Amber Archive Apr 2024 by thread
93 messages
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Starting
Mon Apr 01 2024 - 01:30:02 PDT,
Ending
Tue Apr 30 2024 - 08:00:03 PDT
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[AMBER] antechamber - running sqm in parallel
Giorgos Lambrinidis via AMBER
(Mon Apr 01 2024 - 01:11:22 PDT)
Re: [AMBER] antechamber - running sqm in parallel
David A Case via AMBER
(Mon Apr 01 2024 - 08:47:47 PDT)
[AMBER] Collecting representative snapshots from AMBER MD trajcetory:
Kankana Bhattacharjee via AMBER
(Mon Apr 01 2024 - 02:54:21 PDT)
Re: [AMBER] Collecting representative snapshots from AMBER MD trajcetory:
Carlos Simmerling via AMBER
(Mon Apr 01 2024 - 06:43:35 PDT)
Re: [AMBER] Collecting representative snapshots from AMBER MD trajcetory:
David A Case via AMBER
(Mon Apr 01 2024 - 08:51:39 PDT)
[AMBER] Coordinating atoms and dummy atoms too close in 12-6-4 dummy atom model.
郭 家藩 via AMBER
(Mon Apr 01 2024 - 02:58:05 PDT)
[AMBER] some atom types are missing in leaprc.gaff2 of AmberTools 23
Ye Mei via AMBER
(Mon Apr 01 2024 - 07:04:33 PDT)
[AMBER] Size of water box for MMPBSA
Yang Wei via AMBER
(Mon Apr 01 2024 - 08:29:50 PDT)
Re: [AMBER] Size of water box for MMPBSA
Carlos Simmerling via AMBER
(Mon Apr 01 2024 - 09:35:07 PDT)
Re: [AMBER] Size of water box for MMPBSA
Yang Wei via AMBER
(Wed Apr 03 2024 - 18:01:52 PDT)
Re: [AMBER] Size of water box for MMPBSA
Carlos Simmerling via AMBER
(Thu Apr 04 2024 - 06:52:36 PDT)
Re: [AMBER] Size of water box for MMPBSA
Yang Wei via AMBER
(Fri Apr 05 2024 - 07:01:59 PDT)
[AMBER] Benzene ring planarity
Intravaia, Lauren E via AMBER
(Mon Apr 01 2024 - 12:28:23 PDT)
Re: [AMBER] Benzene ring planarity
Carlos Simmerling via AMBER
(Mon Apr 01 2024 - 12:38:34 PDT)
[AMBER] Regarding constant pH and redox potential simulation:
Kankana Bhattacharjee via AMBER
(Mon Apr 01 2024 - 23:35:25 PDT)
Re: [AMBER] Regarding constant pH and redox potential simulation:
Vinicius Cruzeiro via AMBER
(Tue Apr 02 2024 - 14:07:10 PDT)
[AMBER] Amber installation error - ModuleNotFoundError: No module named 'parmed'
anu chandra via AMBER
(Tue Apr 02 2024 - 08:43:10 PDT)
[AMBER] Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
ABDELATIF MESSAOUDI via AMBER
(Tue Apr 02 2024 - 10:10:58 PDT)
Re: [AMBER] Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
David A Case via AMBER
(Tue Apr 02 2024 - 14:08:25 PDT)
[AMBER] quick.out problem when running TI sander.quick.cuda.MPI
Montalvillo, Fernando via AMBER
(Tue Apr 02 2024 - 11:01:45 PDT)
Re: [AMBER] quick.out problem when running TI sander.quick.cuda.MPI
Goetz, Andreas via AMBER
(Tue Apr 02 2024 - 20:14:59 PDT)
[AMBER] Pre-command is not working
ABDELATIF MESSAOUDI via AMBER
(Tue Apr 02 2024 - 15:54:14 PDT)
Re: [AMBER] Pre-command is not working
David A Case via AMBER
(Tue Apr 02 2024 - 19:33:07 PDT)
[AMBER] Error_MMGBSA Amber22
ABDELATIF MESSAOUDI via AMBER
(Tue Apr 02 2024 - 17:22:41 PDT)
Re: [AMBER] Error_MMGBSA Amber22
Bill Miller III via AMBER
(Tue Apr 02 2024 - 23:16:08 PDT)
Re: [AMBER] Parametrization of a system with missed loop fragments
Enrico Martinez via AMBER
(Wed Apr 03 2024 - 01:46:51 PDT)
Re: [AMBER] Parametrization of a system with missed loop fragments
Enrico Martinez via AMBER
(Wed Apr 03 2024 - 06:39:18 PDT)
[AMBER] match_atomname program
Baptiste Legrand via AMBER
(Wed Apr 03 2024 - 05:31:49 PDT)
Re: [AMBER] match_atomname program
David A Case via AMBER
(Tue Apr 09 2024 - 07:15:42 PDT)
[AMBER] Amber 22 parallel installation error
anu chandra via AMBER
(Wed Apr 03 2024 - 07:25:59 PDT)
