Amber Archive May 2026 by author

53 messages: Starting Mon May 04 2026 - 03:00:02 PDT, Ending Sat May 30 2026 - 09:00:02 PDT
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Anders Frederiksen via AMBER
- Re: [AMBER] bug when running QM/MM with orca as external program (Fri May 29 2026 - 00:28:50 PDT)
- Re: [AMBER] bug when running QM/MM with orca as external program (Tue May 26 2026 - 02:13:21 PDT)
- [AMBER] bug when running QM/MM with orca as external program (Mon May 25 2026 - 06:52:59 PDT)
Arti 2410204 via AMBER
- Re: [AMBER] Vlimit exceeded, box deformation, ligand receptor distance change. (Sat May 30 2026 - 08:36:21 PDT)
- [AMBER] Vlimit exceeded, box deformation, ligand receptor distance change. (Thu May 21 2026 - 03:15:25 PDT)
- [AMBER] Simulation instability during equilibration of protein-ligand-membrane system.(Problem: vlimit exceeded ) (Wed May 20 2026 - 22:58:59 PDT)
- [AMBER] Subject: Peptide ligand movement despite positional restraints in AMBER22 pmemd.cuda (Mon May 11 2026 - 04:17:14 PDT)
Beierlein, Frank via AMBER
- Re: [AMBER] Compilation Issues - also with pmemd26 (Fri May 08 2026 - 02:43:45 PDT)
Bill Miller III via AMBER
- Re: [AMBER] MM-PBSA Problem (Thu May 21 2026 - 08:26:35 PDT)
Carlos Simmerling via AMBER
- Re: [AMBER] Bending in helical region of bHLH Transcription factor (Fri May 15 2026 - 06:30:13 PDT)
- Re: [AMBER] DNA-Protein MMPBSA (Tue May 12 2026 - 04:50:59 PDT)
- Re: [AMBER] Bending in helical region of bHLH Transcription factor (Wed May 06 2026 - 03:59:55 PDT)
Charo del Genio via AMBER
- Re: [AMBER] problems building pmemd26 with cuda support on ubuntu26. (Thu May 21 2026 - 06:03:40 PDT)
- [AMBER] Three patches for AmberTools26 (Fri May 15 2026 - 07:16:15 PDT)
Clorice Reinhardt via AMBER
- Re: [AMBER] bug when running QM/MM with orca as external program (Mon May 25 2026 - 14:54:21 PDT)
Daniel Roe via AMBER
- Re: [AMBER] Help understanding CPPTRAJ rst command for generating AMBER distance restraints. (Wed May 13 2026 - 10:22:06 PDT)
David A Case via AMBER
- Re: [AMBER] INQUIRING ABOUT NEED FOR AN UPGRADE. (Sat May 09 2026 - 08:02:30 PDT)
David Case via AMBER
- Re: [AMBER] Compilation Issues - also with pmemd26 (Fri May 08 2026 - 07:53:28 PDT)
Dickson, Callum via AMBER
- Re: [AMBER] Vlimit exceeded, box deformation, ligand receptor distance change. (Thu May 21 2026 - 06:11:19 PDT)
ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER
- [AMBER] MM-PBSA Problem (Thu May 21 2026 - 05:49:22 PDT)
- [AMBER] Protonation Question (Mon May 04 2026 - 10:54:37 PDT)
Elvis Martis via AMBER
- Re: [AMBER] Bending in helical region of bHLH Transcription factor (Tue May 05 2026 - 23:49:30 PDT)
Gert Kruger via AMBER
- [AMBER] From Punch Cards to AI-Powered HPC: A 40-Year Journey in Computational Chemistry Infrastructure (Thu May 21 2026 - 03:08:35 PDT)
Goetz, Andreas via AMBER
- Re: [AMBER] bug when running QM/MM with orca as external program (Tue May 26 2026 - 21:09:21 PDT)
James Kress via AMBER
