Amber Archive May 2025 by author

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