Amber Archive Dec 2025: by thread

[AMBER] Custom Caps in AMBER and Compatibility with GROMACS Xenidis, Vasilis via AMBER (Tue Dec 02 2025 - 08:41:40 PST)
- Re: [AMBER] Custom Caps in AMBER and Compatibility with GROMACS Carlos Simmerling via AMBER (Tue Dec 02 2025 - 08:55:32 PST)
- Re: [AMBER] Custom Caps in AMBER and Compatibility with GROMACS Téletchéa Stéphane via AMBER (Tue Dec 02 2025 - 09:38:11 PST)
[AMBER] LINMIN failure Sangita Kachhap via AMBER (Wed Dec 03 2025 - 07:12:06 PST)
[AMBER] Request download AmberTools24 source code Arsene Marian Alain via AMBER (Thu Dec 04 2025 - 01:21:21 PST)
- Re: [AMBER] Request download AmberTools24 source code David A Case via AMBER (Sat Dec 06 2025 - 10:03:27 PST)
[AMBER] Question: Box size change during parametrization of rbLDH in 1M trehalose cai.hanfeng--- via AMBER (Fri Dec 05 2025 - 10:55:44 PST)
- Re: [AMBER] Question: Box size change during parametrization of rbLDH in 1M trehalose Arun Srikanth via AMBER (Fri Dec 05 2025 - 12:25:00 PST)
- Re: [AMBER] Question: Box size change during parametrization of rbLDH in 1M trehalose David A Case via AMBER (Sat Dec 06 2025 - 10:15:37 PST)
[AMBER] Radius of phosphate Reza Khayat via AMBER (Fri Dec 05 2025 - 12:01:05 PST)
- Re: [AMBER] Radius of phosphate David A Case via AMBER (Sat Dec 06 2025 - 10:06:59 PST)
[AMBER] Calculating a dot product between eigenvectors Osman, Roman via AMBER (Wed Dec 10 2025 - 19:29:58 PST)
- Re: [AMBER] Calculating a dot product between eigenvectors Daniel Roe via AMBER (Thu Dec 11 2025 - 05:40:36 PST)
[AMBER] Error: Bad topology file. Sum of ATOMS_PER_MOLECULE does not equal NATOM Siavoush Dastmalchi via AMBER (Thu Dec 11 2025 - 04:34:39 PST)
[AMBER] &wt type='rest' not applied in Amber22 pmemd.cuda Emme Burgin via AMBER (Thu Dec 11 2025 - 08:36:38 PST)
- Re: [AMBER] &wt type='rest' not applied in Amber22 pmemd.cuda David A Case via AMBER (Sat Dec 13 2025 - 08:32:27 PST)
[AMBER] pmemd.cuda.MPI run stops (amber24) Dulal Mondal via AMBER (Thu Dec 11 2025 - 22:51:05 PST)
- Re: [AMBER] pmemd.cuda.MPI run stops (amber24) Dulal Mondal via AMBER (Fri Dec 12 2025 - 23:48:03 PST)
- Re: [AMBER] pmemd.cuda.MPI run stops (amber24) David A Case via AMBER (Sat Dec 13 2025 - 08:23:29 PST)
  - Re: [AMBER] pmemd.cuda.MPI run stops (amber24) Dulal Mondal via AMBER (Sat Dec 13 2025 - 22:49:10 PST)
    - Re: [AMBER] pmemd.cuda.MPI run stops (amber24) Dulal Mondal via AMBER (Sun Dec 21 2025 - 07:05:09 PST)
    - Re: [AMBER] pmemd.cuda.MPI run stops (amber24) Carlos Simmerling via AMBER (Sun Dec 21 2025 - 10:46:30 PST)
[AMBER] Errors in MMPBSA Priyasha Majee via AMBER (Mon Dec 15 2025 - 05:59:21 PST)
- Re: [AMBER] Errors in MMPBSA Dr. Anselm Horn via AMBER (Tue Dec 16 2025 - 05:35:05 PST)
- Re: [AMBER] Errors in MMPBSA Priyasha Majee via AMBER (Thu Dec 18 2025 - 00:53:50 PST)
  - Re: [AMBER] Errors in MMPBSA Bill Miller III via AMBER (Thu Dec 18 2025 - 07:24:35 PST)
[AMBER] Umbrella Sampling | WHAM mish via AMBER (Tue Dec 16 2025 - 09:01:05 PST)
[AMBER] Old Amber installation PIETRO DAL CIN via AMBER (Thu Dec 18 2025 - 08:20:05 PST)
[AMBER] Issue with MMGBSA Calculation for Protein–siRNA Complex YASHIKA . via AMBER (Fri Dec 19 2025 - 00:30:26 PST)
- Re: [AMBER] Issue with MMGBSA Calculation for Protein–siRNA Complex Tomás Benjamín Cáceres Madariaga via AMBER (Fri Dec 19 2025 - 06:31:43 PST)
  - Re: [AMBER] Issue with MMGBSA Calculation for Protein–siRNA Complex YASHIKA . via AMBER (Fri Dec 19 2025 - 08:03:39 PST)
    - Re: [AMBER] Issue with MMGBSA Calculation for Protein–siRNA Complex Bill Miller III via AMBER (Fri Dec 19 2025 - 10:33:30 PST)
[AMBER] Issues with sander-ORCA interface when using ORCA 6.1.0 喵Junmin via AMBER (Fri Dec 19 2025 - 06:32:48 PST)
[AMBER] NetCDF Format Error When Using mpirun with sander, and CPU Usage Query Tan Rua via AMBER (Sun Dec 21 2025 - 01:19:10 PST)
- Re: [AMBER] NetCDF Format Error When Using mpirun with sander, and CPU Usage Query David A Case via AMBER (Sun Dec 21 2025 - 06:40:38 PST)
[AMBER] Invitation to BioEM Marek Malý via AMBER (Mon Dec 22 2025 - 04:22:53 PST)
[AMBER] Query regarding AMBER24 - "KMMD" CMAKE ERROR - Requesting clarification. MANASA BHARATH via AMBER (Tue Dec 23 2025 - 01:51:05 PST)
- Re: [AMBER] Query regarding AMBER24 - "KMMD" CMAKE ERROR - Requesting clarification. David A Case via AMBER (Sun Dec 28 2025 - 07:56:33 PST)
[AMBER] Query regarding AMBER24 - "KMMD" CMAKE ERROR - Requesting clarification. MANASA BHARATH via AMBER (Tue Dec 23 2025 - 20:48:16 PST)
[AMBER] OPC water model misread by NAMD Guillaume Petit via AMBER (Wed Dec 24 2025 - 00:44:28 PST)
[AMBER] Query regarding AMBER24 - "KMMD" CMAKE ERROR - Requesting clarification. MANASA BHARATH via AMBER (Wed Dec 24 2025 - 01:06:12 PST)
[AMBER] Query regarding AMBER24 - "KMMD" CMAKE ERROR - Requesting clarification. MANASA BHARATH via AMBER (Wed Dec 24 2025 - 01:09:33 PST)
[AMBER] Query regarding AMBER24 - "KMMD" CMAKE ERROR - Requesting clarification. MANASA BHARATH via AMBER (Wed Dec 24 2025 - 01:13:00 PST)
[AMBER] Error while running MMPBSA using Amber16 input script on BRaF cluster YASHIKA . via AMBER (Tue Dec 30 2025 - 02:18:02 PST)
- Re: [AMBER] Error while running MMPBSA using Amber16 input script on BRaF cluster Elvis Martis via AMBER (Tue Dec 30 2025 - 03:31:36 PST)

Amber Archive Dec 2025 by thread