Amber Archive May 2025: by thread

Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences maya nair via AMBER (Wed Apr 30 2025 - 11:35:02 PDT)
- Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences Téletchéa Stéphane via AMBER (Mon May 05 2025 - 10:12:28 PDT)
  - Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences Mariangela Dametto via AMBER (Mon May 05 2025 - 10:13:27 PDT)
- Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences Cenk Andac via AMBER (Mon May 05 2025 - 20:00:58 PDT)
[AMBER] AmberTools 25 and MBIS Trevor Kramer via AMBER (Thu May 01 2025 - 04:42:30 PDT)
- Re: [AMBER] AmberTools 25 and MBIS David A Case via AMBER (Thu May 01 2025 - 20:22:21 PDT)
- Re: [AMBER] AmberTools 25 and MBIS Adrian Roitberg via AMBER (Fri May 02 2025 - 11:56:07 PDT)
[AMBER] Does mbar in fe-toolkit support linear conbination distance as a CV when reconstructing FES from US? Ameni BEN ABDELJAOUED via AMBER (Thu May 01 2025 - 09:16:32 PDT)
- Re: [AMBER] Does mbar in fe-toolkit support linear conbination distance as a CV when reconstructing FES from US? Timothy Giese via AMBER (Thu May 01 2025 - 10:10:23 PDT)
- Re: [AMBER] Does mbar in fe-toolkit support linear conbination distance as a CV when reconstructing FES from US? Timothy Giese via AMBER (Thu May 01 2025 - 10:42:20 PDT)
[AMBER] ante-MMPBSA ERROR: Creating complex topology failed Righteous via AMBER (Sun May 04 2025 - 09:50:43 PDT)
- Re: [AMBER] ante-MMPBSA ERROR: Creating complex topology failed Bill Miller III via AMBER (Sun May 04 2025 - 09:57:43 PDT)
Re: [AMBER] Release of AmberTools25 Vedran Miletic via AMBER (Mon May 05 2025 - 00:57:56 PDT)
[AMBER] Weird atomic valence Kehinde Idowu via AMBER (Mon May 05 2025 - 08:45:49 PDT)
- Re: [AMBER] Weird atomic valence David A Case via AMBER (Tue May 06 2025 - 06:26:12 PDT)
[AMBER] pmemd.cuda Aborted: "double free or corruption (out)" during minimization Devid Sahu via AMBER (Mon May 05 2025 - 23:31:17 PDT)
- Re: [AMBER] pmemd.cuda Aborted: "double free or corruption (out)" during minimization David A Case via AMBER (Tue May 06 2025 - 06:31:25 PDT)
[AMBER] Constant ph molecular dynamics simulation Dulal Mondal via AMBER (Wed May 07 2025 - 01:00:03 PDT)
- Re: [AMBER] Constant ph molecular dynamics simulation Dr. Anselm Horn via AMBER (Tue May 13 2025 - 03:17:29 PDT)
[AMBER] Mutation TI simulation values King Wang via AMBER (Wed May 07 2025 - 19:48:29 PDT)
[AMBER] RMSD calculation Ibrahim Said via AMBER (Sat May 10 2025 - 12:02:36 PDT)
[AMBER] AMBER installation Serguei Vassiliev via AMBER (Mon May 12 2025 - 06:06:01 PDT)
[AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Abhisek Jana via AMBER (Wed May 14 2025 - 04:16:42 PDT)
- Re: [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Carlos Simmerling via AMBER (Wed May 14 2025 - 04:29:04 PDT)
- Re: [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Mlynsky Vojtech via AMBER (Wed May 14 2025 - 12:46:17 PDT)
  - Re: [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Maria Nagan via AMBER (Wed May 14 2025 - 13:17:54 PDT)
[AMBER] Difference in atom/residue naming convention in PDB and CRD/TOP files generated from AmberTools Hòa Lê via AMBER (Thu May 15 2025 - 00:10:20 PDT)
[AMBER] Steered MD - Pushing RNA micro helix to protein's pocket Sidharth E K via AMBER (Thu May 15 2025 - 04:44:53 PDT)
- Re: [AMBER] Steered MD - Pushing RNA micro helix to protein's pocket Carlos Simmerling via AMBER (Thu May 15 2025 - 05:31:30 PDT)
- Re: [AMBER] Steered MD - Pushing RNA micro helix to protein's pocket Adrian Roitberg via AMBER (Thu May 15 2025 - 09:10:28 PDT)
[AMBER] Can't read CRD file Hòa Lê via AMBER (Fri May 16 2025 - 02:16:47 PDT)
