Amber Archive Jan 2025 by thread
85 messages
:
Starting
Wed Jan 01 2025 - 03:00:02 PST,
Ending
Tue Jan 14 2025 - 21:30:02 PST
This period
:
Most recent messages
sort by
: [ thread ] [
author
] [
date
] [
subject
] [
attachment
]
[AMBER] Dimension problem for a huge rod-like system
PD Dr. Anselm Horn via AMBER
(Wed Jan 01 2025 - 02:34:18 PST)
Re: [AMBER] Dimension problem for a huge rod-like system
David A Case via AMBER
(Sat Jan 04 2025 - 21:23:18 PST)
Re: [AMBER] Dimension problem for a huge rod-like system
Dr. Anselm Horn via AMBER
(Tue Jan 07 2025 - 08:11:30 PST)
Re: [AMBER] Regarding polarizable continuum solvation model:
David A Case via AMBER
(Wed Jan 01 2025 - 10:09:33 PST)
[AMBER] process_mdout.perl doesn't extract Density data
LI An-Bang via AMBER
(Wed Jan 01 2025 - 18:21:30 PST)
Re: [AMBER] process_mdout.perl doesn't extract Density data
David A Case via AMBER
(Sat Jan 04 2025 - 21:06:41 PST)
[AMBER] nastruct
Jing Qu via AMBER
(Thu Jan 02 2025 - 04:30:00 PST)
Re: [AMBER] nastruct
Daniel Roe via AMBER
(Thu Jan 02 2025 - 08:07:30 PST)
[AMBER] Error installing amber on and GPUs
Wong, Sergio E. via AMBER
(Thu Jan 02 2025 - 05:06:52 PST)
Re: [AMBER] Error installing amber on and GPUs
David A Case via AMBER
(Thu Jan 02 2025 - 15:17:08 PST)
Re: [AMBER] Regarding QM-MM_MD setup calculation:
Goetz, Andreas via AMBER
(Thu Jan 02 2025 - 14:04:31 PST)
Re: [AMBER] Regarding QM-MM_MD setup calculation:
Kankana Bhattacharjee via AMBER
(Fri Jan 03 2025 - 09:19:33 PST)
Re: [AMBER] Regarding QM-MM_MD setup calculation:
Goetz, Andreas via AMBER
(Fri Jan 03 2025 - 13:25:16 PST)
[AMBER] Regarding QMMM simulation run error:
Kankana Bhattacharjee via AMBER
(Fri Jan 03 2025 - 10:52:53 PST)
Re: [AMBER] Regarding QMMM simulation run error:
Goetz, Andreas via AMBER
(Fri Jan 03 2025 - 13:47:26 PST)
Re: [AMBER] Regarding QMMM simulation run error:
David Case via AMBER
(Fri Jan 03 2025 - 15:46:16 PST)
[AMBER] Is this the place to ask about CPPTRAJ issues?
James Kress via AMBER
(Sat Jan 04 2025 - 21:01:28 PST)
Re: [AMBER] Is this the place to ask about CPPTRAJ issues?
Daniel Roe via AMBER
(Sun Jan 05 2025 - 09:58:15 PST)
Re: [AMBER] Regarding QMMM simulation run error:
Kankana Bhattacharjee via AMBER
(Sat Jan 04 2025 - 19:11:02 PST)
Re: [AMBER] Regarding QMMM simulation run error:
SATYAJIT KHATUA via AMBER
(Sat Jan 04 2025 - 19:45:15 PST)
Re: [AMBER] Regarding QMMM simulation run error:
David A Case via AMBER
(Sat Jan 04 2025 - 20:47:02 PST)
Re: [AMBER] CPPTRAJ grid output units
Daniel Roe via AMBER
(Sat Jan 04 2025 - 09:46:27 PST)
[AMBER] tleap error: ligand atom does not have a type
Zeyu Lin via AMBER
(Sat Jan 04 2025 - 09:57:32 PST)
Re: [AMBER] tleap error: ligand atom does not have a type
David A Case via AMBER
(Sat Jan 04 2025 - 10:21:04 PST)
[AMBER] Single Point Energy calculation using Force Fields
Benjamin Shugaev via AMBER
(Sat Jan 04 2025 - 10:46:55 PST)
Re: [AMBER] Single Point Energy calculation using Force Fields
David A Case via AMBER
(Sat Jan 04 2025 - 20:52:13 PST)
[AMBER] aMD run
Dulal Mondal via AMBER
(Sun Jan 05 2025 - 04:39:03 PST)
Re: [AMBER] aMD run
Dulal Mondal via AMBER
