Amber Archive Jan 2025: by date

Wednesday, 1 January 2025
- [AMBER] Dimension problem for a huge rod-like system PD Dr. Anselm Horn via AMBER
- Re: [AMBER] Regarding polarizable continuum solvation model: David A Case via AMBER
- [AMBER] process_mdout.perl doesn't extract Density data LI An-Bang via AMBER
Thursday, 2 January 2025
- [AMBER] nastruct Jing Qu via AMBER
- [AMBER] Error installing amber on and GPUs Wong, Sergio E. via AMBER
- Re: [AMBER] nastruct Daniel Roe via AMBER
- Re: [AMBER] Regarding QM-MM_MD setup calculation: Goetz, Andreas via AMBER
- Re: [AMBER] Error installing amber on and GPUs David A Case via AMBER
Friday, 3 January 2025
- Re: [AMBER] Regarding QM-MM_MD setup calculation: Kankana Bhattacharjee via AMBER
- [AMBER] Regarding QMMM simulation run error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Regarding QM-MM_MD setup calculation: Goetz, Andreas via AMBER
- Re: [AMBER] Regarding QMMM simulation run error: Goetz, Andreas via AMBER
- Re: [AMBER] Regarding QMMM simulation run error: David Case via AMBER
Saturday, 4 January 2025
- Re: [AMBER] CPPTRAJ grid output units Daniel Roe via AMBER
- [AMBER] tleap error: ligand atom does not have a type Zeyu Lin via AMBER
- Re: [AMBER] tleap error: ligand atom does not have a type David A Case via AMBER
- [AMBER] Single Point Energy calculation using Force Fields Benjamin Shugaev via AMBER
- Re: [AMBER] Regarding QMMM simulation run error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] Regarding QMMM simulation run error: SATYAJIT KHATUA via AMBER
- Re: [AMBER] Regarding QMMM simulation run error: David A Case via AMBER
- Re: [AMBER] Single Point Energy calculation using Force Fields David A Case via AMBER
- [AMBER] Is this the place to ask about CPPTRAJ issues? James Kress via AMBER
- Re: [AMBER] process_mdout.perl doesn't extract Density data David A Case via AMBER
- Re: [AMBER] Dimension problem for a huge rod-like system David A Case via AMBER
Sunday, 5 January 2025
- [AMBER] aMD run Dulal Mondal via AMBER
- Re: [AMBER] Is this the place to ask about CPPTRAJ issues? Daniel Roe via AMBER
- [AMBER] Regarding QM-MM error: Kankana Bhattacharjee via AMBER
Monday, 6 January 2025
- Re: [AMBER] aMD run Dulal Mondal via AMBER
- Re: [AMBER] [Sender Not Verified] Re: aMD run Steinbrecher, Thomas via AMBER
- Re: [AMBER] [Sender Not Verified] Re: aMD run Dulal Mondal via AMBER
- Re: [AMBER] aMD run Charo del Genio via AMBER
- Re: [AMBER] aMD run Charo del Genio via AMBER
- Re: [AMBER] Regarding QM-MM error: Goetz, Andreas via AMBER
- Re: [AMBER] Regarding QM-MM error: Kankana Bhattacharjee via AMBER
- [AMBER] Unphysical temperature spikes Kiriko Terai via AMBER
- Re: [AMBER] Unphysical temperature spikes Charo del Genio via AMBER
- Re: [AMBER] Unphysical temperature spikes Guberman-Pfeffer, Matthew via AMBER
- Re: [AMBER] Unphysical temperature spikes Charo del Genio via AMBER
- Re: [AMBER] Unphysical temperature spikes Adrian Roitberg via AMBER
- Re: [AMBER] Unphysical temperature spikes David A Case via AMBER
- [AMBER] Use OPM to add membrane Zeyu Lin via AMBER
- Re: [AMBER] Question about vectors Jing Qu via AMBER
- [AMBER] Regarding the use of the opc3pol water model and the QM-MM calculation error: Kankana Bhattacharjee via AMBER
Tuesday, 7 January 2025
- Re: [AMBER] Dimension problem for a huge rod-like system Dr. Anselm Horn via AMBER
- Re: [AMBER] Use OPM to add membrane David A Case via AMBER
- Re: [AMBER] Regarding the use of the opc3pol water model and the QM-MM calculation error: David A Case via AMBER
- [AMBER] Question regarding rotation matrix value from "rotate" (cpptraj) Dr. Anselm Horn via AMBER
- Re: [AMBER] Question regarding rotation matrix value from "rotate" (cpptraj) Daniel Roe via AMBER
- [AMBER] Issue with generating output files Munazzah Fatima Ansari via AMBER
Wednesday, 8 January 2025
- [AMBER] Problem in stapled peptides Airy Sanjeev via AMBER
- Re: [AMBER] Problem in stapled peptides Airy Sanjeev via AMBER
- Re: [AMBER] Issue with generating output files David A Case via AMBER
Thursday, 9 January 2025
- [AMBER] A monomer move out the simulation box Ibrahim Said via AMBER
- Re: [AMBER] A monomer move out the simulation box Dr. Anselm Horn via AMBER
- [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] A monomer move out the simulation box Ibrahim Said via AMBER
- Re: [AMBER] prmtop and inpcrd file generation error: Timothy Giese via AMBER
- Re: [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER
- [AMBER] [amber-owner.ambermd.org: Re: Problem in stapled peptides] David A Case via AMBER
