[AMBER] Langevin thermostat different gamma_ln giving systematically different energies?
- Thomas Cheatham (Sat Jan 16 2021 - 18:23:48 PST)
- Liao (Sat Jan 16 2021 - 17:44:16 PST)
[AMBER] Lateral movement of membrane bound protein during MD simulation in Amber
- Stephan Schott (Mon Jan 11 2021 - 03:21:37 PST)
- Biplab Ghosh (Sun Jan 10 2021 - 21:27:36 PST)
[AMBER] LEaP Error/questions.
- Sam Walsworth (Researcher) (Fri Jan 15 2021 - 12:58:57 PST)
- David A Case (Fri Jan 15 2021 - 12:41:17 PST)
- Sam Walsworth (Researcher) (Fri Jan 15 2021 - 10:58:38 PST)
- David A Case (Thu Jan 14 2021 - 14:15:21 PST)
- Sam Walsworth (Researcher) (Wed Jan 13 2021 - 12:41:01 PST)
- David A Case (Wed Jan 13 2021 - 08:11:59 PST)
- Sam Walsworth (Researcher) (Wed Jan 13 2021 - 07:06:44 PST)
- Carlos Simmerling (Wed Jan 13 2021 - 06:44:49 PST)
- Sam Walsworth (Researcher) (Wed Jan 13 2021 - 06:38:33 PST)
- Carlos Simmerling (Wed Jan 13 2021 - 06:13:08 PST)
- Daniel Roe (Wed Jan 13 2021 - 06:11:24 PST)
- Sam Walsworth (Researcher) (Wed Jan 13 2021 - 05:27:55 PST)
- Carlos Simmerling (Wed Jan 13 2021 - 04:37:09 PST)
- Sam Walsworth (Researcher) (Wed Jan 13 2021 - 04:30:36 PST)
- David A Case (Tue Jan 12 2021 - 05:21:37 PST)
- David A Case (Tue Jan 12 2021 - 05:17:15 PST)
- Sam Walsworth (Researcher) (Tue Jan 12 2021 - 05:11:39 PST)
- Carlos Simmerling (Tue Jan 12 2021 - 05:05:01 PST)
- Sam Walsworth (Researcher) (Tue Jan 12 2021 - 04:18:08 PST)
- Carlos Simmerling (Mon Jan 11 2021 - 14:09:33 PST)
- Sam Walsworth (Researcher) (Mon Jan 11 2021 - 12:58:04 PST)
- Maria Nagan (Mon Jan 11 2021 - 09:37:46 PST)
- Carlos Simmerling (Mon Jan 11 2021 - 09:29:29 PST)
- Sam Walsworth (Researcher) (Mon Jan 11 2021 - 09:10:26 PST)
- David A Case (Mon Jan 11 2021 - 08:44:16 PST)
- Sam Walsworth (Researcher) (Mon Jan 11 2021 - 05:45:18 PST)
- David A Case (Mon Jan 11 2021 - 05:29:47 PST)
- Sam Walsworth (Researcher) (Mon Jan 11 2021 - 03:45:14 PST)
[AMBER] lj1264 in vacuum
- Pengfei Li (Sat Jan 16 2021 - 19:21:56 PST)
[AMBER] Major Cpptraj Update (GitHub)
- Daniel Roe (Wed Jan 20 2021 - 11:54:44 PST)
[AMBER] makedepend for sander
- Antoine MARION (Wed Jan 20 2021 - 06:14:04 PST)
- David A Case (Wed Jan 20 2021 - 05:09:43 PST)
- Antoine MARION (Wed Jan 20 2021 - 03:26:06 PST)
[AMBER] max pairlist cutoff must be less than unit cell max sphere radius!
- Pinky Mazumder (Thu Jan 28 2021 - 10:31:52 PST)
- David A Case (Thu Jan 28 2021 - 07:07:32 PST)
- Pinky Mazumder (Wed Jan 27 2021 - 13:49:22 PST)
[AMBER] MD GPU Scaling Performance
- David A Case (Fri Jan 08 2021 - 06:47:42 PST)
- Jatin Kashyap (Thu Jan 07 2021 - 14:38:26 PST)
[AMBER] Missing Iron (Fe) DFTB3 parameters for QM/MM simulation of Enzyme
- Goetz, Andreas (Tue Jan 12 2021 - 16:15:54 PST)
[AMBER] MMPBSA calculation cpptraj failed with ligand prmtop
- Sadaf Rani (Sun Jan 24 2021 - 21:03:10 PST)
- Sadaf Rani (Sun Jan 24 2021 - 20:47:03 PST)
- Elvis A F Martis (Wed Jan 20 2021 - 23:52:57 PST)
- Sadaf Rani (Wed Jan 20 2021 - 21:13:09 PST)
[AMBER] MMPBSA.py.MPI not build in Amber20
- Li,Haoxi (Fri Jan 08 2021 - 14:05:16 PST)
- Elvis A F Martis (Fri Jan 08 2021 - 07:35:44 PST)
- David A Case (Fri Jan 08 2021 - 07:10:57 PST)
- Elvis A F Martis (Mon Jan 04 2021 - 09:19:43 PST)
- Li,Haoxi (Mon Jan 04 2021 - 09:13:32 PST)
[AMBER] NaN VDWAALS Error During Minimization
- Jatin Kashyap (Thu Jan 07 2021 - 11:29:05 PST)
- Bill Ross (Wed Jan 06 2021 - 00:48:17 PST)
- David Cerutti (Tue Jan 05 2021 - 22:36:39 PST)
- Jatin Kashyap (Tue Jan 05 2021 - 22:28:52 PST)
- Bill Ross (Tue Jan 05 2021 - 21:51:28 PST)
- Jatin Kashyap (Tue Jan 05 2021 - 21:09:59 PST)
- Thomas Cheatham (Tue Jan 05 2021 - 20:39:56 PST)
- Thomas Cheatham (Tue Jan 05 2021 - 20:33:17 PST)
- Bill Ross (Tue Jan 05 2021 - 20:01:06 PST)
- Bill Ross (Tue Jan 05 2021 - 19:59:23 PST)
- Jatin Kashyap (Tue Jan 05 2021 - 19:53:29 PST)
- Bill Ross (Tue Jan 05 2021 - 19:45:56 PST)
- David A Case (Tue Jan 05 2021 - 19:44:39 PST)
- Jatin Kashyap (Tue Jan 05 2021 - 19:18:47 PST)
- Bill Ross (Tue Jan 05 2021 - 19:05:23 PST)
- David Cerutti (Tue Jan 05 2021 - 17:29:19 PST)
- Jatin Kashyap (Tue Jan 05 2021 - 16:55:17 PST)
[AMBER] Non zero ligand warning
- Kenneth Huang (Sun Jan 31 2021 - 10:14:48 PST)
- David A Case (Sun Jan 31 2021 - 06:24:59 PST)
- Ayesha Fatima (Sun Jan 31 2021 - 05:10:51 PST)
[AMBER] Non-integer/zero charges from RESP fitting?
- Kenneth Huang (Wed Jan 13 2021 - 10:50:29 PST)
- David A Case (Wed Jan 13 2021 - 05:15:17 PST)
- Kenneth Huang (Tue Jan 12 2021 - 11:18:04 PST)
[AMBER] NonUniversalWarning: Modified off-diagonal LJ parameters detected
- David A Case (Sat Jan 16 2021 - 11:22:39 PST)
- Loki (Sat Jan 16 2021 - 09:30:12 PST)
- David A Case (Sat Jan 16 2021 - 06:45:31 PST)
- Loki (Sat Jan 16 2021 - 03:54:54 PST)
[AMBER] Number of na, cl ions
- David A Case (Thu Jan 14 2021 - 14:08:49 PST)
- Женя Елизарова (Thu Jan 14 2021 - 08:10:11 PST)
[AMBER] Nvidia RTX 3080/3090 Servers
- mish (Fri Jan 22 2021 - 06:16:34 PST)
- Ross Walker (Fri Jan 22 2021 - 06:03:53 PST)
- mish (Thu Jan 21 2021 - 18:48:54 PST)
[AMBER] OPC monovalent ion parameters
- Carlos Simmerling (Mon Jan 25 2021 - 12:35:11 PST)
- Sebastian Oleksy (Mon Jan 25 2021 - 10:07:26 PST)
[AMBER] overall and internal correlation function
- Mani Radh (Mon Jan 25 2021 - 09:48:12 PST)
[AMBER] Patches to fix the replica exchange restart bug
- Charo del Genio (Sun Jan 31 2021 - 12:11:59 PST)
[AMBER] pdb4amber error
- David A Case (Wed Jan 27 2021 - 05:14:14 PST)
- Scott Brozell (Tue Jan 26 2021 - 22:37:06 PST)
- Nicy yadav (Mon Jan 25 2021 - 08:24:33 PST)
[AMBER] Potential energy discrepancy in RXSGLD
- Charo del Genio (Fri Jan 29 2021 - 08:28:51 PST)
[AMBER] Preparation of input file for RAMD (Geng Dong)
- 东庚 (Sun Jan 10 2021 - 20:11:12 PST)
[AMBER] PrmtopError: Complex natom != receptor natom + ligand natom
- David A Case (Tue Jan 26 2021 - 11:19:55 PST)
- Renato Araujo (Tue Jan 26 2021 - 08:56:11 PST)
- David A Case (Mon Jan 25 2021 - 19:17:14 PST)
- Renato Araujo (Mon Jan 25 2021 - 17:49:58 PST)
[AMBER] Problem in running cmake
- Airy Sanjeev (Mon Jan 11 2021 - 19:01:15 PST)
- David A Case (Mon Jan 11 2021 - 05:23:31 PST)
- Airy Sanjeev (Sun Jan 10 2021 - 23:17:00 PST)
[AMBER] Problem with cudaMalloc GpuBuffer Allocate failed out of memory
- Elvis A F Martis (Fri Jan 01 2021 - 20:36:06 PST)
- assawin daducale (Fri Jan 01 2021 - 11:07:25 PST)
[AMBER] Problem with PB calculation
- CAVALLARO MATTIA (Sat Jan 02 2021 - 06:24:20 PST)
[AMBER] Problems when running make test.parallel
- Beatriz Gomes Guimaraes (Mon Jan 18 2021 - 10:53:18 PST)
- Daniel Roe (Tue Jan 12 2021 - 08:58:14 PST)
- Beatriz Gomes Guimaraes (Tue Jan 12 2021 - 06:35:36 PST)
[AMBER] Probmlems compiling under macOS
- Gustaf Olsson (Wed Jan 13 2021 - 22:32:01 PST)
- David A Case (Mon Jan 11 2021 - 05:11:29 PST)
- Gustaf Olsson (Sun Jan 10 2021 - 13:37:31 PST)
- Gustaf Olsson (Sun Jan 10 2021 - 09:24:07 PST)
- David A Case (Sun Jan 10 2021 - 05:46:50 PST)
- Gustaf Olsson (Sun Jan 10 2021 - 00:13:00 PST)
[AMBER] PROTEIN-DNA rmsd plot
- Syeda Amna Arshi (Mon Jan 04 2021 - 22:23:40 PST)
- Daniel Roe (Mon Jan 04 2021 - 06:09:10 PST)
- David A Case (Mon Jan 04 2021 - 05:19:42 PST)
- Syeda Amna Arshi (Mon Jan 04 2021 - 00:56:57 PST)
[AMBER] PROTEIN-DNA RMSD plots
- Dr. Anselm Horn (Thu Jan 14 2021 - 04:55:59 PST)
- Carlos Simmerling (Thu Jan 14 2021 - 03:22:06 PST)
- Syeda Amna Arshi (Thu Jan 14 2021 - 03:14:05 PST)
[AMBER] Pull group of atoms together
- Pinky Mazumder (Tue Jan 12 2021 - 11:59:22 PST)
- Carlos Simmerling (Tue Jan 12 2021 - 11:43:09 PST)
- Pinky Mazumder (Tue Jan 12 2021 - 11:30:16 PST)
- Carlos Simmerling (Tue Jan 12 2021 - 11:25:42 PST)
- Pinky Mazumder (Tue Jan 12 2021 - 08:38:42 PST)
- Carlos Simmerling (Mon Jan 11 2021 - 10:43:19 PST)
- Pinky Mazumder (Mon Jan 11 2021 - 10:34:11 PST)
[AMBER] Python Error in MMPBSA.py, only for PBSA on final output
- Lennart Gundelach (Fri Jan 22 2021 - 04:22:07 PST)
- Ray Luo (Sat Jan 16 2021 - 17:48:43 PST)
- Lennart Gundelach (Sat Jan 16 2021 - 02:14:54 PST)
- Ray Luo (Wed Jan 13 2021 - 09:10:46 PST)
- Lennart Gundelach (Wed Jan 13 2021 - 01:43:07 PST)
[AMBER] pytraj in python 3.9
- Abdul-Rashid III Sampaco (Wed Jan 06 2021 - 19:53:50 PST)
- David A Case (Wed Jan 06 2021 - 06:29:39 PST)
- Abdul-Rashid III Sampaco (Tue Jan 05 2021 - 20:54:53 PST)
[AMBER] question
- David A Case (Thu Jan 21 2021 - 05:19:27 PST)
- MYRIAN TORRES RICO (Thu Jan 21 2021 - 03:05:45 PST)
[AMBER] Question of targeted molecular dynamics simulation
- Dr. Anselm Horn (Fri Jan 15 2021 - 09:14:18 PST)
- 吴晓东 (Thu Jan 14 2021 - 18:37:16 PST)
[AMBER] Reproducing Tutorial: Analysis of a nucleic acid simulation
- Carlos Simmerling (Mon Jan 18 2021 - 18:02:55 PST)
- Jatin Kashyap (Mon Jan 18 2021 - 17:40:11 PST)
- Carlos Simmerling (Mon Jan 18 2021 - 17:12:30 PST)
- Jatin Kashyap (Mon Jan 18 2021 - 16:48:50 PST)
- Roitberg,Adrian E (Mon Jan 18 2021 - 16:40:00 PST)
- Jatin Kashyap (Mon Jan 18 2021 - 16:06:35 PST)
- Carlos Simmerling (Mon Jan 18 2021 - 16:01:25 PST)
- Jatin Kashyap (Mon Jan 18 2021 - 15:47:58 PST)
- Carlos Simmerling (Mon Jan 18 2021 - 15:43:41 PST)
- Jatin Kashyap (Mon Jan 18 2021 - 15:32:45 PST)
- Carlos Simmerling (Mon Jan 18 2021 - 15:28:15 PST)
- Jatin Kashyap (Mon Jan 18 2021 - 15:17:02 PST)
[AMBER] RMSD analysis
- Daniel Roe (Fri Jan 08 2021 - 13:09:54 PST)
- Carlos Simmerling (Thu Jan 07 2021 - 17:55:01 PST)
- K Jan (Thu Jan 07 2021 - 15:26:14 PST)
- Kenneth Huang (Thu Jan 07 2021 - 14:45:09 PST)
- K Jan (Thu Jan 07 2021 - 14:34:51 PST)
[AMBER] rotdif analysis in cpptraj
- Adeleh Mokhles Gerami (Wed Jan 27 2021 - 06:41:02 PST)
[AMBER] Running simulations
- David A Case (Tue Jan 26 2021 - 11:24:03 PST)
- richa anand (Sun Jan 24 2021 - 22:41:53 PST)
[AMBER] Sander code doesn’t output trajectory files
- K Jan (Wed Jan 06 2021 - 07:13:49 PST)
- Roitberg,Adrian E (Wed Jan 06 2021 - 07:00:44 PST)
- K Jan (Wed Jan 06 2021 - 06:57:16 PST)
- David A Case (Wed Jan 06 2021 - 06:34:44 PST)
- Carlos Simmerling (Wed Jan 06 2021 - 06:25:48 PST)
- K Jan (Wed Jan 06 2021 - 04:58:23 PST)
[AMBER] Setting PME cutoff in Crystal Simulations
- David A Case (Wed Jan 06 2021 - 06:22:13 PST)
- Matthew Guberman-Pfeffer (Wed Jan 06 2021 - 00:33:05 PST)
- Matthew Guberman-Pfeffer (Tue Jan 05 2021 - 19:03:59 PST)
- David A Case (Tue Jan 05 2021 - 05:35:13 PST)
- Matthew Guberman-Pfeffer (Tue Jan 05 2021 - 01:37:22 PST)
- David A Case (Mon Jan 04 2021 - 05:14:34 PST)
- Matthew Guberman-Pfeffer (Sun Jan 03 2021 - 12:37:09 PST)
[AMBER] SMD & MULTI_RMSD
- Feng Pan (Mon Jan 11 2021 - 12:11:07 PST)
- Fabian Glaser (Mon Jan 11 2021 - 06:19:10 PST)
- Feng Pan (Tue Jan 05 2021 - 06:43:15 PST)
- Fabian Glaser (Sun Jan 03 2021 - 13:09:16 PST)
- Feng Pan (Sun Jan 03 2021 - 12:50:54 PST)
- Fabian Glaser (Sun Jan 03 2021 - 09:47:21 PST)
[AMBER] Spam purewater keyword
- Debarati DasGupta (Mon Jan 11 2021 - 12:49:02 PST)
[AMBER] Steered molecular dynamics Simulation
- Pinky Mazumder (Sat Jan 16 2021 - 13:37:28 PST)
- Pinky Mazumder (Sat Jan 16 2021 - 10:13:35 PST)
- Fabian Glaser (Sat Jan 16 2021 - 06:56:04 PST)
- Pinky Mazumder (Fri Jan 15 2021 - 18:01:53 PST)
[AMBER] Suggestions on crossing energy barrier to break strong HBs
- Kenneth Huang (Sat Jan 30 2021 - 17:10:10 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Jan 29 2021 - 22:27:43 PST)
- David A Case (Fri Jan 29 2021 - 19:06:00 PST)
- Amit Sharma (Asstt. Prof., MCARS) (Fri Jan 29 2021 - 15:40:35 PST)
[AMBER] technical problems with installing amber20
- David A Case (Thu Jan 28 2021 - 07:05:06 PST)
- Игорь Злотников (Wed Jan 27 2021 - 12:29:34 PST)
- David A Case (Wed Jan 27 2021 - 12:21:43 PST)
- Игорь Злотников (Wed Jan 27 2021 - 04:59:02 PST)
[AMBER] The long and winding STSM
- Feng Pan (Fri Jan 29 2021 - 12:37:48 PST)
- Luis Simon (Wed Jan 20 2021 - 07:56:33 PST)
[AMBER] TI simulation blowing up with pmemd.CUDA
- Debarati DasGupta (Mon Jan 11 2021 - 09:41:36 PST)
- Debarati DasGupta (Mon Jan 11 2021 - 07:27:22 PST)
- Debarati DasGupta (Mon Jan 11 2021 - 05:52:01 PST)
- David A Case (Mon Jan 11 2021 - 05:09:12 PST)
- Delwakkada Liyanage, Senal Dinuka (Sun Jan 10 2021 - 12:08:21 PST)
- David A Case (Sun Jan 10 2021 - 11:28:09 PST)
- Delwakkada Liyanage, Senal Dinuka (Sun Jan 10 2021 - 10:07:39 PST)
[AMBER] tinker_to_amber
- David A Case (Fri Jan 08 2021 - 06:57:54 PST)
- Юлия Беляева (Tue Jan 05 2021 - 11:16:01 PST)
[AMBER] Tri-coordination environment in zinc
- Pengfei Li (Sat Jan 16 2021 - 19:29:17 PST)
[AMBER] Typo in update.13 for AmberTools20
- Hashemi, Mohtadin (Fri Jan 15 2021 - 12:28:26 PST)
[AMBER] Understanding File Format Specifications
- Thomas Cheatham (Fri Jan 22 2021 - 14:03:52 PST)
- nguerin (Fri Jan 22 2021 - 12:48:45 PST)
[AMBER] US or SMD for torsion angle steering?
- Feng Pan (Tue Jan 12 2021 - 06:35:32 PST)
- Fabian Glaser (Mon Jan 11 2021 - 06:31:08 PST)
[AMBER] vlimit exceeded for step 0; vmax = 50.6241
- Pinky Mazumder (Tue Jan 19 2021 - 13:50:09 PST)
[AMBER] working with mmpbsa with protein and three ligands in same complex
- Sadaf Rani (Tue Jan 19 2021 - 22:42:20 PST)
- David A Case (Sun Jan 17 2021 - 07:16:54 PST)
- Sadaf Rani (Sun Jan 17 2021 - 02:36:31 PST)
[AMBER] ZAFF force field
- Tabassum Khair Barbhuiya (Wed Jan 20 2021 - 17:09:11 PST)

Amber Archive Jan 2021 by subject