Amber Archive Sep 2025: by thread

[AMBER] HIII ankita mehta via AMBER (Tue Sep 02 2025 - 09:36:49 PDT)
[AMBER] continuous constant pH (chapter 28) Dulal Mondal via AMBER (Wed Sep 03 2025 - 07:58:06 PDT)
- Re: [AMBER] continuous constant pH (chapter 28) Dulal Mondal via AMBER (Wed Sep 03 2025 - 08:15:32 PDT)
- Re: [AMBER] continuous constant pH (chapter 28) Dulal Mondal via AMBER (Wed Sep 03 2025 - 10:10:53 PDT)
[AMBER] Amber EasyBuild taha.elmoudden--- via AMBER (Wed Sep 03 2025 - 08:38:42 PDT)
Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER (Wed Sep 03 2025 - 12:10:26 PDT)
[AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs YASHIKA . via AMBER (Wed Sep 03 2025 - 22:25:42 PDT)
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Elvis Martis via AMBER (Wed Sep 03 2025 - 22:58:03 PDT)
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Thomas Cheatham via AMBER (Wed Sep 03 2025 - 23:00:35 PDT)
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Carlos Simmerling via AMBER (Thu Sep 04 2025 - 03:31:37 PDT)
  - Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Daniel Roe via AMBER (Thu Sep 04 2025 - 08:35:41 PDT)
[AMBER] KeyError of chargedict in MCPB's step 1 Ge Song via AMBER (Thu Sep 04 2025 - 08:47:45 PDT)
- Re: [AMBER] KeyError of chargedict in MCPB's step 1 Li, Zhen via AMBER (Thu Sep 04 2025 - 09:55:28 PDT)
  - Re: [AMBER] KeyError of chargedict in MCPB's step 1 Ge Song via AMBER (Thu Sep 04 2025 - 10:18:06 PDT)
    - Re: [AMBER] KeyError of chargedict in MCPB's step 1 Li, Zhen via AMBER (Thu Sep 04 2025 - 11:48:26 PDT)
    - Re: [AMBER] KeyError of chargedict in MCPB's step 1 Ge Song via AMBER (Thu Sep 04 2025 - 12:09:02 PDT)
    - Re: [AMBER] KeyError of chargedict in MCPB's step 1 Li, Zhen via AMBER (Thu Sep 04 2025 - 16:23:22 PDT)
[AMBER] secondary structure analysis ankita mehta via AMBER (Thu Sep 04 2025 - 09:11:22 PDT)
[AMBER] Hydrogen bond analysis at particular frame ankita mehta via AMBER (Thu Sep 04 2025 - 23:08:52 PDT)
[AMBER] Hydrogen bond analysis on a single frame David A Case via AMBER (Fri Sep 05 2025 - 07:53:19 PDT)
[AMBER] ASH (protonated Asp) at N terminus missing NH3+ Cherry, Kendall via AMBER (Mon Sep 08 2025 - 08:37:24 PDT)
- Re: [AMBER] ASH (protonated Asp) at N terminus missing NH3+ Carlos Simmerling via AMBER (Mon Sep 08 2025 - 08:44:48 PDT)
- Re: [AMBER] ASH (protonated Asp) at N terminus missing NH3+ Carlos Simmerling via AMBER (Wed Sep 10 2025 - 09:28:44 PDT)
[AMBER] Segmentation fault in pmemd.MPI: YASHIKA . via AMBER (Mon Sep 08 2025 - 22:56:28 PDT)
- Re: [AMBER] Segmentation fault in pmemd.MPI: David A Case via AMBER (Thu Sep 11 2025 - 08:52:06 PDT)
[AMBER] Segmentation fault in pmemd.MPI: YASHIKA . via AMBER (Tue Sep 09 2025 - 22:58:06 PDT)
[AMBER] Compatibility of NVIDIA RTX 5060/5070/4060/4080 GPUs with Amber installation Abhisek Jana via AMBER (Tue Sep 09 2025 - 22:50:41 PDT)
- Re: [AMBER] Compatibility of NVIDIA RTX 5060/5070/4060/4080 GPUs with Amber installation Maria Nagan via AMBER (Wed Sep 10 2025 - 16:09:57 PDT)
[AMBER] occasional problem in ABFE in pmemd.cuda Charles-Alexandre Mattelaer via AMBER (Wed Sep 10 2025 - 01:59:28 PDT)
[AMBER] Looking at gaff2 FyD via AMBER (Wed Sep 10 2025 - 23:39:19 PDT)
- Re: [AMBER] Looking at gaff2 FyD via AMBER (Thu Sep 11 2025 - 00:04:56 PDT)
[AMBER] job run error Dulal Mondal via AMBER (Fri Sep 12 2025 - 04:07:29 PDT)
- Re: [AMBER] job run error David A Case via AMBER (Fri Sep 12 2025 - 14:03:27 PDT)
- Re: [AMBER] job run error David A Case via AMBER (Sun Sep 14 2025 - 11:24:08 PDT)
Re: [AMBER] A note about running pmemd.cuda on NVIDIA Blackwell GPUs Oscar Conchillo-Solé via AMBER (Fri Sep 12 2025 - 07:53:33 PDT)
- Re: [AMBER] A note about running pmemd.cuda on NVIDIA Blackwell GPUs David A Case via AMBER (Fri Sep 12 2025 - 14:00:49 PDT)
Re: [AMBER] MMPBSA.py "bad atom type" error with custom Fe(IV) ion David A Case via AMBER (Fri Sep 12 2025 - 14:12:22 PDT)