[AMBER] restraining a possible interaction between solute and ligand
Debarati DasGupta via AMBER
(Thu Apr 04 2024 - 16:24:19 PDT)
Re: [AMBER] restraining a possible interaction between solute and ligand
Carlos Simmerling via AMBER
(Thu Apr 04 2024 - 16:59:17 PDT)
Re: [AMBER] restraining a possible interaction between solute and ligand
Carlos Simmerling via AMBER
(Fri Apr 05 2024 - 10:40:38 PDT)
[AMBER] MScript MMPBSA.py_Amber22
ABDELATIF MESSAOUDI via AMBER
(Thu Apr 04 2024 - 17:49:16 PDT)
Re: [AMBER] MScript MMPBSA.py_Amber22
Todd Minehardt via AMBER
(Fri Apr 05 2024 - 05:54:38 PDT)
[AMBER] Ref Flag for Minimization
William Livernois via AMBER
(Fri Apr 05 2024 - 16:46:24 PDT)
Re: [AMBER] Ref Flag for Minimization
He, Amy via AMBER
(Tue Apr 09 2024 - 15:14:39 PDT)
[AMBER] Error while running minimization
AMANPREET KAUR via AMBER
(Sat Apr 06 2024 - 03:27:09 PDT)
Re: [AMBER] Error while running minimization
David A Case via AMBER
(Mon Apr 08 2024 - 06:42:41 PDT)
Re: [AMBER] Error while running minimization
David A Case via AMBER
(Wed Apr 10 2024 - 11:29:25 PDT)
[AMBER] Minimization of a large water box
Sasha Buzko via AMBER
(Sat Apr 06 2024 - 10:44:39 PDT)
Re: [AMBER] Minimization of a large water box
Carlos Simmerling via AMBER
(Sat Apr 06 2024 - 11:32:33 PDT)
[AMBER] mmpbsa_py_nabnmode failed with prmtop com.prmtop!
SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
(Sun Apr 07 2024 - 02:27:17 PDT)
Re: [AMBER] mmpbsa_py_nabnmode failed with prmtop com.prmtop!
Bill Miller III via AMBER
(Sun Apr 07 2024 - 05:47:24 PDT)
[AMBER] Error while running minimization
AMANPREET KAUR via AMBER
(Sun Apr 07 2024 - 22:40:02 PDT)
[AMBER] Virtual box exceeded
AMANPREET KAUR via AMBER
(Mon Apr 08 2024 - 03:03:43 PDT)
Re: [AMBER] Virtual box exceeded
Daniel Roe via AMBER
(Sun Apr 14 2024 - 09:15:11 PDT)
[AMBER] pdb4amber - Hydrogen missing in ligand!
Abdelrahman, Noureen via AMBER
(Mon Apr 08 2024 - 11:38:11 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
He, Amy via AMBER
(Mon Apr 08 2024 - 12:21:43 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
Abdelrahman, Noureen via AMBER
(Mon Apr 08 2024 - 14:24:42 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
Abdelrahman, Noureen via AMBER
(Mon Apr 08 2024 - 14:26:14 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
Amie Rwxayheee via AMBER
(Mon Apr 08 2024 - 15:53:58 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
He, Amy via AMBER
(Mon Apr 08 2024 - 15:55:35 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
Abdelrahman, Noureen via AMBER
(Tue Apr 09 2024 - 08:51:07 PDT)
Re: [AMBER] pdb4amber - Hydrogen missing in ligand!
Dr. Anselm Horn via AMBER
(Tue Apr 09 2024 - 02:56:52 PDT)
[AMBER] Umbrella Sampling for proteins/ligand into a membrane
Matias Alejandro Marambio Soto via AMBER
(Mon Apr 08 2024 - 12:39:13 PDT)
Re: [AMBER] Umbrella Sampling for proteins/ligand into a membrane
Carlos Simmerling via AMBER
(Mon Apr 08 2024 - 12:49:43 PDT)
[AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj
Md Fulbabu Sk via AMBER
(Mon Apr 08 2024 - 15:34:57 PDT)
Re: [AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj
Dickson, Callum via AMBER
(Tue Apr 09 2024 - 07:55:15 PDT)
Re: [AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj
Daniel Roe via AMBER
(Tue Apr 09 2024 - 09:12:45 PDT)
[AMBER] High RMSD Difference
Priyasha Majee via AMBER
(Mon Apr 08 2024 - 23:00:05 PDT)
Re: [AMBER] High RMSD Difference
Carlos Simmerling via AMBER
(Tue Apr 09 2024 - 02:57:09 PDT)
Re: [AMBER] High RMSD Difference
Dr. Anselm Horn via AMBER
(Tue Apr 09 2024 - 03:06:46 PDT)
[AMBER] A40 benchmark for Amber performance
