Amber Archive Mar 2025: by thread

[AMBER] single point energy examples Benjamin Shugaev via AMBER (Sun Mar 02 2025 - 09:29:22 PST)
- Re: [AMBER] single point energy examples David A Case via AMBER (Sun Mar 02 2025 - 15:40:25 PST)
[AMBER] A problem in parametrizing a fused heteroaromatic compound YOKOI Taiyo via AMBER (Tue Mar 04 2025 - 02:16:41 PST)
- Re: [AMBER] A problem in parametrizing a fused heteroaromatic compound Junmei Wang via AMBER (Mon Mar 10 2025 - 08:11:54 PDT)
Re: [AMBER] Amber metal ions protein multiple chains Iglika Lessigiarska via AMBER (Tue Mar 04 2025 - 10:48:20 PST)
- Re: [AMBER] Amber metal ions protein multiple chains Li, Zhen via AMBER (Tue Mar 04 2025 - 10:59:27 PST)
[AMBER] Compilation errors with CUDA 12.6 RUBEN ANTONIO ROMO MANCILLAS via AMBER (Wed Mar 05 2025 - 09:57:27 PST)
- Re: [AMBER] Compilation errors with CUDA 12.6 James Kress via AMBER (Wed Mar 05 2025 - 10:45:21 PST)
  - Re: [AMBER] Compilation errors with CUDA 12.6 RUBEN ANTONIO ROMO MANCILLAS via AMBER (Wed Mar 05 2025 - 19:23:12 PST)
    - Re: [AMBER] Compilation errors with CUDA 12.6 James Kress via AMBER (Wed Mar 05 2025 - 20:38:41 PST)
    - Re: [AMBER] Compilation errors with CUDA 12.6 Gard Nelson via AMBER (Thu Mar 06 2025 - 13:36:22 PST)
[AMBER] Atom names failed Carlos via AMBER (Thu Mar 06 2025 - 11:54:25 PST)
Re: [AMBER] AMBER Digest, Vol 4648, Issue 1 Patricio Barletta via AMBER (Thu Mar 06 2025 - 12:59:19 PST)
[AMBER] Another way to disable building pbsa.cuda (e.g. for CUDA 12.6) David A Case via AMBER (Fri Mar 07 2025 - 10:14:51 PST)
[AMBER] 'Process abort signal' when running sander or pmemd. ning via AMBER (Sat Mar 08 2025 - 11:31:43 PST)
- Re: [AMBER] 'Process abort signal' when running sander or pmemd. David A Case via AMBER (Wed Mar 12 2025 - 10:35:13 PDT)
[AMBER] ante-MMPBSA.py Error: Creating complex topology failed! Righteous via AMBER (Mon Mar 10 2025 - 01:28:49 PDT)
[AMBER] Issue in using AMBER22 in RTX 4090 TUSHAR GUPTA via AMBER (Wed Mar 12 2025 - 03:41:05 PDT)
- Re: [AMBER] Issue in using AMBER22 in RTX 4090 David A Case via AMBER (Wed Mar 12 2025 - 10:38:01 PDT)
[AMBER] possibly a bug in the CUDA version of PMEMD Ye Mei via AMBER (Sun Mar 16 2025 - 20:56:43 PDT)
- Re: [AMBER] possibly a bug in the CUDA version of PMEMD 1464903098 via AMBER (Tue Mar 18 2025 - 18:51:27 PDT)
[AMBER] NETCDF error message Dulal Mondal via AMBER (Tue Mar 18 2025 - 06:49:15 PDT)
- Re: [AMBER] NETCDF error message Masoud Keramati via AMBER (Tue Mar 18 2025 - 07:33:17 PDT)
[AMBER] How to solve FATAL: Atom .R<*>.A<*> does not have a type. 1464903098 via AMBER (Tue Mar 18 2025 - 18:48:51 PDT)
- Re: [AMBER] How to solve FATAL: Atom .R<*>.A<*> does not have a type. Rodrigo Galindo-Murillo via AMBER (Tue Mar 18 2025 - 18:57:27 PDT)
[AMBER] How to solve FATAL: Atom .R<*>.A<*> does not have a type. 1464903098 via AMBER (Tue Mar 18 2025 - 19:34:33 PDT)
[AMBER] FATAL: Atom .R<*>.A<*> does not have a type. 1464903098 via AMBER (Tue Mar 18 2025 - 19:43:36 PDT)
[AMBER] Different number of processes give different nonbonded energy in sander trajectory analysis Yunhao Mei via AMBER (Thu Mar 20 2025 - 04:43:05 PDT)
- Re: [AMBER] Different number of processes give different nonbonded energy in sander trajectory analysis Daniel Roe via AMBER (Thu Mar 20 2025 - 05:36:11 PDT)
- Re: [AMBER] Different number of processes give different nonbonded energy in sander trajectory analysis Daniel Roe via AMBER (Thu Mar 20 2025 - 06:17:10 PDT)
[AMBER] compiling Amber24 on Rocky9 HPC cluster Latorraca, Naomi R. via AMBER (Thu Mar 20 2025 - 06:57:35 PDT)