[AMBER] per frame residue interactions Debarati DasGupta via AMBER (Mon Sep 15 2025 - 12:59:38 PDT)
- Re: [AMBER] per frame residue interactions Rodrigo Galindo-Murillo via AMBER (Mon Sep 15 2025 - 13:11:49 PDT)
- Re: [AMBER] per frame residue interactions Gard Nelson via AMBER (Mon Sep 15 2025 - 13:13:52 PDT)
[AMBER] dihedralrms is complex Debarati DasGupta via AMBER (Wed Sep 17 2025 - 14:24:30 PDT)
- Re: [AMBER] dihedralrms is complex Daniel Roe via AMBER (Thu Sep 25 2025 - 05:30:13 PDT)
[AMBER] Error in Steered QM/MM MD Kriti Shukla via AMBER (Fri Sep 19 2025 - 05:52:07 PDT)
- Re: [AMBER] Error in Steered QM/MM MD Ramdhan,Peter A via AMBER (Fri Sep 19 2025 - 05:57:50 PDT)
  - Re: [AMBER] Error in Steered QM/MM MD Kriti Shukla via AMBER (Fri Sep 19 2025 - 06:02:10 PDT)
  - Re: [AMBER] Error in Steered QM/MM MD Adrian Roitberg via AMBER (Fri Sep 19 2025 - 06:04:04 PDT)
    - Re: [AMBER] Error in Steered QM/MM MD Goetz, Andreas via AMBER (Fri Sep 19 2025 - 15:27:49 PDT)
[AMBER] How to define COM of two domains in the DISANG file for Steered Molecular Dynamics Simulation in AMBER? Gourav Das via AMBER (Fri Sep 19 2025 - 23:49:07 PDT)
- Re: [AMBER] How to define COM of two domains in the DISANG file for Steered Molecular Dynamics Simulation in AMBER? Carlos Simmerling via AMBER (Sat Sep 20 2025 - 06:19:56 PDT)
[AMBER] Stacking calculations Debarati DasGupta via AMBER (Sat Sep 20 2025 - 08:40:43 PDT)
- Re: [AMBER] Stacking calculations Rodrigo Galindo-Murillo via AMBER (Sat Sep 20 2025 - 08:44:08 PDT)
[AMBER] Error Kapali Suri via AMBER (Sun Sep 21 2025 - 13:50:03 PDT)
[AMBER] Error in nad+ Kapali Suri via AMBER (Sun Sep 21 2025 - 13:59:12 PDT)
- Re: [AMBER] Error in nad+ David A Case via AMBER (Mon Sep 22 2025 - 09:27:30 PDT)
[AMBER] Updated Amber 24 benchmarks Ross Walker via AMBER (Mon Sep 22 2025 - 14:18:09 PDT)
- Re: [AMBER] Updated Amber 24 benchmarks Oscar Conchillo-Solé via AMBER (Tue Sep 23 2025 - 08:17:27 PDT)
  - Re: [AMBER] Updated Amber 24 benchmarks David A Case via AMBER (Thu Sep 25 2025 - 11:45:03 PDT)
- Re: [AMBER] Updated Amber 24 benchmarks Emme Burgin via AMBER (Fri Sep 26 2025 - 12:35:33 PDT)
  - Re: [AMBER] Updated Amber 24 benchmarks Ross Walker via AMBER (Fri Sep 26 2025 - 12:39:11 PDT)
[AMBER] Review of a covalent ligand-cysteine (CYX) simulation setup js jeon via AMBER (Mon Sep 22 2025 - 23:02:48 PDT)
- Re: [AMBER] Review of a covalent ligand-cysteine (CYX) simulation setup Carlos Simmerling via AMBER (Tue Sep 23 2025 - 06:36:39 PDT)
[AMBER] Problems changing LJ distances by atom type. James Ross via AMBER (Tue Sep 23 2025 - 02:08:47 PDT)
- Re: [AMBER] Problems changing LJ distances by atom type. Carlos Simmerling via AMBER (Tue Sep 23 2025 - 06:31:51 PDT)
[AMBER] Segmentation Fault with Bonded Parameter Fitting Tutorial (Stage 2) js jeon via AMBER (Tue Sep 23 2025 - 23:33:23 PDT)
[AMBER] MMPBSA protein–protein calculation: PB Bomb error (No radius assigned for OG/OZ atom) angad sharma via AMBER (Wed Sep 24 2025 - 05:30:48 PDT)
[AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations Li, Zhen via AMBER (Wed Sep 24 2025 - 07:21:44 PDT)
- Re: [AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations Timothy Giese via AMBER (Wed Sep 24 2025 - 07:47:32 PDT)
  - Re: [AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations Timothy Giese via AMBER (Wed Sep 24 2025 - 07:58:04 PDT)
[AMBER] miniconda error with Amber24 Jiang, Wei via AMBER (Thu Sep 25 2025 - 12:46:51 PDT)
- Re: [AMBER] miniconda error with Amber24 David A Case via AMBER (Thu Sep 25 2025 - 13:20:22 PDT)
- Re: [AMBER] miniconda error with Amber24 Skanda Sastry via AMBER (Thu Sep 25 2025 - 16:44:08 PDT)
[AMBER] Compiling Amber24 fails after changing gti_controlVariable.i for GaMD-PPI Christian Seitz via AMBER (Tue Sep 30 2025 - 15:54:36 PDT)

Amber Archive Sep 2025 by thread