Amber Archive Sep 2025 by date

72 messages: Starting Tue Sep 02 2025 - 10:00:03 PDT, Ending Tue Sep 30 2025 - 16:00:02 PDT
This period: Most recent messages
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Tuesday, 2 September 2025
- [AMBER] HIII ankita mehta via AMBER
Wednesday, 3 September 2025
- [AMBER] continuous constant pH (chapter 28) Dulal Mondal via AMBER
- Re: [AMBER] continuous constant pH (chapter 28) Dulal Mondal via AMBER
- [AMBER] Amber EasyBuild taha.elmoudden--- via AMBER
- Re: [AMBER] continuous constant pH (chapter 28) Dulal Mondal via AMBER
- Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters? Cherry, Kendall via AMBER
- [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs YASHIKA . via AMBER
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Elvis Martis via AMBER
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Thomas Cheatham via AMBER
Thursday, 4 September 2025
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Carlos Simmerling via AMBER
- Re: [AMBER] Difference in cpptraj output structures between NVT equilibration and NPT production runs Daniel Roe via AMBER
- [AMBER] KeyError of chargedict in MCPB's step 1 Ge Song via AMBER
- [AMBER] secondary structure analysis ankita mehta via AMBER
- Re: [AMBER] KeyError of chargedict in MCPB's step 1 Li, Zhen via AMBER
- Re: [AMBER] KeyError of chargedict in MCPB's step 1 Ge Song via AMBER
- Re: [AMBER] KeyError of chargedict in MCPB's step 1 Li, Zhen via AMBER
- Re: [AMBER] KeyError of chargedict in MCPB's step 1 Ge Song via AMBER
- Re: [AMBER] KeyError of chargedict in MCPB's step 1 Li, Zhen via AMBER
- [AMBER] Hydrogen bond analysis at particular frame ankita mehta via AMBER
Friday, 5 September 2025
- [AMBER] Hydrogen bond analysis on a single frame David A Case via AMBER
Monday, 8 September 2025
- [AMBER] ASH (protonated Asp) at N terminus missing NH3+ Cherry, Kendall via AMBER
- Re: [AMBER] ASH (protonated Asp) at N terminus missing NH3+ Carlos Simmerling via AMBER
- [AMBER] Segmentation fault in pmemd.MPI: YASHIKA . via AMBER
Tuesday, 9 September 2025
- [AMBER] Segmentation fault in pmemd.MPI: YASHIKA . via AMBER
- [AMBER] Compatibility of NVIDIA RTX 5060/5070/4060/4080 GPUs with Amber installation Abhisek Jana via AMBER
Wednesday, 10 September 2025
- [AMBER] occasional problem in ABFE in pmemd.cuda Charles-Alexandre Mattelaer via AMBER
- Re: [AMBER] ASH (protonated Asp) at N terminus missing NH3+ Carlos Simmerling via AMBER
- Re: [AMBER] Compatibility of NVIDIA RTX 5060/5070/4060/4080 GPUs with Amber installation Maria Nagan via AMBER
- [AMBER] Looking at gaff2 FyD via AMBER
Thursday, 11 September 2025
- Re: [AMBER] Looking at gaff2 FyD via AMBER
- Re: [AMBER] Segmentation fault in pmemd.MPI: David A Case via AMBER
Friday, 12 September 2025
- [AMBER] job run error Dulal Mondal via AMBER
- Re: [AMBER] A note about running pmemd.cuda on NVIDIA Blackwell GPUs Oscar Conchillo-Solé via AMBER
- Re: [AMBER] A note about running pmemd.cuda on NVIDIA Blackwell GPUs David A Case via AMBER
- Re: [AMBER] job run error David A Case via AMBER
- Re: [AMBER] MMPBSA.py "bad atom type" error with custom Fe(IV) ion David A Case via AMBER
Sunday, 14 September 2025
- Re: [AMBER] job run error David A Case via AMBER
Monday, 15 September 2025
- [AMBER] per frame residue interactions Debarati DasGupta via AMBER
- Re: [AMBER] per frame residue interactions Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] per frame residue interactions Gard Nelson via AMBER
Wednesday, 17 September 2025
- [AMBER] dihedralrms is complex Debarati DasGupta via AMBER
Friday, 19 September 2025
- [AMBER] Error in Steered QM/MM MD Kriti Shukla via AMBER
- Re: [AMBER] Error in Steered QM/MM MD Ramdhan,Peter A via AMBER
- Re: [AMBER] Error in Steered QM/MM MD Kriti Shukla via AMBER
- Re: [AMBER] Error in Steered QM/MM MD Adrian Roitberg via AMBER
- Re: [AMBER] Error in Steered QM/MM MD Goetz, Andreas via AMBER
- [AMBER] How to define COM of two domains in the DISANG file for Steered Molecular Dynamics Simulation in AMBER? Gourav Das via AMBER
Saturday, 20 September 2025
- Re: [AMBER] How to define COM of two domains in the DISANG file for Steered Molecular Dynamics Simulation in AMBER? Carlos Simmerling via AMBER
- Re: [AMBER] Stacking calculations Rodrigo Galindo-Murillo via AMBER
- [AMBER] Stacking calculations Debarati DasGupta via AMBER
Sunday, 21 September 2025
- [AMBER] Error Kapali Suri via AMBER
- [AMBER] Error in nad+ Kapali Suri via AMBER
Monday, 22 September 2025
- Re: [AMBER] Error in nad+ David A Case via AMBER
- [AMBER] Updated Amber 24 benchmarks Ross Walker via AMBER
- [AMBER] Review of a covalent ligand-cysteine (CYX) simulation setup js jeon via AMBER
Tuesday, 23 September 2025
- [AMBER] Problems changing LJ distances by atom type. James Ross via AMBER
- Re: [AMBER] Problems changing LJ distances by atom type. Carlos Simmerling via AMBER
- Re: [AMBER] Review of a covalent ligand-cysteine (CYX) simulation setup Carlos Simmerling via AMBER
- Re: [AMBER] Updated Amber 24 benchmarks Oscar Conchillo-Solé via AMBER
- [AMBER] Segmentation Fault with Bonded Parameter Fitting Tutorial (Stage 2) js jeon via AMBER
Wednesday, 24 September 2025
- [AMBER] MMPBSA protein–protein calculation: PB Bomb error (No radius assigned for OG/OZ atom) angad sharma via AMBER
- [AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations Li, Zhen via AMBER
- Re: [AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations Timothy Giese via AMBER
- Re: [AMBER] sander.MPI appears to be incompatible with QUICK API while doing free energy calculations Timothy Giese via AMBER
Thursday, 25 September 2025
- Re: [AMBER] dihedralrms is complex Daniel Roe via AMBER
- Re: [AMBER] Updated Amber 24 benchmarks David A Case via AMBER
- [AMBER] miniconda error with Amber24 Jiang, Wei via AMBER
- Re: [AMBER] miniconda error with Amber24 David A Case via AMBER
- Re: [AMBER] miniconda error with Amber24 Skanda Sastry via AMBER
Friday, 26 September 2025
- Re: [AMBER] Updated Amber 24 benchmarks Emme Burgin via AMBER
- Re: [AMBER] Updated Amber 24 benchmarks Ross Walker via AMBER
Tuesday, 30 September 2025
- [AMBER] Compiling Amber24 fails after changing gti_controlVariable.i for GaMD-PPI Christian Seitz via AMBER

Last message date: Tue Sep 30 2025 - 16:00:02 PDT
Archived on: Mon Oct 27 2025 - 05:56:21 PDT