Amber Archive Apr 2026: by thread

Re: [AMBER] [EXTERN] Re: Ligand Prepartion Stéphane Téletchéa via AMBER (Wed Apr 01 2026 - 02:51:01 PDT)
- Re: [AMBER] [EXTERN] Re: Ligand Prepartion Sarah Witzke via AMBER (Wed Apr 01 2026 - 03:46:59 PDT)
[AMBER] Help needed with MCPB.py for Ru complex ABDELATIF MESSAOUDI via AMBER (Fri Apr 03 2026 - 08:26:45 PDT)
- Re: [AMBER] Help needed with MCPB.py for Ru complex Pengfei Li via AMBER (Wed Apr 08 2026 - 19:23:48 PDT)
[AMBER] Installation issue - xray module Frederico Henrique Ferreira via AMBER (Sat Apr 04 2026 - 14:36:40 PDT)
- Re: [AMBER] Installation issue - xray module Brent Krueger via AMBER (Sat Apr 04 2026 - 15:53:52 PDT)
- Re: [AMBER] Installation issue - xray module Frederico Henrique Ferreira via AMBER (Mon Apr 06 2026 - 06:33:19 PDT)
[AMBER] TI simulation instability with truncated octahedron box Kalandadze, Nino via AMBER (Mon Apr 06 2026 - 11:29:16 PDT)
- Re: [AMBER] TI simulation instability with truncated octahedron box Timothy Giese via AMBER (Mon Apr 06 2026 - 11:59:16 PDT)
[AMBER] help with non-canonical DNA backbone: 3'-3' and 5'-5' phosphodiester linkages Carmen Cerchia via AMBER (Wed Apr 08 2026 - 12:32:04 PDT)
Re: [AMBER] Possible caveats in using HMR with ZAFF modeling Pengfei Li via AMBER (Wed Apr 08 2026 - 19:24:59 PDT)
[AMBER] Restarting simulation error ULPG:Hickey.Niamh via AMBER (Thu Apr 09 2026 - 02:07:47 PDT)
- Re: [AMBER] Restarting simulation error David A Case via AMBER (Thu Apr 09 2026 - 09:20:35 PDT)
Re: [AMBER] PhD defense milestone — Amber supported my research David A Case via AMBER (Fri Apr 10 2026 - 20:15:22 PDT)
[AMBER] Please help fix this input file for qmmm (Amber24, GAMESS v2023) A R via AMBER (Sat Apr 11 2026 - 01:32:13 PDT)
[AMBER] QMMM (Amber24, gamess.2023.R1) A R via AMBER (Sat Apr 11 2026 - 02:09:02 PDT)
- Re: [AMBER] QMMM (Amber24, gamess.2023.R1) Goetz, Andreas via AMBER (Sat Apr 11 2026 - 16:19:41 PDT)
  - [AMBER] Unsubscribe Christopher Jesudason via AMBER (Sat Apr 11 2026 - 19:15:45 PDT)
- [AMBER] Unsubscribe Christopher Jesudason via AMBER (Sat Apr 11 2026 - 19:57:28 PDT)
Re: [AMBER] Question about steered MD parameters Baker, Joseph via AMBER (Mon Apr 13 2026 - 10:46:33 PDT)
- Re: [AMBER] Question about steered MD parameters Adrian Roitberg via AMBER (Mon Apr 13 2026 - 11:12:36 PDT)
[AMBER] Uasge of Nastruct command Priyasha Majee via AMBER (Tue Apr 14 2026 - 04:06:27 PDT)
- Re: [AMBER] Uasge of Nastruct command Rodrigo Galindo-Murillo via AMBER (Tue Apr 14 2026 - 06:11:52 PDT)
- Re: [AMBER] Uasge of Nastruct command Leung, Jeremy via AMBER (Tue Apr 14 2026 - 09:20:38 PDT)
  - Re: [AMBER] Uasge of Nastruct command Priyasha Majee via AMBER (Wed Apr 15 2026 - 04:59:27 PDT)
    - Re: [AMBER] Uasge of Nastruct command Leung, Jeremy via AMBER (Wed Apr 15 2026 - 08:33:30 PDT)
[AMBER] AMBER and P450 Harshini Karthikeyan via AMBER (Tue Apr 14 2026 - 14:08:15 PDT)
- Re: [AMBER] AMBER and P450 Maria Nagan via AMBER (Tue Apr 14 2026 - 14:20:24 PDT)
[AMBER] Question regarding the relaxation of a system and the use of HMR saverio lemme via AMBER (Wed Apr 15 2026 - 03:04:53 PDT)
- Re: [AMBER] Question regarding the relaxation of a system and the use of HMR Adrian Roitberg via AMBER (Wed Apr 15 2026 - 06:30:29 PDT)
