Amber Archive Mar 2025 by date

75 messages: Starting Sun Mar 02 2025 - 10:00:02 PST, Ending Mon Mar 31 2025 - 15:30:02 PDT
This period: Most recent messages
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Sunday, 2 March 2025
- [AMBER] single point energy examples Benjamin Shugaev via AMBER
- Re: [AMBER] single point energy examples David A Case via AMBER
Tuesday, 4 March 2025
- [AMBER] A problem in parametrizing a fused heteroaromatic compound YOKOI Taiyo via AMBER
- Re: [AMBER] Amber metal ions protein multiple chains Iglika Lessigiarska via AMBER
- Re: [AMBER] Amber metal ions protein multiple chains Li, Zhen via AMBER
Wednesday, 5 March 2025
- [AMBER] Compilation errors with CUDA 12.6 RUBEN ANTONIO ROMO MANCILLAS via AMBER
- Re: [AMBER] Compilation errors with CUDA 12.6 James Kress via AMBER
- Re: [AMBER] Compilation errors with CUDA 12.6 RUBEN ANTONIO ROMO MANCILLAS via AMBER
- Re: [AMBER] Compilation errors with CUDA 12.6 James Kress via AMBER
Thursday, 6 March 2025
- [AMBER] Atom names failed Carlos via AMBER
- Re: [AMBER] AMBER Digest, Vol 4648, Issue 1 Patricio Barletta via AMBER
- Re: [AMBER] Compilation errors with CUDA 12.6 Gard Nelson via AMBER
Friday, 7 March 2025
- [AMBER] Another way to disable building pbsa.cuda (e.g. for CUDA 12.6) David A Case via AMBER
Saturday, 8 March 2025
- [AMBER] 'Process abort signal' when running sander or pmemd. ning via AMBER
Monday, 10 March 2025
- [AMBER] ante-MMPBSA.py Error: Creating complex topology failed! Righteous via AMBER
- Re: [AMBER] A problem in parametrizing a fused heteroaromatic compound Junmei Wang via AMBER
Wednesday, 12 March 2025
- [AMBER] Issue in using AMBER22 in RTX 4090 TUSHAR GUPTA via AMBER
- Re: [AMBER] Issue in using AMBER22 in RTX 4090 David A Case via AMBER
- Re: [AMBER] 'Process abort signal' when running sander or pmemd. David A Case via AMBER
Sunday, 16 March 2025
- [AMBER] possibly a bug in the CUDA version of PMEMD Ye Mei via AMBER
Tuesday, 18 March 2025
- [AMBER] NETCDF error message Dulal Mondal via AMBER
- Re: [AMBER] NETCDF error message Masoud Keramati via AMBER
- [AMBER] How to solve FATAL: Atom .R<*>.A<*> does not have a type. 1464903098 via AMBER
- Re: [AMBER] possibly a bug in the CUDA version of PMEMD 1464903098 via AMBER
- Re: [AMBER] How to solve FATAL: Atom .R<*>.A<*> does not have a type. Rodrigo Galindo-Murillo via AMBER
- [AMBER] How to solve FATAL: Atom .R<*>.A<*> does not have a type. 1464903098 via AMBER
- [AMBER] FATAL: Atom .R<*>.A<*> does not have a type. 1464903098 via AMBER
Thursday, 20 March 2025
- [AMBER] Different number of processes give different nonbonded energy in sander trajectory analysis Yunhao Mei via AMBER
- Re: [AMBER] Different number of processes give different nonbonded energy in sander trajectory analysis Daniel Roe via AMBER
- Re: [AMBER] Different number of processes give different nonbonded energy in sander trajectory analysis Daniel Roe via AMBER
- [AMBER] compiling Amber24 on Rocky9 HPC cluster Latorraca, Naomi R. via AMBER
- [AMBER] modified amino acid residue error while using antechamber fateme haghighi via AMBER
- Re: [AMBER] modified amino acid residue error while using antechamber Lauren Raguette via AMBER
Friday, 21 March 2025
- [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList Gross, Craig via AMBER
- Re: [AMBER] compiling Amber24 on Rocky9 HPC cluster David A Case via AMBER
- Re: [AMBER-Developers] [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList David A Case via AMBER-Developers