- Re: [AMBER] compiling Amber24 on Rocky9 HPC cluster David A Case via AMBER (Fri Mar 21 2025 - 09:21:51 PDT)
  - Re: [AMBER] compiling Amber24 on Rocky9 HPC cluster SATYAJIT KHATUA via AMBER (Fri Mar 21 2025 - 09:40:09 PDT)
- Re: [AMBER] compiling Amber24 on Rocky9 HPC cluster Patricio Barletta via AMBER (Sat Mar 22 2025 - 12:21:00 PDT)
[AMBER] modified amino acid residue error while using antechamber fateme haghighi via AMBER (Thu Mar 20 2025 - 09:23:03 PDT)
- Re: [AMBER] modified amino acid residue error while using antechamber Lauren Raguette via AMBER (Thu Mar 20 2025 - 10:04:06 PDT)
[AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList Gross, Craig via AMBER (Fri Mar 21 2025 - 05:54:24 PDT)
- Re: [AMBER-Developers] [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList David A Case via AMBER-Developers (Fri Mar 21 2025 - 09:27:18 PDT)
- Re: [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList Patricio Barletta via AMBER (Fri Mar 21 2025 - 15:01:43 PDT)
  - Re: [AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList Gross, Craig via AMBER (Mon Mar 24 2025 - 14:58:35 PDT)
[AMBER] MMPBSA is not working Ibrahim Said via AMBER (Sat Mar 22 2025 - 02:35:06 PDT)
[AMBER] AMD GPU executable reads different gb parameters Wong, Sergio E. via AMBER (Sun Mar 23 2025 - 01:06:30 PDT)
- Re: [AMBER] AMD GPU executable reads different gb parameters David A Case via AMBER (Sun Mar 23 2025 - 12:59:27 PDT)
[AMBER] Amber24 installation +cuda fateme haghighi via AMBER (Sun Mar 23 2025 - 11:27:52 PDT)
- Re: [AMBER] Amber24 installation +cuda David A Case via AMBER (Sun Mar 23 2025 - 13:03:33 PDT)
[AMBER] Help with ZINC Paramterisation using MCPB.py DIPANKAR DAS 20012 via AMBER (Tue Mar 25 2025 - 07:37:21 PDT)
[AMBER] Query: Generating Force Field Parameters for TCO and TCNitro FRET Probes in DNA System Rahul Singal via AMBER (Tue Mar 25 2025 - 23:26:20 PDT)
- Re: [AMBER] Query: Generating Force Field Parameters for TCO and TCNitro FRET Probes in DNA System Rodrigo Galindo-Murillo via AMBER (Wed Mar 26 2025 - 07:40:48 PDT)
[AMBER] DFTB/MM result from SQM does not match Sander? Ge Song via AMBER (Wed Mar 26 2025 - 07:30:27 PDT)
- Re: [AMBER] DFTB/MM result from SQM does not match Sander? Timothy Giese via AMBER (Wed Mar 26 2025 - 09:10:09 PDT)
- Re: [AMBER] DFTB/MM result from SQM does not match Sander? Ge Song via AMBER (Wed Mar 26 2025 - 13:32:48 PDT)
  - Re: [AMBER] DFTB/MM result from SQM does not match Sander? Ge Song via AMBER (Wed Mar 26 2025 - 13:42:21 PDT)
[AMBER] Installation Issue: cudaMemcpyToSymbol: SetSim copy to cSim failed no kernel image is available for execution on the device Johannes Loeffler via AMBER (Wed Mar 26 2025 - 22:22:22 PDT)
[AMBER] Errors in Antechamber Devid Sahu via AMBER (Wed Mar 26 2025 - 22:51:24 PDT)
- Re: [AMBER] Errors in Antechamber Patricio Barletta via AMBER (Thu Mar 27 2025 - 13:23:21 PDT)
- Re: [AMBER] Errors in Antechamber Devid Sahu via AMBER (Fri Mar 28 2025 - 02:39:24 PDT)
[AMBER] Issue with PMF Calculation in AMBER Umbrella Sampling SANKAR MAITY via AMBER (Wed Mar 26 2025 - 23:34:55 PDT)
- Re: [AMBER] Issue with PMF Calculation in AMBER Umbrella Sampling Christina Bergonzo via AMBER (Thu Mar 27 2025 - 05:30:22 PDT)
[AMBER] MCPB.py usage Hantz, Eric via AMBER (Thu Mar 27 2025 - 11:50:46 PDT)
- Re: [AMBER] MCPB.py usage Pengfei Li via AMBER (Thu Mar 27 2025 - 13:41:26 PDT)
[AMBER] Installation Error: Russell Bertrand via AMBER (Fri Mar 28 2025 - 02:24:05 PDT)

Amber Archive Mar 2025 by thread