Amber Archive May 2026: by thread

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

Amber Archive May 2026 by thread