Amber Archive Jun 2025: by thread

[AMBER] RAMD Dhananjay via AMBER (Tue Jun 03 2025 - 19:42:35 PDT)
[AMBER] spc/fw water model Dulal Mondal via AMBER (Wed Jun 04 2025 - 08:00:55 PDT)
- Re: [AMBER] spc/fw water model Timothy Giese via AMBER (Wed Jun 04 2025 - 08:58:50 PDT)
  - Re: [AMBER] spc/fw water model Dulal Mondal via AMBER (Wed Jun 04 2025 - 10:43:41 PDT)
    - Re: [AMBER] spc/fw water model Dulal Mondal via AMBER (Wed Jun 04 2025 - 23:53:04 PDT)
[AMBER] Possible bug in restraint mask parsing during minimization in AMBER24 (works in AMBER22) Pedro Martínez Zaragoza via AMBER (Fri Jun 06 2025 - 03:30:11 PDT)
- Re: [AMBER] Possible bug in restraint mask parsing during minimization in AMBER24 (works in AMBER22) Adrian Roitberg via AMBER (Fri Jun 06 2025 - 11:26:41 PDT)
[AMBER] Steered MD with two variables Kriti Shukla via AMBER (Fri Jun 06 2025 - 22:03:06 PDT)
[AMBER] Segmentation fault occurred when using Amber with Plumed Jiahua Deng via AMBER (Sun Jun 08 2025 - 20:44:35 PDT)
[AMBER] whether the PM6-DH+ method supports cuda acceleration xurui via AMBER (Mon Jun 09 2025 - 07:06:16 PDT)
- Re: [AMBER] whether the PM6-DH+ method supports cuda acceleration David A Case via AMBER (Mon Jun 09 2025 - 20:39:27 PDT)
[AMBER] Segmentation fault when running TI with lambda scheduling for restraints on AMBER 24 (AMD GPU) Yuxuan Zhuang via AMBER (Mon Jun 09 2025 - 12:09:14 PDT)
[AMBER] errors in total energy Sudipti Priyadarsinee via AMBER (Tue Jun 10 2025 - 06:29:07 PDT)
- Re: [AMBER] errors in total energy Elvis Martis via AMBER (Tue Jun 10 2025 - 06:40:21 PDT)
- Re: [AMBER] errors in total energy Carlos Simmerling via AMBER (Tue Jun 10 2025 - 07:17:30 PDT)
- Re: [AMBER] errors in total energy Daniel Roe via AMBER (Thu Jun 12 2025 - 08:18:54 PDT)
[AMBER] Accelerating NMA Calculations in MMPBSA.py for Large Number of Structures Rahul Singal via AMBER (Tue Jun 10 2025 - 23:42:25 PDT)
- Re: [AMBER] Accelerating NMA Calculations in MMPBSA.py for Large Number of Structures David A Case via AMBER (Wed Jun 11 2025 - 07:45:05 PDT)
[AMBER] TIP3P Water issue with MCPB.py Jasmin Güven via AMBER (Wed Jun 11 2025 - 07:44:40 PDT)
- Re: [AMBER] TIP3P Water issue with MCPB.py Li, Zhen via AMBER (Wed Jun 11 2025 - 11:25:21 PDT)
  - Re: [AMBER] TIP3P Water issue with MCPB.py Jasmin Güven via AMBER (Wed Jun 11 2025 - 11:41:19 PDT)
[AMBER] Can cpptraj calculate electron density for molecular surface? Hòa Lê via AMBER (Wed Jun 11 2025 - 20:40:29 PDT)
- Re: [AMBER] Can cpptraj calculate electron density for molecular surface? Hòa Lê via AMBER (Mon Jun 16 2025 - 13:27:45 PDT)
[AMBER] Illegal Memory Access Oke, Elizabeth Damilola via AMBER (Thu Jun 12 2025 - 08:30:33 PDT)
- Re: [AMBER] Illegal Memory Access Daniel Roe via AMBER (Thu Jun 12 2025 - 08:47:19 PDT)
[AMBER] gaff2.dat Kelly, Katie Lynette via AMBER (Thu Jun 12 2025 - 08:43:31 PDT)
- Re: [AMBER] gaff2.dat Christina Bergonzo via AMBER (Thu Jun 12 2025 - 08:56:50 PDT)
[AMBER] Error in saving prmtop of a DNA:RNA hybrid structure Sruthi Sudhakar via AMBER (Fri Jun 13 2025 - 11:41:50 PDT)
- Re: [AMBER] Error in saving prmtop of a DNA:RNA hybrid structure Sruthi Sudhakar via AMBER (Sat Jun 14 2025 - 11:43:41 PDT)
[AMBER] Number of frames loaded in doing MMPBSA.py Jong Young Joung via AMBER (Sun Jun 15 2025 - 23:49:50 PDT)
- [AMBER] Fwd: Number of frames loaded in doing MMPBSA.py Jong Young Joung via AMBER (Mon Jun 16 2025 - 00:10:53 PDT)
[AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER (Mon Jun 16 2025 - 09:28:33 PDT)
- Re: [AMBER] Building double bilayer using packmol-memgen Stephan Schott via AMBER (Thu Jun 19 2025 - 00:24:59 PDT)
  - Re: [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER (Thu Jun 19 2025 - 06:48:49 PDT)
- Re: [AMBER] Building double bilayer using packmol-memgen Stephan Schott via AMBER (Fri Jun 20 2025 - 03:47:45 PDT)
  - Re: [AMBER] Building double bilayer using packmol-memgen Cherry, Kendall via AMBER (Fri Jun 20 2025 - 04:17:05 PDT)
[AMBER] Steered MD - Pulling RNA micro helix from protein's pocket Sidharth E K via AMBER (Tue Jun 17 2025 - 06:09:33 PDT)
[AMBER] Recommended barostat for membrane protein simulations? Cherry, Kendall via AMBER (Wed Jun 18 2025 - 09:53:21 PDT)
- Re: [AMBER] Recommended barostat for membrane protein simulations? Dickson, Callum via AMBER (Wed Jun 18 2025 - 16:00:43 PDT)
  - Re: [AMBER] Recommended barostat for membrane protein simulations? Cherry, Kendall via AMBER (Thu Jun 19 2025 - 08:19:54 PDT)
    - Re: [AMBER] Recommended barostat for membrane protein simulations? Dickson, Callum via AMBER (Thu Jun 19 2025 - 09:59:00 PDT)
    - Re: [AMBER] Recommended barostat for membrane protein simulations? Cherry, Kendall via AMBER (Thu Jun 19 2025 - 10:08:58 PDT)
[AMBER] How can I pack a protein (not GPCR) into the centre of bilayer membrane and perpendicular to the xy plane? yumura.seigo967--- via AMBER (Wed Jun 18 2025 - 22:15:01 PDT)
- Re: [AMBER] How can I pack a protein (not GPCR) into the centre of bilayer membrane and perpendicular to the xy plane? Stephan Schott via AMBER (Thu Jun 19 2025 - 00:18:39 PDT)
[AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER (Thu Jun 19 2025 - 13:57:03 PDT)
- Re: [AMBER] Antechamber and flying ligand problem Dr. Anselm Horn via AMBER (Fri Jun 20 2025 - 02:41:45 PDT)
  - Re: [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER (Mon Jun 23 2025 - 10:48:34 PDT)
    - Re: [AMBER] Antechamber and flying ligand problem Dr. Anselm Horn via AMBER (Tue Jun 24 2025 - 03:15:46 PDT)
    - Re: [AMBER] Antechamber and flying ligand problem Pitambar Poudel via AMBER (Tue Jun 24 2025 - 03:35:02 PDT)
Re: [AMBER] [EXTERNAL] AMBER Digest, Vol 4731, Issue 1 Md Imran Ahmed via AMBER (Mon Jun 23 2025 - 02:27:17 PDT)
- Re: [AMBER] [EXTERNAL] AMBER Digest, Vol 4731, Issue 1 Dr. Anselm Horn via AMBER (Mon Jun 23 2025 - 03:57:25 PDT)
- Re: [AMBER] [EXTERNAL] AMBER Digest, Vol 4731, Issue 1 David A Case via AMBER (Tue Jun 24 2025 - 10:51:21 PDT)
  - [AMBER] Getting started with Amber tutorials David A Case via AMBER (Tue Jun 24 2025 - 11:00:20 PDT)
[AMBER] MM-GBSA Ven, Wouter van de via AMBER (Mon Jun 23 2025 - 08:10:01 PDT)
[AMBER] cpptraj: nonbond energies calculated by "energy" and "lie" are not the same Игорь Упоров via AMBER (Tue Jun 24 2025 - 05:34:50 PDT)
- Re: [AMBER] cpptraj: nonbond energies calculated by "energy" and "lie" are not the same Daniel Roe via AMBER (Tue Jun 24 2025 - 06:08:08 PDT)
- Re: [AMBER] cpptraj: nonbond energies calculated by "energy" and "lie" are not the same Daniel Roe via AMBER (Tue Jun 24 2025 - 08:19:47 PDT)
[AMBER] flatwell restraints MANVENDRA SINGH via AMBER (Tue Jun 24 2025 - 09:50:50 PDT)
- Re: [AMBER] flatwell restraints David A Case via AMBER (Tue Jun 24 2025 - 10:47:40 PDT)

Amber Archive Jun 2025 by thread