Amber Archive Nov 2024 by date

82 messages: Starting Sat Nov 02 2024 - 09:30:02 PDT, Ending Wed Nov 27 2024 - 08:00:02 PST
This period: Most recent messages
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Saturday, 2 November 2024
- Re: [AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21) David A Case via AMBER
- Re: [AMBER] Installing Amber24 and AmberTools24 David A Case via AMBER
- Re: [AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21) Carlos Simmerling via AMBER
Monday, 4 November 2024
- Re: [AMBER] BZIP2 Error when building Amber24 Li, Zhen via AMBER
- [AMBER] BZIP2 Error when building Amber24 Patricio Barletta via AMBER
- Re: [AMBER] BZIP2 Error when building Amber24 Li, Zhen via AMBER
- [AMBER] Guidance on WHAM PMF graph Frederico Henrique Ferreira via AMBER
Tuesday, 5 November 2024
- Re: [AMBER] Installing Amber24 and AmberTools24 Gerald Monard via AMBER
Thursday, 7 November 2024
- [AMBER] Question about cpptraj for PBC removal Enrico Martinez via AMBER
- Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER
- Re: [AMBER] AMBER Digest, Vol 4547, Issue 1 袁浩亮 via AMBER
- Re: [AMBER] Installation of Amber on Ubuntu 22.04 David A Case via AMBER
Friday, 8 November 2024
- [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Maciej Spiegel via AMBER
- Re: [AMBER] Question about cpptraj for PBC removal Téletchéa Stéphane via AMBER
- Re: [AMBER] Question about cpptraj for PBC removal Enrico Martinez via AMBER
- Re: [AMBER] Question about cpptraj for PBC removal Enrico Martinez via AMBER
- Re: [AMBER] BZIP2 Error when building Amber24 Téletchéa Stéphane via AMBER
- [AMBER] md simulations running very slow Rosa Teijeiro Juiz via AMBER
- [AMBER] FF for Amino Acid side chains analogs mish via AMBER
- Re: [AMBER] md simulations running very slow David A Case via AMBER
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. David A Case via AMBER
Saturday, 9 November 2024
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Maciej Spiegel via AMBER
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Carlos Simmerling via AMBER
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Maciej Spiegel via AMBER
- [AMBER] AMBER24 install Error: nvcc fatal : Unsupported gpu architecture 'compute_30' Md Fulbabu Sk via AMBER
Sunday, 10 November 2024
- [AMBER] Automatic cation an anion detection for GAFF Husak Michal via AMBER
- Re: [AMBER] AMBER24 install Error: nvcc fatal : Unsupported gpu architecture 'compute_30' Goetz, Andreas via AMBER
- [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the forces from the gaussian output file and the forces reported in the mdfrc file Ge Song via AMBER
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the forces from the gaussian output file and the forces reported in the mdfrc file Goetz, Andreas via AMBER
- Re: [AMBER] QM/MM using Amber and Gaussian: Discrepancies between the forces from the gaussian output file and the forces reported in the mdfrc file Ge Song via AMBER
- [AMBER] CPPTRAJ, unit cell not X-aligned? Guberman-Pfeffer, Matthew via AMBER
- Re: [AMBER] [Sender Not Verified] CPPTRAJ, unit cell not X-aligned? Steinbrecher, Thomas via AMBER
- Re: [AMBER] [Sender Not Verified] Automatic cation an anion detection for GAFF Steinbrecher, Thomas via AMBER
Monday, 11 November 2024
- [AMBER] Cpptraj: is it possible to perform 2D RMSD analysis from average data of several simulations? Nikolay Kuzmich via AMBER
- Re: [AMBER] Cpptraj: is it possible to perform 2D RMSD analysis from average data of several simulations? Carlos Simmerling via AMBER
- [AMBER] extraction of ph specific trajectory from constant ph replica exchange Dulal Mondal via AMBER
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER
- Re: [AMBER] AMBER24 install Error: nvcc fatal : Unsupported gpu architecture 'compute_30' Md Fulbabu Sk via AMBER
Tuesday, 12 November 2024
- Re: [AMBER] FF for Amino Acid side chains analogs Dr. Anselm Horn via AMBER
- [AMBER] How to compile with SANDER API Guberman-Pfeffer, Matthew via AMBER
- Re: [AMBER] FF for Amino Acid side chains analogs mish via AMBER
- Re: [AMBER] How to compile with SANDER API David A Case via AMBER
Wednesday, 13 November 2024
- Re: [AMBER] extraction of ph specific trajectory from constant ph replica exchange Dulal Mondal via AMBER
Thursday, 14 November 2024
- Re: [AMBER] extraction of ph specific trajectory from constant ph replica exchange Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER
Friday, 15 November 2024
- [AMBER] Download for Amber 22? Loris Bennett via AMBER
Saturday, 16 November 2024
- [AMBER] Swapping the use of gms or Gaussian for ORCA in the MCPB.py example YESID ARMANDO ARISTIZABAL SALAZAR via AMBER
Monday, 18 November 2024
- [AMBER] Question about restrainmask Enrico Martinez via AMBER
- Re: [AMBER] Cpptraj: is it possible to perform 2D RMSD analysis from average data of several simulations? Carlos Simmerling via AMBER
- [AMBER] PeptidoGlycans Angelo Gallo via AMBER
Tuesday, 19 November 2024
- Re: [AMBER] PeptidoGlycans Warren, Kyle Benjamin via AMBER
Wednesday, 20 November 2024
- [AMBER] Help with Bad atom type error in MMPBSA Osman, Roman via AMBER
- Re: [AMBER] Help with Bad atom type error in MMPBSA Carlos Simmerling via AMBER
Thursday, 21 November 2024
- [AMBER] GOLD ions Enrico Martinez via AMBER
Friday, 22 November 2024
- Re: [AMBER] GOLD ions Enrico Martinez via AMBER
- [AMBER] ERROR: PMEMD does not support single H residues! Christian Seitz via AMBER
- Re: [AMBER] ERROR: PMEMD does not support single H residues! Carlos Simmerling via AMBER
- [AMBER] question about steered MD Ramdhan,Peter A via AMBER
- Re: [AMBER] question about steered MD Carlos Simmerling via AMBER
- Re: [AMBER] question about steered MD Carlos Simmerling via AMBER
- [AMBER] Regarding PBC correction issue for trimeric complex: Kankana Bhattacharjee via AMBER
Saturday, 23 November 2024
- Re: [AMBER] Regarding PBC correction issue for trimeric complex: Carlos Simmerling via AMBER
- Re: [AMBER] Regarding PBC correction issue for trimeric complex: Carlos Simmerling via AMBER
Sunday, 24 November 2024
- [AMBER] Accelerating microsecond-scale simulations on GPUs Maciej Spiegel via AMBER
- Re: [AMBER] Accelerating microsecond-scale simulations on GPUs Carlos Simmerling via AMBER
- Re: [AMBER] Accelerating microsecond-scale simulations on GPUs Carlos Simmerling via AMBER
- Re: [AMBER] Accelerating microsecond-scale simulations on GPUs Carlos Simmerling via AMBER
- