Amber Archive Jan 2025: by subject

[AMBER] [Sender Not Verified] Error calculation halted in pmemd.cuda
- Steinbrecher, Thomas via AMBER (Fri Jan 10 2025 - 03:20:27 PST)
[AMBER] A monomer move out the simulation box
- Ibrahim Said via AMBER (Thu Jan 09 2025 - 12:14:41 PST)
- Dr. Anselm Horn via AMBER (Thu Jan 09 2025 - 09:57:57 PST)
- Ibrahim Said via AMBER (Thu Jan 09 2025 - 09:30:36 PST)
[AMBER] Amber metal ions protein multiple chains
- Solen Ekesan via AMBER (Tue Jan 21 2025 - 07:25:32 PST)
- Iglika Lessigiarska via AMBER (Tue Jan 21 2025 - 01:52:03 PST)
- Li, Zhen via AMBER (Mon Jan 13 2025 - 12:13:58 PST)
- Solen Ekesan via AMBER (Mon Jan 13 2025 - 11:55:41 PST)
- David A Case via AMBER (Mon Jan 13 2025 - 07:26:05 PST)
- Iglika Lessigiarska via AMBER (Mon Jan 13 2025 - 03:19:59 PST)
[AMBER] aMD run
- Charo del Genio via AMBER (Mon Jan 06 2025 - 06:39:09 PST)
- Charo del Genio via AMBER (Mon Jan 06 2025 - 06:04:11 PST)
- Dulal Mondal via AMBER (Mon Jan 06 2025 - 01:45:33 PST)
- Dulal Mondal via AMBER (Sun Jan 05 2025 - 04:39:03 PST)
[AMBER] Best method to calculate vdW energies between residue side chains
- Dr. Anselm Horn via AMBER (Tue Jan 14 2025 - 02:54:42 PST)
- Intravaia, Lauren E via AMBER (Mon Jan 13 2025 - 12:23:59 PST)
[AMBER] Calculating charges by Gastieger procedure in Antechamber ...
- Michal Husak via AMBER (Tue Jan 14 2025 - 06:03:56 PST)
[AMBER] Compiling on AMD MI50 chips
- David A Case via AMBER (Tue Jan 21 2025 - 20:24:25 PST)
- Wong, Sergio E. via AMBER (Tue Jan 21 2025 - 13:57:07 PST)
[AMBER] Convert Gromacs RB dihedrals to AMBER dihedrals
- Abdelrahman, Noureen via AMBER (Sat Jan 25 2025 - 00:24:46 PST)
[AMBER] CPPTRAJ grid output units
- Daniel Roe via AMBER (Sat Jan 04 2025 - 09:46:27 PST)
[AMBER] Dimension problem for a huge rod-like system
- Dr. Anselm Horn via AMBER (Tue Jan 07 2025 - 08:11:30 PST)
- David A Case via AMBER (Sat Jan 04 2025 - 21:23:18 PST)
- PD Dr. Anselm Horn via AMBER (Wed Jan 01 2025 - 02:34:18 PST)
[AMBER] Error calculation halted in pmemd.cuda
- Bhattacharjee, Sinjini via AMBER (Fri Jan 10 2025 - 03:04:56 PST)
[AMBER] Error in make install
- INDAH LANGITASARI via AMBER (Sun Jan 26 2025 - 00:14:37 PST)
- TUSHAR GUPTA via AMBER (Wed Jan 15 2025 - 17:05:52 PST)
[AMBER] Error installing amber on and GPUs
- David A Case via AMBER (Thu Jan 02 2025 - 15:17:08 PST)
- Wong, Sergio E. via AMBER (Thu Jan 02 2025 - 05:06:52 PST)
[AMBER] Force field parameters modification
- Tej Tarun Sharma 2310225 via AMBER (Wed Jan 15 2025 - 23:17:56 PST)
[AMBER] GBNeck parameters modification to incorporate CustomGBForce calculations of OpenMM in Amber
- Tej Tarun Sharma 2310225 via AMBER (Tue Jan 21 2025 - 04:16:39 PST)
[AMBER] Interactions of GAFF2 force field with Lipid21 and BSC1 force fields
- David A Case via AMBER (Tue Jan 21 2025 - 09:04:46 PST)
- Victor Nazarychev via AMBER (Fri Jan 17 2025 - 02:53:35 PST)
[AMBER] Is this the place to ask about CPPTRAJ issues?
