Amber Archive Apr 2024: by thread

[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)

Amber Archive Apr 2024 by thread