[AMBER] Problem with selecting chains from TOP + CRD files for Hòa Lê via AMBER (Fri May 16 2025 - 03:59:35 PDT)
[AMBER] There seems to be a bug in the CPPTRAJ software Michael Shokhen via AMBER (Fri May 16 2025 - 08:45:29 PDT)
- Re: [AMBER] There seems to be a bug in the CPPTRAJ software Timothy Giese via AMBER (Fri May 16 2025 - 08:56:36 PDT)
- Re: [AMBER] There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER (Fri May 16 2025 - 09:08:52 PDT)
[AMBER] Fw: There seems to be a bug in the CPPTRAJ software Michael Shokhen via AMBER (Fri May 16 2025 - 09:55:58 PDT)
- Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER (Fri May 16 2025 - 11:04:31 PDT)
  - Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER (Sat May 17 2025 - 06:52:54 PDT)
    - Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Michael Shokhen via AMBER (Sat May 17 2025 - 22:16:53 PDT)
    - Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER (Mon May 19 2025 - 10:45:21 PDT)
  - Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER (Tue May 20 2025 - 09:08:46 PDT)
[AMBER] runtime error in AmberTools25 tests and pmemd24 license for computing center Motoshi Kamiya via AMBER (Mon May 19 2025 - 00:47:39 PDT)
- Re: [AMBER] runtime error in AmberTools25 tests and pmemd24 license for computing center David A Case via AMBER (Thu May 22 2025 - 09:09:59 PDT)
[AMBER] Issue with VdW Energies in MMGBSA Calculations Mar Llorca Torres via AMBER (Mon May 19 2025 - 03:27:45 PDT)
- Re: [AMBER] Issue with VdW Energies in MMGBSA Calculations Bill Miller III via AMBER (Mon May 19 2025 - 07:45:01 PDT)
[AMBER] Unable to build Darrin Bath via AMBER (Tue May 20 2025 - 08:32:42 PDT)
- Re: [AMBER] Unable to build David A Case via AMBER (Thu May 22 2025 - 09:04:06 PDT)
[AMBER] missing angle/dihedral parameters issue after MCPB.py/tleap Aliakbartehrani Zahra via AMBER (Wed May 21 2025 - 00:41:48 PDT)
- Re: [AMBER] missing angle/dihedral parameters issue after MCPB.py/tleap Li, Zhen via AMBER (Mon May 26 2025 - 21:02:01 PDT)
[AMBER] Strange bond connecting the ends of two separate chains Hòa Lê via AMBER (Wed May 21 2025 - 04:51:07 PDT)
[AMBER] Question regarding fixing cispeptides in modelled loops and protonation states Jenny 148 via AMBER (Thu May 22 2025 - 09:40:37 PDT)
- Re: [AMBER] Question regarding fixing cispeptides in modelled loops and protonation states Adrian Roitberg via AMBER (Fri May 23 2025 - 06:12:44 PDT)
[AMBER] How to parametrize these RNA structure with "N" bases in the structure Debarati DasGupta via AMBER (Thu May 22 2025 - 13:53:38 PDT)
- Re: [AMBER] How to parametrize these RNA structure with "N" bases in the structure Carlos Simmerling via AMBER (Thu May 22 2025 - 14:12:38 PDT)
[AMBER] Missing Angle Parameter Issue Nematipour, Adel \(drf5jn\) via AMBER (Fri May 23 2025 - 11:17:31 PDT)
[AMBER] Bug in CPPTRAJ following alignment Helmut Carter via AMBER (Tue May 27 2025 - 09:34:25 PDT)
- Re: [AMBER] Bug in CPPTRAJ following alignment Carlos Simmerling via AMBER (Tue May 27 2025 - 09:38:19 PDT)
Re: [AMBER] [EXTERNAL]Re: Bug in CPPTRAJ following alignment Carlos Simmerling via AMBER (Tue May 27 2025 - 09:53:13 PDT)
[AMBER] AmberTools 25 fails to compile with Python 3.13 Charo del Genio via AMBER (Wed May 28 2025 - 03:34:24 PDT)
- Re: [AMBER] AmberTools 25 fails to compile with Python 3.13 Vedran Miletic via AMBER (Wed May 28 2025 - 05:26:12 PDT)
  - Re: [AMBER] AmberTools 25 fails to compile with Python 3.13 Charo del Genio via AMBER (Wed May 28 2025 - 06:06:33 PDT)
[AMBER] pbsa warning/error Professor Mark Wilson via AMBER (Wed May 28 2025 - 13:19:50 PDT)
[AMBER] GROMAC's insert-molecule equivalent in AMBER Russell Bertrand via AMBER (Thu May 29 2025 - 02:51:00 PDT)

Amber Archive May 2025 by thread