Pooja Pooja via AMBER
(Mon Apr 08 2024 - 23:46:06 PDT)
[AMBER] Need help to setup pulling force
Enrico Martinez via AMBER
(Wed Apr 10 2024 - 00:47:23 PDT)
[AMBER] the rms command
百毒不侵√ via AMBER
(Wed Apr 10 2024 - 06:32:24 PDT)
Re: [AMBER] the rms command
Daniel Roe via AMBER
(Wed Apr 10 2024 - 06:56:05 PDT)
[AMBER] Amber Mail Archive
Onur İŞCİL via AMBER
(Wed Apr 10 2024 - 14:02:40 PDT)
Re: [AMBER] Amber Mail Archive
He, Amy via AMBER
(Wed Apr 10 2024 - 14:06:59 PDT)
Re: [AMBER] Amber Mail Archive
Adrian Roitberg via AMBER
(Wed Apr 10 2024 - 15:14:45 PDT)
[AMBER] constant pH MD: reference energy calculation using finddgrep.py
Dulal Mondal via AMBER
(Wed Apr 10 2024 - 21:29:16 PDT)
Re: [AMBER] constant pH MD: reference energy calculation using finddgrep.py
Adrian Roitberg via AMBER
(Thu Apr 11 2024 - 07:25:06 PDT)
[AMBER] Error: Could not determine format of topology name.prmtop
Priyasha Majee via AMBER
(Wed Apr 10 2024 - 23:23:05 PDT)
Re: [AMBER] Error: Could not determine format of topology name.prmtop
David A Case via AMBER
(Fri Apr 12 2024 - 11:35:33 PDT)
[AMBER] R: Help for the value of #SBATCH --cpus-per-task on a cluster when using only one GPU for pmemd.cuda_SPFP.MPI
saverio lemme via AMBER
(Thu Apr 11 2024 - 07:45:31 PDT)
Re: [AMBER] MM-GBSA and MM-PBSA Results Interpretation
Carlos Simmerling via AMBER
(Thu Apr 11 2024 - 12:35:46 PDT)
[AMBER] AMBER22 pmemd.cuda running error while involving GaMD and Mg2+ ions with a 12-6-4 LJ-type nonbonded model
沈扬 via AMBER
(Mon Apr 15 2024 - 00:42:18 PDT)
Re: [AMBER] Possible bug in PMEMD (appearence of synchronization artifacts between parallel tasks)
Charo del Genio via AMBER
(Mon Apr 15 2024 - 08:25:10 PDT)
[AMBER] How to solve Amber xleap PDB preparation error "atom does not have a type"?
ABDELATIF MESSAOUDI via AMBER
(Mon Apr 15 2024 - 16:17:24 PDT)
Re: [AMBER] How to solve Amber xleap PDB preparation error "atom does not have a type"?
Carlos Simmerling via AMBER
(Mon Apr 15 2024 - 17:49:42 PDT)
Re: [AMBER] How to solve Amber xleap PDB preparation error "atom does not have a type"?
Carlos Simmerling via AMBER
(Thu Apr 18 2024 - 06:17:28 PDT)
[AMBER] ambermd.org does not work
Crescenzo Coppa via AMBER
(Tue Apr 16 2024 - 01:21:06 PDT)
Re: [AMBER] How to fix "FATAL: Atom .R<***> does not have a type"?
Carlos Simmerling via AMBER
(Wed Apr 17 2024 - 18:07:03 PDT)
[AMBER] Setting two groups of positional restraints
Parth Bandivadekar via AMBER
(Thu Apr 18 2024 - 16:48:02 PDT)
Re: [AMBER] Tleap parametrization of DNA system
Enrico Martinez via AMBER
(Mon Apr 22 2024 - 08:42:02 PDT)
Re: [AMBER] Adding missing atoms of the DNA structure
Enrico Martinez via AMBER
(Fri Apr 26 2024 - 06:01:57 PDT)
[AMBER] Native Contact Analysis in cpptraj input script
Priyasha Majee via AMBER
(Mon Apr 29 2024 - 02:11:12 PDT)
[AMBER] Problems with water solvatation
Matias Alejandro Marambio Soto via AMBER
(Mon Apr 29 2024 - 08:55:17 PDT)
Re: [AMBER] Problems with water solvatation
David A Case via AMBER
(Tue Apr 30 2024 - 07:39:48 PDT)
[AMBER] Nativecontact command in Cpptraj
Md Fulbabu Sk via AMBER
(Mon Apr 29 2024 - 09:11:06 PDT)
Re: [AMBER] Nativecontact command in Cpptraj
Diego Gomes via AMBER
(Mon Apr 29 2024 - 13:04:12 PDT)
[AMBER] Thermodynamic Integration calculation:
Kankana Bhattacharjee via AMBER
(Tue Apr 30 2024 - 04:38:50 PDT)
Re: [AMBER] Thermodynamic Integration calculation:
Maria Nagan via AMBER
(Tue Apr 30 2024 - 07:30:47 PDT)
Last message date
:
Tue Apr 30 2024 - 08:00:03 PDT
Archived on
: Sun Nov 10 2024 - 05:56:14 PST
93 messages
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