Amber Archive Oct 2024: by date

Tuesday, 1 October 2024
- [AMBER] plumed patch with amber24 Dulal Mondal via AMBER
- [AMBER] cpinutil.py error: AmberWarning: Molecule atoms are not contiguous! Abdelrahman, Noureen via AMBER
- Re: [AMBER] cpinutil.py error: AmberWarning: Molecule atoms are not contiguous! Adrian Roitberg via AMBER
- [AMBER] Doing alignment on a specific region and run RMSF on ther reagion with CPPTRAJ Maghsoud, Yazdan via AMBER
- [AMBER] Paramfit X ForceBalance - Was: Forcefield Builder analogs in Amber Jones de Andrade via AMBER
Wednesday, 2 October 2024
- [AMBER] issue with packmol-memgen from amber-tools 2024 Enrico Martinez via AMBER
- [AMBER] Length of translation vector from "rmsd" via cpptraj? Dr. Anselm Horn via AMBER
- [AMBER] Question about Steered QM/MM/MD Ramdhan,Peter A via AMBER
- Re: [AMBER] Length of translation vector from "rmsd" via cpptraj? Daniel Roe via AMBER
- Re: [AMBER] Doing alignment on a specific region and run RMSF on ther reagion with CPPTRAJ Daniel Roe via AMBER
Thursday, 3 October 2024
- Re: [AMBER] Doing alignment on a specific region and run RMSF on ther reagion with CPPTRAJ Daniel Roe via AMBER
- [AMBER] Send pmemd output to stdout? Gard Nelson via AMBER
Friday, 4 October 2024
- Re: [AMBER] Length of translation vector from "rmsd" via cpptraj? Dr. Anselm Horn via AMBER
- [AMBER] Question about QM with Gaussian using GPU Ramdhan,Peter A via AMBER
- [AMBER] QM/MM simulation with SHAKE using Sander QUICK module Dutta, Ankita via AMBER
- Re: [AMBER] QM/MM simulation with SHAKE using Sander QUICK module Ramdhan,Peter A via AMBER
Saturday, 5 October 2024
- [AMBER] Inquiry on problems with CDH2 Zinc Finger Force Field Parameters 戚苗苗 via AMBER
Monday, 7 October 2024
- [AMBER] Installation: Amber24 with MVAPICH2-GDR Nitin Kulhar via AMBER
- [AMBER] Saving trajectory during minimization Alexander Hung Lee via AMBER
Tuesday, 8 October 2024
- Re: [AMBER] [Sender Not Verified] Saving trajectory during minimization Alexander Hung Lee via AMBER
- [AMBER] BZIP2 Error when building Amber24 Robert Palmere via AMBER
Wednesday, 9 October 2024
- [AMBER] Error when starting PPI GaMD simulation Nikolay Kuzmich via AMBER
Thursday, 10 October 2024
- Re: [AMBER] BZIP2 Error when building Amber24 Téletchéa Stéphane via AMBER
- [AMBER] System Administrator Position, NIH/NHLBI Daniel Roe via AMBER
- [AMBER] Enforcing Chirality in DNA Simulations Maciej Spiegel via AMBER
- [AMBER] segmentation faults and randomly stopping simulations Ryan Woltz via AMBER
- Re: [AMBER] segmentation faults and randomly stopping simulations Masoud Keramati via AMBER
- Re: [AMBER] segmentation faults and randomly stopping simulations Ryan Woltz via AMBER
- Re: [AMBER] BZIP2 Error when building Amber24 David A Case via AMBER
- Re: [AMBER] Enforcing Chirality in DNA Simulations David A Case via AMBER
Friday, 11 October 2024
- [AMBER] AMBER-ORCA Interface Ramdhan,Peter A via AMBER
- [AMBER] Problems building Amber Martin Cuma via AMBER
- Re: [AMBER] Enforcing Chirality in DNA Simulations Maciej Spiegel via AMBER
- Re: [AMBER] Enforcing Chirality in DNA Simulations Carlos Simmerling via AMBER
- Re: [AMBER] Enforcing Chirality in DNA Simulations Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] AMBER-ORCA Interface Martin Juhás via AMBER
- Re: [AMBER] Enforcing Chirality in DNA Simulations FyD via AMBER
Saturday, 12 October 2024
- [AMBER] CPPTRAJ is unable to handle the specified arguments Maciej Spiegel via AMBER
- Re: [AMBER] CPPTRAJ is unable to handle the specified arguments Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ is unable to handle the specified arguments Maciej Spiegel via AMBER
- Re: [AMBER] segmentation faults and randomly stopping simulations David A Case via AMBER
- Re: [AMBER] CPPTRAJ is unable to handle the specified arguments Daniel Roe via AMBER
Tuesday, 15 October 2024
- [AMBER] What forcefield for DNA-RNA duplex Maciej Spiegel via AMBER
- Re: [AMBER] What forcefield for DNA-RNA duplex Christina Bergonzo via AMBER
Wednesday, 16 October 2024
- Re: [AMBER] What forcefield for DNA-RNA duplex Mlynsky Vojtech via AMBER
- [AMBER] Using Steered MD in NPT vs NVT vs NVE Ramdhan,Peter A via AMBER
- [AMBER] AMBER CUDA version support Martin Cuma via AMBER
Thursday, 17 October 2024
- [AMBER] multiple solvent system Enrico Martinez via AMBER
- Re: [AMBER] segmentation faults and randomly stopping simulations Daniel Roe via AMBER
- Re: [AMBER] AMBER CUDA version support Daniel Roe via AMBER
Friday, 18 October 2024
- Re: [AMBER] multiple solvent system FyD via AMBER