  - [AMBER] R: Question regarding the relaxation of a system and the use of HMR saverio lemme via AMBER (Wed Apr 15 2026 - 07:33:49 PDT)
    - Re: [AMBER] R: Question regarding the relaxation of a system and the use of HMR Li, Zhen via AMBER (Wed Apr 15 2026 - 10:41:44 PDT)
    - Re: [AMBER] R: Question regarding the relaxation of a system and the use of HMR Li, Zhen via AMBER (Wed Apr 15 2026 - 10:45:01 PDT)
    - Re: [AMBER] R: Question regarding the relaxation of a system and the use of HMR Adrian Roitberg via AMBER (Wed Apr 15 2026 - 11:15:17 PDT)
- Re: [AMBER] Question regarding the relaxation of a system and the use of HMR Timothy Giese via AMBER (Wed Apr 15 2026 - 07:09:14 PDT)
  - [AMBER] R: Question regarding the relaxation of a system and the use of HMR saverio lemme via AMBER (Wed Apr 15 2026 - 07:11:52 PDT)
[AMBER] Restart less efficient than Initial ULPG:Hickey.Niamh via AMBER (Mon Apr 20 2026 - 08:44:02 PDT)
- Re: [AMBER] Restart less efficient than Initial Adrian Roitberg via AMBER (Mon Apr 20 2026 - 10:54:03 PDT)
[AMBER] PatchingError: using update_pmemd saverio lemme via AMBER (Mon Apr 20 2026 - 11:50:03 PDT)
- Re: [AMBER] PatchingError: using update_pmemd David A Case via AMBER (Tue Apr 21 2026 - 07:25:49 PDT)
[AMBER] Questions Regarding Structure Preparation and Protonation Errors for MD Simulation ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER (Wed Apr 22 2026 - 04:50:09 PDT)
[AMBER] Compilation Issues Beierlein, Frank via AMBER (Thu Apr 23 2026 - 07:01:05 PDT)
- Re: [AMBER] Compilation Issues Matt Thompson via AMBER (Thu Apr 23 2026 - 08:46:26 PDT)
  - Re: [AMBER] Compilation Issues anu chandra via AMBER (Fri Apr 24 2026 - 09:04:48 PDT)
  - Re: [AMBER] Compilation Issues Frank Beierlein via AMBER (Tue Apr 28 2026 - 06:35:15 PDT)
[AMBER] Need help in proceeding with md sim ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER (Fri Apr 24 2026 - 08:05:39 PDT)
- Re: [AMBER] Need help in proceeding with md sim Adrian Roitberg via AMBER (Fri Apr 24 2026 - 08:59:06 PDT)
  - Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER (Fri Apr 24 2026 - 09:29:32 PDT)
    - Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim Christina Bergonzo via AMBER (Fri Apr 24 2026 - 10:06:12 PDT)
    - Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim David A Case via AMBER (Fri Apr 24 2026 - 13:22:05 PDT)
    - Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim Thomas Cheatham via AMBER (Fri Apr 24 2026 - 13:36:52 PDT)
    - Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim Pedro Guillem via AMBER (Fri Apr 24 2026 - 17:27:18 PDT)
    - Re: [AMBER] [EXTERN] Re: Need help in proceeding with md sim ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER (Sun Apr 26 2026 - 10:24:38 PDT)
[AMBER] How to check if the structure potential energies converged to better state ? ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER (Mon Apr 27 2026 - 08:36:38 PDT)
[AMBER] Question about QM/MM parallelization in sander.MPI 张玮豪 via AMBER (Wed Apr 29 2026 - 01:43:29 PDT)
- Re: [AMBER] Question about QM/MM parallelization in sander.MPI Adrian Roitberg via AMBER (Wed Apr 29 2026 - 07:54:01 PDT)
Re: [AMBER] Miniforge fails during install + Fix Leung, Jeremy via AMBER (Thu Apr 30 2026 - 12:05:42 PDT)

Amber Archive Apr 2026 by thread