Amber Archive May 2025 by date

63 messages: Starting Wed Apr 30 2025 - 12:00:02 PDT, Ending Thu May 29 2025 - 03:00:02 PDT
This period: Most recent messages
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Wednesday, 30 April 2025
- Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences maya nair via AMBER
Thursday, 1 May 2025
- [AMBER] AmberTools 25 and MBIS Trevor Kramer via AMBER
- [AMBER] Does mbar in fe-toolkit support linear conbination distance as a CV when reconstructing FES from US? Ameni BEN ABDELJAOUED via AMBER
- Re: [AMBER] Does mbar in fe-toolkit support linear conbination distance as a CV when reconstructing FES from US? Timothy Giese via AMBER
- Re: [AMBER] Does mbar in fe-toolkit support linear conbination distance as a CV when reconstructing FES from US? Timothy Giese via AMBER
- Re: [AMBER] AmberTools 25 and MBIS David A Case via AMBER
Friday, 2 May 2025
- Re: [AMBER] AmberTools 25 and MBIS Adrian Roitberg via AMBER
Sunday, 4 May 2025
- [AMBER] ante-MMPBSA ERROR: Creating complex topology failed Righteous via AMBER
- Re: [AMBER] ante-MMPBSA ERROR: Creating complex topology failed Bill Miller III via AMBER
Monday, 5 May 2025
- Re: [AMBER] Release of AmberTools25 Vedran Miletic via AMBER
- [AMBER] Weird atomic valence Kehinde Idowu via AMBER
- Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences Téletchéa Stéphane via AMBER
- Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences Mariangela Dametto via AMBER
- Re: [AMBER] Congratulations on Dr. Case's election to the new member of the National Academy of Sciences Cenk Andac via AMBER
- [AMBER] pmemd.cuda Aborted: "double free or corruption (out)" during minimization Devid Sahu via AMBER
Tuesday, 6 May 2025
- Re: [AMBER] Weird atomic valence David A Case via AMBER
- Re: [AMBER] pmemd.cuda Aborted: "double free or corruption (out)" during minimization David A Case via AMBER
Wednesday, 7 May 2025
- [AMBER] Constant ph molecular dynamics simulation Dulal Mondal via AMBER
- [AMBER] Mutation TI simulation values King Wang via AMBER
Saturday, 10 May 2025
- [AMBER] RMSD calculation Ibrahim Said via AMBER
Monday, 12 May 2025
- [AMBER] AMBER installation Serguei Vassiliev via AMBER
Tuesday, 13 May 2025
- Re: [AMBER] Constant ph molecular dynamics simulation Dr. Anselm Horn via AMBER
Wednesday, 14 May 2025
- [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Abhisek Jana via AMBER
- Re: [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Carlos Simmerling via AMBER
- Re: [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Mlynsky Vojtech via AMBER
- Re: [AMBER] siRNA Base Pairing Instability Beyond 17-mer in MD Simulation Maria Nagan via AMBER
Thursday, 15 May 2025
- [AMBER] Difference in atom/residue naming convention in PDB and CRD/TOP files generated from AmberTools Hòa Lê via AMBER
- [AMBER] Steered MD - Pushing RNA micro helix to protein's pocket Sidharth E K via AMBER
- Re: [AMBER] Steered MD - Pushing RNA micro helix to protein's pocket Carlos Simmerling via AMBER
- Re: [AMBER] Steered MD - Pushing RNA micro helix to protein's pocket Adrian Roitberg via AMBER
Friday, 16 May 2025
- [AMBER] Can't read CRD file Hòa Lê via AMBER
- [AMBER] Problem with selecting chains from TOP + CRD files for Hòa Lê via AMBER
- [AMBER] There seems to be a bug in the CPPTRAJ software Michael Shokhen via AMBER
- Re: [AMBER] There seems to be a bug in the CPPTRAJ software Timothy Giese via AMBER
- Re: [AMBER] There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER
- [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Michael Shokhen via AMBER
- Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER
Saturday, 17 May 2025
- Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER
- Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Michael Shokhen via AMBER
Monday, 19 May 2025
- [AMBER] runtime error in AmberTools25 tests and pmemd24 license for computing center Motoshi Kamiya via AMBER
- [AMBER] Issue with VdW Energies in MMGBSA Calculations Mar Llorca Torres via AMBER
- Re: [AMBER] Issue with VdW Energies in MMGBSA Calculations Bill Miller III via AMBER
- Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER
Tuesday, 20 May 2025
- [AMBER] Unable to build Darrin Bath via AMBER
- Re: [AMBER] Fw: There seems to be a bug in the CPPTRAJ software Daniel Roe via AMBER
Wednesday, 21 May 2025
- [AMBER] missing angle/dihedral parameters issue after MCPB.py/tleap Aliakbartehrani Zahra via AMBER
- [AMBER] Strange bond connecting the ends of two separate chains Hòa Lê via AMBER
Thursday, 22 May 2025
- Re: [AMBER] Unable to build David A Case via AMBER
- Re: [AMBER] runtime error in AmberTools25 tests and pmemd24 license for computing center David A Case via AMBER
- [AMBER] Question regarding fixing cispeptides in modelled loops and protonation states Jenny 148 via AMBER
- [AMBER] How to parametrize these RNA structure with "N" bases in the structure Debarati DasGupta via AMBER
- Re: [AMBER] How to parametrize these RNA structure with "N" bases in the structure Carlos Simmerling via AMBER
Friday, 23 May 2025
- Re: [AMBER] Question regarding fixing cispeptides in modelled loops and protonation states Adrian Roitberg via AMBER
- [AMBER] Missing Angle Parameter Issue Nematipour, Adel \(drf5jn\) via AMBER
Monday, 26 May 2025
- Re: [AMBER] missing angle/dihedral parameters issue after MCPB.py/tleap Li, Zhen via AMBER
Tuesday, 27 May 2025
- [AMBER] Bug in CPPTRAJ following alignment Helmut Carter via AMBER
- Re: [AMBER] Bug in CPPTRAJ following alignment Carlos Simmerling via AMBER
- Re: [AMBER] [EXTERNAL]Re: Bug in CPPTRAJ following alignment Carlos Simmerling via AMBER
Wednesday, 28 May 2025
- [AMBER] AmberTools 25 fails to compile with Python 3.13 Charo del Genio via AMBER
- Re: [AMBER] AmberTools 25 fails to compile with Python 3.13 Vedran Miletic via AMBER
- Re: [AMBER] AmberTools 25 fails to compile with Python 3.13 Charo del Genio via AMBER
- [AMBER] pbsa warning/error Professor Mark Wilson via AMBER
Thursday, 29 May 2025
- [AMBER] GROMAC's insert-molecule equivalent in AMBER Russell Bertrand via AMBER

Last message date: Thu May 29 2025 - 03:00:02 PDT
Archived on: Wed Jun 25 2025 - 05:56:20 PDT