(Mon Jan 06 2025 - 01:45:33 PST)
Re: [AMBER] [Sender Not Verified] Re: aMD run
Steinbrecher, Thomas via AMBER
(Mon Jan 06 2025 - 04:17:02 PST)
Re: [AMBER] [Sender Not Verified] Re: aMD run
Dulal Mondal via AMBER
(Mon Jan 06 2025 - 05:47:03 PST)
Re: [AMBER] aMD run
Charo del Genio via AMBER
(Mon Jan 06 2025 - 06:04:11 PST)
Re: [AMBER] aMD run
Charo del Genio via AMBER
(Mon Jan 06 2025 - 06:39:09 PST)
[AMBER] Regarding QM-MM error:
Kankana Bhattacharjee via AMBER
(Sun Jan 05 2025 - 23:13:39 PST)
Re: [AMBER] Regarding QM-MM error:
Goetz, Andreas via AMBER
(Mon Jan 06 2025 - 08:53:26 PST)
Re: [AMBER] Regarding QM-MM error:
Kankana Bhattacharjee via AMBER
(Mon Jan 06 2025 - 09:04:53 PST)
[AMBER] Unphysical temperature spikes
Kiriko Terai via AMBER
(Mon Jan 06 2025 - 09:13:17 PST)
Re: [AMBER] Unphysical temperature spikes
Charo del Genio via AMBER
(Mon Jan 06 2025 - 09:23:03 PST)
Re: [AMBER] Unphysical temperature spikes
Guberman-Pfeffer, Matthew via AMBER
(Mon Jan 06 2025 - 09:41:59 PST)
Re: [AMBER] Unphysical temperature spikes
Charo del Genio via AMBER
(Mon Jan 06 2025 - 10:19:05 PST)
Re: [AMBER] Unphysical temperature spikes
Adrian Roitberg via AMBER
(Mon Jan 06 2025 - 10:32:25 PST)
Re: [AMBER] Unphysical temperature spikes
David A Case via AMBER
(Mon Jan 06 2025 - 12:25:35 PST)
[AMBER] Use OPM to add membrane
Zeyu Lin via AMBER
(Mon Jan 06 2025 - 19:08:46 PST)
Re: [AMBER] Use OPM to add membrane
David A Case via AMBER
(Tue Jan 07 2025 - 08:49:59 PST)
[AMBER] Question regarding rotation matrix value from "rotate" (cpptraj)
Dr. Anselm Horn via AMBER
(Tue Jan 07 2025 - 09:22:20 PST)
Re: [AMBER] Question regarding rotation matrix value from "rotate" (cpptraj)
Daniel Roe via AMBER
(Tue Jan 07 2025 - 12:43:33 PST)
Re: [AMBER] Question about vectors
Jing Qu via AMBER
(Mon Jan 06 2025 - 19:57:37 PST)
[AMBER] Regarding the use of the opc3pol water model and the QM-MM calculation error:
Kankana Bhattacharjee via AMBER
(Mon Jan 06 2025 - 23:43:08 PST)
Re: [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)
[AMBER] Issue with generating output files
Munazzah Fatima Ansari via AMBER
(Tue Jan 07 2025 - 23:35:53 PST)
Re: [AMBER] Issue with generating output files
David A Case via AMBER
(Wed Jan 08 2025 - 08:17:46 PST)
[AMBER] Problem in stapled peptides
Airy Sanjeev via AMBER
(Wed Jan 08 2025 - 06:03:14 PST)
Re: [AMBER] Problem in stapled peptides
Airy Sanjeev via AMBER
(Wed Jan 08 2025 - 06:04:08 PST)
[AMBER] A monomer move out the simulation box
Ibrahim Said via AMBER
(Thu Jan 09 2025 - 09:30:36 PST)
Re: [AMBER] A monomer move out the simulation box
Dr. Anselm Horn via AMBER
(Thu Jan 09 2025 - 09:57:57 PST)
Re: [AMBER] A monomer move out the simulation box
Ibrahim Said via AMBER
(Thu Jan 09 2025 - 12:14:41 PST)
[AMBER] prmtop and inpcrd file generation error:
Kankana Bhattacharjee via AMBER
(Thu Jan 09 2025 - 10:46:14 PST)
Re: [AMBER] prmtop and inpcrd file generation error:
Timothy Giese via AMBER
(Thu Jan 09 2025 - 12:52:50 PST)
Re: [AMBER] prmtop and inpcrd file generation error:
Kankana Bhattacharjee via AMBER
(Thu Jan 09 2025 - 20:30:31 PST)
Re: [AMBER] prmtop and inpcrd file generation error:
