Amber Archive Mar 2025: by subject

[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)
[AMBER] 'Process abort signal' when running sander or pmemd.
- David A Case via AMBER (Wed Mar 12 2025 - 10:35:13 PDT)
- ning via AMBER (Sat Mar 08 2025 - 11:31:43 PST)
[AMBER] A problem in parametrizing a fused heteroaromatic compound
- Junmei Wang via AMBER (Mon Mar 10 2025 - 08:11:54 PDT)
- YOKOI Taiyo via AMBER (Tue Mar 04 2025 - 02:16:41 PST)
[AMBER] AMBER Digest, Vol 4648, Issue 1
- Patricio Barletta via AMBER (Thu Mar 06 2025 - 12:59:19 PST)
[AMBER] Amber metal ions protein multiple chains
- Li, Zhen via AMBER (Tue Mar 04 2025 - 10:59:27 PST)
- Iglika Lessigiarska via AMBER (Tue Mar 04 2025 - 10:48:20 PST)
[AMBER] Amber24 installation +cuda
- David A Case via AMBER (Sun Mar 23 2025 - 13:03:33 PDT)
- fateme haghighi via AMBER (Sun Mar 23 2025 - 11:27:52 PDT)
[AMBER] AMD GPU executable reads different gb parameters
- David A Case via AMBER (Sun Mar 23 2025 - 12:59:27 PDT)
- Wong, Sergio E. via AMBER (Sun Mar 23 2025 - 01:06:30 PDT)
[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] ante-MMPBSA.py Error: Creating complex topology failed!
- Righteous via AMBER (Mon Mar 10 2025 - 01:28:49 PDT)
[AMBER] Atom names failed
- Carlos via AMBER (Thu Mar 06 2025 - 11:54:25 PST)
[AMBER] Compilation errors with CUDA 12.6
- Gard Nelson via AMBER (Thu Mar 06 2025 - 13:36:22 PST)
- James Kress via AMBER (Wed Mar 05 2025 - 20:38:41 PST)
- RUBEN ANTONIO ROMO MANCILLAS via AMBER (Wed Mar 05 2025 - 19:23:12 PST)
- James Kress via AMBER (Wed Mar 05 2025 - 10:45:21 PST)
- RUBEN ANTONIO ROMO MANCILLAS via AMBER (Wed Mar 05 2025 - 09:57:27 PST)
[AMBER] compiling Amber24 on Rocky9 HPC cluster
- Patricio Barletta via AMBER (Sat Mar 22 2025 - 12:21:00 PDT)
- SATYAJIT KHATUA via AMBER (Fri Mar 21 2025 - 09:40:09 PDT)
- David A Case via AMBER (Fri Mar 21 2025 - 09:21:51 PDT)
- Latorraca, Naomi R. via AMBER (Thu Mar 20 2025 - 06:57:35 PDT)
[AMBER] compiling Amber24 with gcc 14.2.1/cuda 12.4.1
- Vlad Cojocaru via AMBER (Sun Mar 30 2025 - 03:58:31 PDT)
- Vlad Cojocaru via AMBER (Sat Mar 29 2025 - 13:13:43 PDT)
[AMBER] DFTB/MM result from SQM does not match Sander?
- Ge Song via AMBER (Wed Mar 26 2025 - 13:42:21 PDT)
- Ge Song via AMBER (Wed Mar 26 2025 - 13:32:48 PDT)
- Timothy Giese via AMBER (Wed Mar 26 2025 - 09:10:09 PDT)
- Ge Song via AMBER (Wed Mar 26 2025 - 07:30:27 PDT)
[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)
- Daniel Roe via AMBER (Thu Mar 20 2025 - 05:36:11 PDT)
- Yunhao Mei via AMBER (Thu Mar 20 2025 - 04:43:05 PDT)
[AMBER] Errors in Antechamber
- David A Case via AMBER (Sat Mar 29 2025 - 10:51:57 PDT)
- Devid Sahu via AMBER (Fri Mar 28 2025 - 02:39:24 PDT)
- Patricio Barletta via AMBER (Thu Mar 27 2025 - 13:23:21 PDT)
- Devid Sahu via AMBER (Wed Mar 26 2025 - 22:51:24 PDT)
[AMBER] FATAL: Atom .R<*>.A<*> does not have a type.
