Amber Archive Apr 2024: by author

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

Amber Archive Apr 2024 by author