Kankana Bhattacharjee via AMBER
(Thu Jan 09 2025 - 20:37:34 PST)
Re: [AMBER] prmtop and inpcrd file generation error:
Kankana Bhattacharjee via AMBER
(Thu Jan 09 2025 - 20:52:20 PST)
Re: [AMBER] prmtop and inpcrd file generation error:
Timothy Giese via AMBER
(Fri Jan 10 2025 - 06:12:40 PST)
Re: [AMBER] prmtop and inpcrd file generation error:
Kankana Bhattacharjee via AMBER
(Fri Jan 10 2025 - 08:57:57 PST)
[AMBER] [amber-owner.ambermd.org: Re: Problem in stapled peptides]
David A Case via AMBER
(Thu Jan 09 2025 - 21:51:16 PST)
[AMBER] [amber-owner.ambermd.org: Re: prmtop and inpcrd file generation error:]
David A Case via AMBER
(Thu Jan 09 2025 - 21:50:54 PST)
[AMBER] Error calculation halted in pmemd.cuda
Bhattacharjee, Sinjini via AMBER
(Fri Jan 10 2025 - 03:04:56 PST)
Re: [AMBER] [Sender Not Verified] Error calculation halted in pmemd.cuda
Steinbrecher, Thomas via AMBER
(Fri Jan 10 2025 - 03:20:27 PST)
[AMBER] Calculating charges by Gastieger procedure in Antechamber ...
Michal Husak via AMBER
(Tue Jan 14 2025 - 06:03:56 PST)
[AMBER] sander.quick.cuda error:
Kankana Bhattacharjee via AMBER
(Fri Jan 10 2025 - 09:16:40 PST)
Re: [AMBER] sander.quick.cuda error:
Timothy Giese via AMBER
(Fri Jan 10 2025 - 09:53:16 PST)
Re: [AMBER] sander.quick.cuda error:
Kankana Bhattacharjee via AMBER
(Fri Jan 10 2025 - 10:28:06 PST)
Re: [AMBER] sander.quick.cuda error:
Goetz, Andreas via AMBER
(Fri Jan 10 2025 - 12:27:57 PST)
[AMBER] QM steered md question
Ramdhan,Peter A via AMBER
(Sat Jan 11 2025 - 14:55:16 PST)
[AMBER] Amber metal ions protein multiple chains
Iglika Lessigiarska via AMBER
(Mon Jan 13 2025 - 03:19:59 PST)
Re: [AMBER] Amber metal ions protein multiple chains
David A Case via AMBER
(Mon Jan 13 2025 - 07:26:05 PST)
Re: [AMBER] Amber metal ions protein multiple chains
Solen Ekesan via AMBER
(Mon Jan 13 2025 - 11:55:41 PST)
Re: [AMBER] Amber metal ions protein multiple chains
Li, Zhen via AMBER
(Mon Jan 13 2025 - 12:13:58 PST)
[AMBER] problem in installing Amber24
TUSHAR GUPTA via AMBER
(Mon Jan 13 2025 - 05:13:06 PST)
Re: [AMBER] problem in installing Amber24
David A Case via AMBER
(Mon Jan 13 2025 - 07:37:09 PST)
Re: [AMBER] problem in installing Amber24
James Kress via AMBER
(Mon Jan 13 2025 - 09:35:56 PST)
Re: [AMBER] problem in installing Amber24
TUSHAR GUPTA via AMBER
(Tue Jan 14 2025 - 19:39:45 PST)
Re: [AMBER] problem in installing Amber24
James Kress via AMBER
(Tue Jan 14 2025 - 21:14:30 PST)
[AMBER] Best method to calculate vdW energies between residue side chains
Intravaia, Lauren E via AMBER
(Mon Jan 13 2025 - 12:23:59 PST)
Re: [AMBER] Best method to calculate vdW energies between residue side chains
Dr. Anselm Horn via AMBER
(Tue Jan 14 2025 - 02:54:42 PST)
[AMBER] reporting ΔG? or ΔΔG? vs experimental ΔG using FEP+ and TI
King Wang via AMBER
(Mon Jan 13 2025 - 15:52:54 PST)
Re: [AMBER] reporting ΔG? or ΔΔG? vs experimental ΔG using FEP+ and TI
Brian Radak via AMBER
(Tue Jan 14 2025 - 11:23:11 PST)
Last message date
:
Tue Jan 14 2025 - 21:30:02 PST
Archived on
: Wed Jan 15 2025 - 05:56:15 PST
85 messages
sort by
: [ thread ] [
author
] [
date
] [
subject
] [
attachment
]
Custom Search