- [AMBER] [amber-owner.ambermd.org: Re: prmtop and inpcrd file generation error:] David A Case via AMBER
Friday, 10 January 2025
- [AMBER] Error calculation halted in pmemd.cuda Bhattacharjee, Sinjini via AMBER
- Re: [AMBER] [Sender Not Verified] Error calculation halted in pmemd.cuda Steinbrecher, Thomas via AMBER
- Re: [AMBER] prmtop and inpcrd file generation error: Timothy Giese via AMBER
- Re: [AMBER] prmtop and inpcrd file generation error: Kankana Bhattacharjee via AMBER
- [AMBER] sander.quick.cuda error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] sander.quick.cuda error: Timothy Giese via AMBER
- Re: [AMBER] sander.quick.cuda error: Kankana Bhattacharjee via AMBER
- Re: [AMBER] sander.quick.cuda error: Goetz, Andreas via AMBER
Saturday, 11 January 2025
- [AMBER] QM steered md question Ramdhan,Peter A via AMBER
Monday, 13 January 2025
- [AMBER] Amber metal ions protein multiple chains Iglika Lessigiarska via AMBER
- [AMBER] problem in installing Amber24 TUSHAR GUPTA via AMBER
- Re: [AMBER] Amber metal ions protein multiple chains David A Case via AMBER
- Re: [AMBER] problem in installing Amber24 David A Case via AMBER
- Re: [AMBER] problem in installing Amber24 James Kress via AMBER
- Re: [AMBER] Amber metal ions protein multiple chains Solen Ekesan via AMBER
- [AMBER] Best method to calculate vdW energies between residue side chains Intravaia, Lauren E via AMBER
- Re: [AMBER] Amber metal ions protein multiple chains Li, Zhen via AMBER
- [AMBER] reporting ΔG? or ΔΔG? vs experimental ΔG using FEP+ and TI King Wang via AMBER
Tuesday, 14 January 2025
- Re: [AMBER] Best method to calculate vdW energies between residue side chains Dr. Anselm Horn via AMBER
- [AMBER] Calculating charges by Gastieger procedure in Antechamber ... Michal Husak via AMBER
- Re: [AMBER] reporting ΔG? or ΔΔG? vs experimental ΔG using FEP+ and TI Brian Radak via AMBER
- Re: [AMBER] problem in installing Amber24 TUSHAR GUPTA via AMBER
- Re: [AMBER] problem in installing Amber24 James Kress via AMBER
Wednesday, 15 January 2025
- [AMBER] Quick Cuda Matt Goff via AMBER
- [AMBER] Error in make install TUSHAR GUPTA via AMBER
- Re: [AMBER] Quick Cuda Goetz, Andreas via AMBER
- Re: [AMBER] Quick Cuda Matt Goff via AMBER
- Re: [AMBER] Quick Cuda Goetz, Andreas via AMBER
- Re: [AMBER] Quick Cuda Matt Goff via AMBER
- Re: [AMBER] Quick Cuda Manathunga Mudiyanselage, Madushanka via AMBER
- [AMBER] Force field parameters modification Tej Tarun Sharma 2310225 via AMBER
Thursday, 16 January 2025
- [AMBER] Problems installing Amber24 on M3 Mac Sommers, Rachel C. via AMBER
- Re: [AMBER] Problems installing Amber24 on M3 Mac Adrian Roitberg via AMBER
- Re: [AMBER] Problems installing Amber24 on M3 Mac Adrian Roitberg via AMBER
Friday, 17 January 2025
- [AMBER] Interactions of GAFF2 force field with Lipid21 and BSC1 force fields Victor Nazarychev via AMBER
Saturday, 18 January 2025
- [AMBER] MMPBSA Error (Topology I think) Vishwaa Kannan via AMBER
- Re: [AMBER] MMPBSA Error (Topology I think) Ray Luo via AMBER
Sunday, 19 January 2025
- Re: [AMBER] MMPBSA Error (Topology I think) Vishwaa Kannan via AMBER
Monday, 20 January 2025
- Re: [AMBER] MMPBSA Error (Topology I think) Ray Luo via AMBER
Tuesday, 21 January 2025
- Re: [AMBER] Amber metal ions protein multiple chains Iglika Lessigiarska via AMBER
- [AMBER] GBNeck parameters modification to incorporate CustomGBForce calculations of OpenMM in Amber Tej Tarun Sharma 2310225 via AMBER
- Re: [AMBER] Amber metal ions protein multiple chains Solen Ekesan via AMBER
- Re: [AMBER] Interactions of GAFF2 force field with Lipid21 and BSC1 force fields David A Case via AMBER
- [AMBER] Compiling on AMD MI50 chips Wong, Sergio E. via AMBER
- Re: [AMBER] Compiling on AMD MI50 chips David A Case via AMBER
Thursday, 23 January 2025
- [AMBER] single point energy calculation Benjamin Shugaev via AMBER
Friday, 24 January 2025
- Re: [AMBER] single point energy calculation Dr. Anselm Horn via AMBER
Saturday, 25 January 2025
- [AMBER] Convert Gromacs RB dihedrals to AMBER dihedrals Abdelrahman, Noureen via AMBER
Sunday, 26 January 2025
- [AMBER] Error in make install INDAH LANGITASARI via AMBER
- [AMBER] protonated imidazole but post antechamber two N+ in ring.... Debarati DasGupta via AMBER
- [AMBER] MCPB.py RESP Value Issues Dratch, Benjamin via AMBER
Thursday, 30 January 2025
- [AMBER] Simulating LES with noe restraints Кунина, Елизавета Игоревна via AMBER

Last message date: Fri Jan 31 2025 - 00:30:02 PST
Archived on: Wed Feb 05 2025 - 05:56:24 PST

Amber Archive Jan 2025 by date