- Re: [AMBER] compiling Amber24 on Rocky9 HPC cluster SATYAJIT KHATUA via AMBER
- Re: [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList Patricio Barletta via AMBER
Saturday, 22 March 2025
- [AMBER] MMPBSA is not working Ibrahim Said via AMBER
- Re: [AMBER] compiling Amber24 on Rocky9 HPC cluster Patricio Barletta via AMBER
Sunday, 23 March 2025
- [AMBER] AMD GPU executable reads different gb parameters Wong, Sergio E. via AMBER
- [AMBER] Amber24 installation +cuda fateme haghighi via AMBER
- Re: [AMBER] AMD GPU executable reads different gb parameters David A Case via AMBER
- Re: [AMBER] Amber24 installation +cuda David A Case via AMBER
Monday, 24 March 2025
- Re: [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList Gross, Craig via AMBER
Tuesday, 25 March 2025
- [AMBER] Help with ZINC Paramterisation using MCPB.py DIPANKAR DAS 20012 via AMBER
- [AMBER] Query: Generating Force Field Parameters for TCO and TCNitro FRET Probes in DNA System Rahul Singal via AMBER
Wednesday, 26 March 2025
- [AMBER] DFTB/MM result from SQM does not match Sander? Ge Song via AMBER
- Re: [AMBER] Query: Generating Force Field Parameters for TCO and TCNitro FRET Probes in DNA System Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] DFTB/MM result from SQM does not match Sander? Timothy Giese via AMBER
- Re: [AMBER] DFTB/MM result from SQM does not match Sander? Ge Song via AMBER
- Re: [AMBER] DFTB/MM result from SQM does not match Sander? Ge Song via AMBER
- [AMBER] Installation Issue: cudaMemcpyToSymbol: SetSim copy to cSim failed no kernel image is available for execution on the device Johannes Loeffler via AMBER
- [AMBER] Errors in Antechamber Devid Sahu via AMBER
- [AMBER] Issue with PMF Calculation in AMBER Umbrella Sampling SANKAR MAITY via AMBER
Thursday, 27 March 2025
- Re: [AMBER] Issue with PMF Calculation in AMBER Umbrella Sampling Christina Bergonzo via AMBER
- [AMBER] MCPB.py usage Hantz, Eric via AMBER
- Re: [AMBER] Errors in Antechamber Patricio Barletta via AMBER
- Re: [AMBER] MCPB.py usage Pengfei Li via AMBER
Friday, 28 March 2025
- [AMBER] Installation Error: Russell Bertrand via AMBER
- Re: [AMBER] Errors in Antechamber Devid Sahu via AMBER
- Re: [AMBER] Installation Error: Daniel Roe via AMBER
- [AMBER] force field combination for a protein-RNA complex Sruthi Sudhakar via AMBER
- Re: [AMBER] Help with ZINC Paramterisation using MCPB.py Li, Zhen via AMBER
- Re: [AMBER] Help with ZINC Paramterisation using MCPB.py Li, Zhen via AMBER
- Re: [AMBER] Help with ZINC Paramterisation using MCPB.py DIPANKAR DAS 20012 via AMBER
Saturday, 29 March 2025
- Re: [AMBER] Installation Error: Daniel Roe via AMBER
- Re: [AMBER] Errors in Antechamber David A Case via AMBER
- [AMBER] compiling Amber24 with gcc 14.2.1/cuda 12.4.1 Vlad Cojocaru via AMBER
Sunday, 30 March 2025
- Re: [AMBER] compiling Amber24 with gcc 14.2.1/cuda 12.4.1 Vlad Cojocaru via AMBER
- [AMBER] Help with Missing Torsion Parameters for TCO and TCNitro FRET Probes in DNA System Rahul Singal via AMBER
Monday, 31 March 2025
- [AMBER] reading/imaging NAMD DCD trajectories with AMBER topologies in CPPTRAJ Vlad Cojocaru via AMBER
- Re: [AMBER] reading/imaging NAMD DCD trajectories with AMBER topologies in CPPTRAJ David A Case via AMBER
- Re: [AMBER] Help with Missing Torsion Parameters for TCO and TCNitro FRET Probes in DNA System David A Case via AMBER
- [AMBER] MCPB Tutorial Ligand missing vdW and other parameters Hantz, Eric via AMBER

Last message date: Mon Mar 31 2025 - 15:30:02 PDT
Archived on: Wed Apr 23 2025 - 05:56:30 PDT