Amber Archive Apr 2024 by date

93 messages: Starting Mon Apr 01 2024 - 01:30:02 PDT, Ending Tue Apr 30 2024 - 08:00:03 PDT
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Monday, 1 April 2024
- [AMBER] antechamber - running sqm in parallel Giorgos Lambrinidis via AMBER
- [AMBER] Collecting representative snapshots from AMBER MD trajcetory: Kankana Bhattacharjee via AMBER
- [AMBER] Coordinating atoms and dummy atoms too close in 12-6-4 dummy atom model. 郭家藩 via AMBER
- Re: [AMBER] Collecting representative snapshots from AMBER MD trajcetory: Carlos Simmerling via AMBER
- [AMBER] some atom types are missing in leaprc.gaff2 of AmberTools 23 Ye Mei via AMBER
- [AMBER] Size of water box for MMPBSA Yang Wei via AMBER
- Re: [AMBER] antechamber - running sqm in parallel David A Case via AMBER
- Re: [AMBER] Collecting representative snapshots from AMBER MD trajcetory: David A Case via AMBER
- Re: [AMBER] Size of water box for MMPBSA Carlos Simmerling via AMBER
- [AMBER] Benzene ring planarity Intravaia, Lauren E via AMBER
- Re: [AMBER] Benzene ring planarity Carlos Simmerling via AMBER
- [AMBER] Regarding constant pH and redox potential simulation: Kankana Bhattacharjee via AMBER
Tuesday, 2 April 2024
- [AMBER] Amber installation error - ModuleNotFoundError: No module named 'parmed' anu chandra via AMBER
- [AMBER] Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL ABDELATIF MESSAOUDI via AMBER
- [AMBER] quick.out problem when running TI sander.quick.cuda.MPI Montalvillo, Fernando via AMBER
- Re: [AMBER] Regarding constant pH and redox potential simulation: Vinicius Cruzeiro via AMBER
- Re: [AMBER] Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL David A Case via AMBER
- [AMBER] Pre-command is not working ABDELATIF MESSAOUDI via AMBER
- [AMBER] Error_MMGBSA Amber22 ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] Pre-command is not working David A Case via AMBER
- Re: [AMBER] quick.out problem when running TI sander.quick.cuda.MPI Goetz, Andreas via AMBER
- Re: [AMBER] Error_MMGBSA Amber22 Bill Miller III via AMBER
Wednesday, 3 April 2024
- Re: [AMBER] Parametrization of a system with missed loop fragments Enrico Martinez via AMBER
- [AMBER] match_atomname program Baptiste Legrand via AMBER
- Re: [AMBER] Parametrization of a system with missed loop fragments Enrico Martinez via AMBER
- [AMBER] Amber 22 parallel installation error anu chandra via AMBER
- Re: [AMBER] Size of water box for MMPBSA Yang Wei via AMBER
Thursday, 4 April 2024
- Re: [AMBER] Size of water box for MMPBSA Carlos Simmerling via AMBER
- [AMBER] restraining a possible interaction between solute and ligand Debarati DasGupta via AMBER
- Re: [AMBER] restraining a possible interaction between solute and ligand Carlos Simmerling via AMBER
- [AMBER] MScript MMPBSA.py_Amber22 ABDELATIF MESSAOUDI via AMBER
Friday, 5 April 2024
- Re: [AMBER] MScript MMPBSA.py_Amber22 Todd Minehardt via AMBER
- Re: [AMBER] Size of water box for MMPBSA Yang Wei via AMBER
- Re: [AMBER] restraining a possible interaction between solute and ligand Carlos Simmerling via AMBER
- [AMBER] Ref Flag for Minimization William Livernois via AMBER
Saturday, 6 April 2024
- [AMBER] Error while running minimization AMANPREET KAUR via AMBER
- [AMBER] Minimization of a large water box Sasha Buzko via AMBER
- Re: [AMBER] Minimization of a large water box Carlos Simmerling via AMBER
Sunday, 7 April 2024
- [AMBER] mmpbsa_py_nabnmode failed with prmtop com.prmtop! SUBHASMITA MAHAPATRA MAHAPATRA via AMBER
- Re: [AMBER] mmpbsa_py_nabnmode failed with prmtop com.prmtop! Bill Miller III via AMBER
- [AMBER] Error while running minimization AMANPREET KAUR via AMBER
Monday, 8 April 2024
- [AMBER] Virtual box exceeded AMANPREET KAUR via AMBER
- Re: [AMBER] Error while running minimization David A Case via AMBER
- [AMBER] pdb4amber - Hydrogen missing in ligand! Abdelrahman, Noureen via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! He, Amy via AMBER
- [AMBER] Umbrella Sampling for proteins/ligand into a membrane Matias Alejandro Marambio Soto via AMBER