- Daniel Roe via AMBER (Sun Jan 05 2025 - 09:58:15 PST)
- James Kress via AMBER (Sat Jan 04 2025 - 21:01:28 PST)
[AMBER] Issue with generating output files
- David A Case via AMBER (Wed Jan 08 2025 - 08:17:46 PST)
- Munazzah Fatima Ansari via AMBER (Tue Jan 07 2025 - 23:35:53 PST)
[AMBER] MCPB.py RESP Value Issues
- Dratch, Benjamin via AMBER (Sun Jan 26 2025 - 08:52:54 PST)
[AMBER] MMPBSA Error (Topology I think)
- Ray Luo via AMBER (Mon Jan 20 2025 - 18:38:33 PST)
- Vishwaa Kannan via AMBER (Sun Jan 19 2025 - 18:48:34 PST)
- Ray Luo via AMBER (Sat Jan 18 2025 - 14:36:01 PST)
- Vishwaa Kannan via AMBER (Sat Jan 18 2025 - 13:33:58 PST)
[AMBER] nastruct
- Daniel Roe via AMBER (Thu Jan 02 2025 - 08:07:30 PST)
- Jing Qu via AMBER (Thu Jan 02 2025 - 04:30:00 PST)
[AMBER] prmtop and inpcrd file generation error:
- Kankana Bhattacharjee via AMBER (Fri Jan 10 2025 - 08:57:57 PST)
- Timothy Giese via AMBER (Fri Jan 10 2025 - 06:12:40 PST)
- Kankana Bhattacharjee via AMBER (Thu Jan 09 2025 - 20:52:20 PST)
- Kankana Bhattacharjee via AMBER (Thu Jan 09 2025 - 20:30:31 PST)
- Kankana Bhattacharjee via AMBER (Thu Jan 09 2025 - 20:37:34 PST)
- Timothy Giese via AMBER (Thu Jan 09 2025 - 12:52:50 PST)
- Kankana Bhattacharjee via AMBER (Thu Jan 09 2025 - 10:46:14 PST)
[AMBER] problem in installing Amber24
- James Kress via AMBER (Tue Jan 14 2025 - 21:14:30 PST)
- TUSHAR GUPTA via AMBER (Tue Jan 14 2025 - 19:39:45 PST)
- James Kress via AMBER (Mon Jan 13 2025 - 09:35:56 PST)
- David A Case via AMBER (Mon Jan 13 2025 - 07:37:09 PST)
- TUSHAR GUPTA via AMBER (Mon Jan 13 2025 - 05:13:06 PST)
[AMBER] Problem in stapled peptides
- Airy Sanjeev via AMBER (Wed Jan 08 2025 - 06:04:08 PST)
- Airy Sanjeev via AMBER (Wed Jan 08 2025 - 06:03:14 PST)
[AMBER] Problems installing Amber24 on M3 Mac
- Adrian Roitberg via AMBER (Thu Jan 16 2025 - 13:32:17 PST)
- Adrian Roitberg via AMBER (Thu Jan 16 2025 - 08:44:32 PST)
- Sommers, Rachel C. via AMBER (Thu Jan 16 2025 - 06:16:42 PST)
[AMBER] process_mdout.perl doesn't extract Density data
- David A Case via AMBER (Sat Jan 04 2025 - 21:06:41 PST)
- LI An-Bang via AMBER (Wed Jan 01 2025 - 18:21:30 PST)
[AMBER] protonated imidazole but post antechamber two N+ in ring....
- Debarati DasGupta via AMBER (Sun Jan 26 2025 - 08:21:36 PST)
[AMBER] QM steered md question
- Ramdhan,Peter A via AMBER (Sat Jan 11 2025 - 14:55:16 PST)
[AMBER] Question about vectors
- Jing Qu via AMBER (Mon Jan 06 2025 - 19:57:37 PST)
[AMBER] Question regarding rotation matrix value from "rotate" (cpptraj)
- Daniel Roe via AMBER (Tue Jan 07 2025 - 12:43:33 PST)
- Dr. Anselm Horn via AMBER (Tue Jan 07 2025 - 09:22:20 PST)
[AMBER] Quick Cuda
- Manathunga Mudiyanselage, Madushanka via AMBER (Wed Jan 15 2025 - 18:25:49 PST)
- Matt Goff via AMBER (Wed Jan 15 2025 - 18:31:47 PST)
- Goetz, Andreas via AMBER (Wed Jan 15 2025 - 18:15:28 PST)
- Matt Goff via AMBER (Wed Jan 15 2025 - 18:06:46 PST)
- Goetz, Andreas via AMBER (Wed Jan 15 2025 - 18:00:19 PST)
- Matt Goff via AMBER (Wed Jan 15 2025 - 16:16:02 PST)
[AMBER] Regarding polarizable continuum solvation model:
- David A Case via AMBER (Wed Jan 01 2025 - 10:09:33 PST)
[AMBER] Regarding QM-MM error:
- Kankana Bhattacharjee via AMBER (Mon Jan 06 2025 - 09:04:53 PST)
- Goetz, Andreas via AMBER (Mon Jan 06 2025 - 08:53:26 PST)
- Kankana Bhattacharjee via AMBER (Sun Jan 05 2025 - 23:13:39 PST)
[AMBER] Regarding QM-MM_MD setup calculation:
- Goetz, Andreas via AMBER (Fri Jan 03 2025 - 13:25:16 PST)
- Kankana Bhattacharjee via AMBER (Fri Jan 03 2025 - 09:19:33 PST)
- Goetz, Andreas via AMBER (Thu Jan 02 2025 - 14:04:31 PST)
[AMBER] Regarding QMMM simulation run error:
- David A Case via AMBER (Sat Jan 04 2025 - 20:47:02 PST)
- SATYAJIT KHATUA via AMBER (Sat Jan 04 2025 - 19:45:15 PST)
- Kankana Bhattacharjee via AMBER (Sat Jan 04 2025 - 19:11:02 PST)
- David Case via AMBER (Fri Jan 03 2025 - 15:46:16 PST)
- Goetz, Andreas via AMBER (Fri Jan 03 2025 - 13:47:26 PST)
- Kankana Bhattacharjee via AMBER (Fri Jan 03 2025 - 10:52:53 PST)
[AMBER] Regarding the use of the opc3pol water model and the QM-MM calculation error:
- David A Case via AMBER (Tue Jan 07 2025 - 09:04:49 PST)
- Kankana Bhattacharjee via AMBER (Mon Jan 06 2025 - 23:43:08 PST)
[AMBER] reporting ΔG? or ΔΔG? vs experimental ΔG using FEP+ and TI
- Brian Radak via AMBER (Tue Jan 14 2025 - 11:23:11 PST)
- King Wang via AMBER (Mon Jan 13 2025 - 15:52:54 PST)
[AMBER] sander.quick.cuda error:
- Goetz, Andreas via AMBER (Fri Jan 10 2025 - 12:27:57 PST)
- Kankana Bhattacharjee via AMBER (Fri Jan 10 2025 - 10:28:06 PST)
- Timothy Giese via AMBER (Fri Jan 10 2025 - 09:53:16 PST)
- Kankana Bhattacharjee via AMBER (Fri Jan 10 2025 - 09:16:40 PST)
[AMBER] Simulating LES with noe restraints
- Кунина, Елизавета Игоревна via AMBER (Thu Jan 30 2025 - 23:58:57 PST)
[AMBER] single point energy calculation
- Dr. Anselm Horn via AMBER (Fri Jan 24 2025 - 00:52:22 PST)
- Benjamin Shugaev via AMBER (Thu Jan 23 2025 - 15:11:43 PST)
[AMBER] Single Point Energy calculation using Force Fields
- David A Case via AMBER (Sat Jan 04 2025 - 20:52:13 PST)
- Benjamin Shugaev via AMBER (Sat Jan 04 2025 - 10:46:55 PST)
[AMBER] tleap error: ligand atom does not have a type
- David A Case via AMBER (Sat Jan 04 2025 - 10:21:04 PST)
- Zeyu Lin via AMBER (Sat Jan 04 2025 - 09:57:32 PST)
[AMBER] Unphysical temperature spikes
- David A Case via AMBER (Mon Jan 06 2025 - 12:25:35 PST)
- Adrian Roitberg via AMBER (Mon Jan 06 2025 - 10:32:25 PST)
- Charo del Genio via AMBER (Mon Jan 06 2025 - 10:19:05 PST)
- Guberman-Pfeffer, Matthew via AMBER (Mon Jan 06 2025 - 09:41:59 PST)
- Charo del Genio via AMBER (Mon Jan 06 2025 - 09:23:03 PST)
- Kiriko Terai via AMBER (Mon Jan 06 2025 - 09:13:17 PST)
[AMBER] Use OPM to add membrane
- David A Case via AMBER (Tue Jan 07 2025 - 08:49:59 PST)
- Zeyu Lin via AMBER (Mon Jan 06 2025 - 19:08:46 PST)
aMD run
- Dulal Mondal via AMBER (Mon Jan 06 2025 - 05:47:03 PST)
- Steinbrecher, Thomas via AMBER (Mon Jan 06 2025 - 04:17:02 PST)
prmtop and inpcrd file generation error:]
- David A Case via AMBER (Thu Jan 09 2025 - 21:50:54 PST)
Problem in stapled peptides]
- David A Case via AMBER (Thu Jan 09 2025 - 21:51:16 PST)

Amber Archive Jan 2025 by subject