- Re: [AMBER] bug when running QM/MM with orca as external program (Tue May 26 2026 - 10:38:58 PDT)
Jiri Sponer via AMBER
- Re: [AMBER] Bending in helical region of bHLH Transcription factor (Thu May 14 2026 - 23:44:04 PDT)
Kevin Hauser via AMBER
- Re: [AMBER] DNA-Protein MMPBSA (Mon May 11 2026 - 07:53:30 PDT)
- Re: [AMBER] DNA-Protein MMPBSA (Mon May 11 2026 - 07:03:40 PDT)
Manasa Bharath ic44158 via AMBER
- [AMBER] Help understanding CPPTRAJ rst command for generating AMBER distance restraints. (Mon May 11 2026 - 03:40:29 PDT)
MANASA BHARATH via AMBER
- [AMBER] INQUIRING ABOUT NEED FOR AN UPGRADE. (Mon May 04 2026 - 03:02:56 PDT)
Oscar Conchillo-Solé via AMBER
- Re: [AMBER] Installing Amber on Grace Hopper GPUs with CUDA 13 (Tue May 05 2026 - 01:23:23 PDT)
Pedro Ojeda May via AMBER
- Re: [AMBER] Installing Amber on Grace Hopper GPUs with CUDA 13 (Mon May 04 2026 - 23:30:12 PDT)
- [AMBER] Installing Amber on Grace Hopper GPUs with CUDA 13 (Mon May 04 2026 - 22:18:21 PDT)
Pengfei Li via AMBER
- Re: [AMBER] Error Occurred When Using MCPB.py to Build a Nonbonded Model for a Ligand-Bound Metalloprotein (Tue May 19 2026 - 19:02:32 PDT)
- Re: [AMBER] Error Occurred When Using MCPB.py to Build a Nonbonded Model for a Ligand-Bound Metalloprotein (Tue May 19 2026 - 18:52:12 PDT)
Raghuvir Pissurlenkar via AMBER
- Re: [AMBER] AMBER Digest, Vol 4956, Issue 1 (Fri May 08 2026 - 15:07:21 PDT)
- Re: [AMBER] AMBER Digest, Vol 4952, Issue 1 (Mon May 04 2026 - 02:29:54 PDT)
Ray Luo via AMBER
- Re: [AMBER] DNA-Protein MMPBSA (Mon May 11 2026 - 13:35:47 PDT)
Scott McCullough via AMBER
- [AMBER] problems building pmemd26 with cuda support on ubuntu26. (Thu May 21 2026 - 05:57:02 PDT)
Stephan Schott via AMBER
- Re: [AMBER] pmemd26 vs ambertools26 (Fri May 15 2026 - 07:00:34 PDT)
- Re: [AMBER] pmemd26 vs ambertools26 (Wed May 13 2026 - 09:40:26 PDT)
- Re: [AMBER] Protonation Question (Tue May 05 2026 - 01:51:08 PDT)
- Re: [AMBER] Installing Amber on Grace Hopper GPUs with CUDA 13 (Tue May 05 2026 - 00:20:28 PDT)
- Re: [AMBER] Installing Amber on Grace Hopper GPUs with CUDA 13 (Mon May 04 2026 - 22:59:03 PDT)
Surabhi Singh 24933024 via AMBER
- Re: [AMBER] Bending in helical region of bHLH Transcription factor (Thu May 14 2026 - 21:53:59 PDT)
- [AMBER] DNA-Protein MMPBSA (Mon May 11 2026 - 06:04:05 PDT)
- [AMBER] Bending in helical region of bHLH Transcription factor (Tue May 05 2026 - 23:37:42 PDT)
Téletchéa Stéphane via AMBER
- Re: [AMBER] bug when running QM/MM with orca as external program (Tue May 26 2026 - 08:52:57 PDT)
Weatherby,Gerard via AMBER
- Re: [AMBER] pmemd26 vs ambertools26 (Wed May 13 2026 - 12:55:03 PDT)
- [AMBER] pmemd26 vs ambertools26 (Wed May 13 2026 - 07:47:20 PDT)
Zihao Bai via AMBER
- [AMBER] ambermd.org is Down (Thu May 07 2026 - 19:10:09 PDT)
喵Junmin via AMBER
- Re: [AMBER] bug when running QM/MM with orca as external program (Tue May 26 2026 - 10:46:54 PDT)
张玮豪 via AMBER
- [AMBER] Error Occurred When Using MCPB.py to Build a Nonbonded Model for a Ligand-Bound Metalloprotein (Tue May 19 2026 - 00:35:04 PDT)