- Re: [AMBER] Umbrella Sampling for proteins/ligand into a membrane Carlos Simmerling via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! Abdelrahman, Noureen via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! Abdelrahman, Noureen via AMBER
- [AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj Md Fulbabu Sk via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! Amie Rwxayheee via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! He, Amy via AMBER
- [AMBER] High RMSD Difference Priyasha Majee via AMBER
- [AMBER] A40 benchmark for Amber performance Pooja Pooja via AMBER
Tuesday, 9 April 2024
- Re: [AMBER] High RMSD Difference Carlos Simmerling via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! Dr. Anselm Horn via AMBER
- Re: [AMBER] High RMSD Difference Dr. Anselm Horn via AMBER
- Re: [AMBER] match_atomname program David A Case via AMBER
- Re: [AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj Dickson, Callum via AMBER
- Re: [AMBER] pdb4amber - Hydrogen missing in ligand! Abdelrahman, Noureen via AMBER
- Re: [AMBER] Printing X Y Z coordinates of selected atom or group of atoms in cpptraj Daniel Roe via AMBER
- Re: [AMBER] Ref Flag for Minimization He, Amy via AMBER
Wednesday, 10 April 2024
- [AMBER] Need help to setup pulling force Enrico Martinez via AMBER
- [AMBER] the rms command 百毒不侵√ via AMBER
- Re: [AMBER] the rms command Daniel Roe via AMBER
- Re: [AMBER] Error while running minimization David A Case via AMBER
- [AMBER] Amber Mail Archive Onur İŞCİL via AMBER
- Re: [AMBER] Amber Mail Archive He, Amy via AMBER
- Re: [AMBER] Amber Mail Archive Adrian Roitberg via AMBER
- [AMBER] constant pH MD: reference energy calculation using finddgrep.py Dulal Mondal via AMBER
- [AMBER] Error: Could not determine format of topology name.prmtop Priyasha Majee via AMBER
Thursday, 11 April 2024
- Re: [AMBER] constant pH MD: reference energy calculation using finddgrep.py Adrian Roitberg 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 saverio lemme via AMBER
- Re: [AMBER] MM-GBSA and MM-PBSA Results Interpretation Carlos Simmerling via AMBER
Friday, 12 April 2024
- Re: [AMBER] Error: Could not determine format of topology name.prmtop David A Case via AMBER
Sunday, 14 April 2024
- Re: [AMBER] Virtual box exceeded Daniel Roe via AMBER
Monday, 15 April 2024
- [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
- Re: [AMBER] Possible bug in PMEMD (appearence of synchronization artifacts between parallel tasks) Charo del Genio via AMBER
- [AMBER] How to solve Amber xleap PDB preparation error "atom does not have a type"? ABDELATIF MESSAOUDI via AMBER
- Re: [AMBER] How to solve Amber xleap PDB preparation error "atom does not have a type"? Carlos Simmerling via AMBER
Tuesday, 16 April 2024
- [AMBER] ambermd.org does not work Crescenzo Coppa via AMBER
Wednesday, 17 April 2024
- Re: [AMBER] How to fix "FATAL: Atom .R<***> does not have a type"? Carlos Simmerling via AMBER
Thursday, 18 April 2024
- Re: [AMBER] How to solve Amber xleap PDB preparation error "atom does not have a type"? Carlos Simmerling via AMBER
- [AMBER] Setting two groups of positional restraints Parth Bandivadekar via AMBER
Monday, 22 April 2024
- Re: [AMBER] Tleap parametrization of DNA system Enrico Martinez via AMBER
Friday, 26 April 2024
- Re: [AMBER] Adding missing atoms of the DNA structure Enrico Martinez via AMBER
Monday, 29 April 2024
- [AMBER] Native Contact Analysis in cpptraj input script Priyasha Majee via AMBER
- [AMBER] Problems with water solvatation Matias Alejandro Marambio Soto via AMBER
- [AMBER] Nativecontact command in Cpptraj Md Fulbabu Sk via AMBER
- Re: [AMBER] Nativecontact command in Cpptraj Diego Gomes via AMBER
Tuesday, 30 April 2024
- [AMBER] Thermodynamic Integration calculation: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Thermodynamic Integration calculation: Maria Nagan via AMBER
- Re: [AMBER] Problems with water solvatation David A Case via AMBER

Last message date: Tue Apr 30 2024 - 08:00:03 PDT
Archived on: Fri May 17 2024 - 05:56:09 PDT