- 1464903098 via AMBER (Tue Mar 18 2025 - 19:43:36 PDT)
[AMBER] force field combination for a protein-RNA complex
- Sruthi Sudhakar via AMBER (Fri Mar 28 2025 - 12:19:20 PDT)
[AMBER] Help with ZINC Paramterisation using MCPB.py
- DIPANKAR DAS 20012 via AMBER (Fri Mar 28 2025 - 20:21:59 PDT)
- Li, Zhen via AMBER (Fri Mar 28 2025 - 20:09:32 PDT)
- Li, Zhen via AMBER (Fri Mar 28 2025 - 19:43:59 PDT)
- DIPANKAR DAS 20012 via AMBER (Tue Mar 25 2025 - 07:37:21 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)
- Rodrigo Galindo-Murillo via AMBER (Tue Mar 18 2025 - 18:57:27 PDT)
- 1464903098 via AMBER (Tue Mar 18 2025 - 18:48:51 PDT)
[AMBER] Installation Error:
- Daniel Roe via AMBER (Sat Mar 29 2025 - 08:01:55 PDT)
- Daniel Roe via AMBER (Fri Mar 28 2025 - 06:21:29 PDT)
- Russell Bertrand via AMBER (Fri Mar 28 2025 - 02:24:05 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] Issue in using AMBER22 in RTX 4090
- David A Case via AMBER (Wed Mar 12 2025 - 10:38:01 PDT)
- TUSHAR GUPTA via AMBER (Wed Mar 12 2025 - 03:41:05 PDT)
[AMBER] Issue with PMF Calculation in AMBER Umbrella Sampling
- Christina Bergonzo via AMBER (Thu Mar 27 2025 - 05:30:22 PDT)
- SANKAR MAITY via AMBER (Wed Mar 26 2025 - 23:34:55 PDT)
[AMBER] MCPB.py usage
- Pengfei Li via AMBER (Thu Mar 27 2025 - 13:41:26 PDT)
- Hantz, Eric via AMBER (Thu Mar 27 2025 - 11:50:46 PDT)
[AMBER] MMPBSA is not working
- Ibrahim Said via AMBER (Sat Mar 22 2025 - 02:35:06 PDT)
[AMBER] modified amino acid residue error while using antechamber
- Lauren Raguette via AMBER (Thu Mar 20 2025 - 10:04:06 PDT)
- fateme haghighi via AMBER (Thu Mar 20 2025 - 09:23:03 PDT)
[AMBER] NETCDF error message
- Masoud Keramati via AMBER (Tue Mar 18 2025 - 07:33:17 PDT)
- Dulal Mondal via AMBER (Tue Mar 18 2025 - 06:49:15 PDT)
[AMBER] pmemd.cuda error: invalid argument launching kernel kgBuildSpecial2RestNBPreList
- Gross, Craig via AMBER (Mon Mar 24 2025 - 14:58:35 PDT)
- Patricio Barletta via AMBER (Fri Mar 21 2025 - 15:01:43 PDT)
- Gross, Craig via AMBER (Fri Mar 21 2025 - 05:54:24 PDT)
[AMBER] possibly a bug in the CUDA version of PMEMD
- 1464903098 via AMBER (Tue Mar 18 2025 - 18:51:27 PDT)
- Ye Mei via AMBER (Sun Mar 16 2025 - 20:56:43 PDT)
[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)
- Rahul Singal via AMBER (Tue Mar 25 2025 - 23:26:20 PDT)
[AMBER] single point energy examples
- David A Case via AMBER (Sun Mar 02 2025 - 15:40:25 PST)
- Benjamin Shugaev via AMBER (Sun Mar 02 2025 - 09:29:22 PST)

Amber Archive Mar 2025 by subject