- [AMBER] Installing Amber24 and AmberTools24 Andriy Kovalenko via AMBER
- [AMBER] MBAR options causing error in reading namelist cntrl Charlie Holdship via AMBER
- Re: [AMBER] Problems building Amber David A Case via AMBER
- Re: [AMBER] Installation: Amber24 with MVAPICH2-GDR Nitin Kulhar via AMBER
- Re: [AMBER] Installation: Amber24 with MVAPICH2-GDR Scott Brozell via AMBER
Saturday, 19 October 2024
- Re: [AMBER] Installation: Amber24 with MVAPICH2-GDR Nitin Kulhar via AMBER
Sunday, 20 October 2024
- [AMBER] Atommap doesn't change atom names Maciej Spiegel via AMBER
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- [AMBER] Seeking Automated Torsional Re-parameterization Tools for GAFF/GAFF2 Marawan Hussien via AMBER
- Re: [AMBER] Seeking Automated Torsional Re-parameterization Tools for GAFF/GAFF2 Carlos Simmerling via AMBER
- Re: [AMBER] Seeking Automated Torsional Re-parameterization Tools for GAFF/GAFF2 Carlos Simmerling via AMBER
Monday, 21 October 2024
- [AMBER] Assistance Required with MCPB.py and Non-Standard Residue Handling 郑逸非 via AMBER
- Re: [AMBER] Seeking Automated Torsional Re-parameterization Tools for GAFF/GAFF2 Juraj Dobias via AMBER
- Re: [AMBER] Assistance Required with MCPB.py and Non-Standard Residue Handling Dr. Anselm Horn via AMBER
- Re: [AMBER] MBAR options causing error in reading namelist cntrl Timothy Giese via AMBER
- Re: [AMBER] MBAR options causing error in reading namelist cntrl Charlie Holdship via AMBER
- [AMBER] AMBER24 compilation - MPI Fortran Yasser Almeida via AMBER
- Re: [AMBER] Seeking Automated Torsional Re-parameterization Tools for GAFF/GAFF2 Marawan Hussien via AMBER
- Re: [AMBER] AMBER24 compilation - MPI Fortran Masoud Keramati via AMBER
- Re: [AMBER] Seeking Automated Torsional Re-parameterization Tools for GAFF/GAFF2 Carlos Simmerling via AMBER
- Re: [AMBER] AMBER CUDA version support Téletchéa Stéphane via AMBER
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- Re: [AMBER] Installation: Amber24 with MVAPICH2-GDR Scott Brozell via AMBER
- Re: [AMBER] Installation: Amber24 with MVAPICH2-GDR Nitin Kulhar via AMBER
- Re: [AMBER] Assistance Required with MCPB.py and Non-Standard Residue Handling Li, Zhen via AMBER
Tuesday, 22 October 2024
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- [AMBER] Question about MCPB.py tutorial with GAMESS-US Silva Carvalho, Felipe via AMBER
Wednesday, 23 October 2024
- [AMBER] MCPB.py: GAMESS-US has no fchk file but seminario requires it. Li, Zhen via AMBER
- Re: [AMBER] Question about MCPB.py tutorial with GAMESS-US Li, Zhen via AMBER
- Re: [AMBER] Question about MCPB.py tutorial with GAMESS-US Silva Carvalho, Felipe via AMBER
- Re: [AMBER] Question about MCPB.py tutorial with GAMESS-US Li, Zhen via AMBER
Thursday, 24 October 2024
- Re: [AMBER] Question about MCPB.py tutorial with GAMESS-US FyD via AMBER
- Re: [AMBER] segmentation faults and randomly stopping simulations Daniel Roe via AMBER
Friday, 25 October 2024
- [AMBER] Question about protein-ligand system: how to add copy of ligands to the solvent ? Enrico Martinez via AMBER
- Re: [AMBER] Question about protein-ligand system: how to add copy of ligands to the solvent ? Enrico Martinez via AMBER
- Re: [AMBER] Question about protein-ligand system: how to add copy of ligands to the solvent ? Enrico Martinez via AMBER
- [AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21) Maciej Spiegel via AMBER
Saturday, 26 October 2024
- Re: [AMBER] Question about the use of MCPB.py(Handling of proteins with non-standard residues in the chain) Li, Zhen via AMBER
Monday, 28 October 2024
- Re: [AMBER] AMBER-ORCA Interface Ramdhan,Peter A via AMBER
- Re: [AMBER] AMBER-ORCA Interface Martin Juhás via AMBER
- [AMBER] patch plumed in amber24 Dulal Mondal via AMBER
- Re: [AMBER] AMBER-ORCA Interface James Kress via AMBER
Tuesday, 29 October 2024
- Re: [AMBER] AMBER24 compilation - MPI Fortran Yasser Almeida via AMBER
- Re: [AMBER] AMBER24 compilation - MPI Fortran Yasser Almeida via AMBER
- Re: [AMBER] patch plumed in amber24 Dulal Mondal via AMBER
- Re: [AMBER] AMBER24 compilation - MPI Fortran Masoud Keramati via AMBER
- Re: [AMBER] patch plumed in amber24 Adrian Roitberg via AMBER
Wednesday, 30 October 2024
- Re: [AMBER] AMBER24 compilation - MPI Fortran Yasser Almeida via AMBER
Thursday, 31 October 2024
- Re: [AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21) David A Case via AMBER
- Re: [AMBER] AMBER24 compilation - MPI Fortran David A Case via AMBER

Last message date: Thu Oct 31 2024 - 08:30:02 PDT
Archived on: Sun Dec 22 2024 - 05:56:18 PST

Amber Archive Oct 2024 by date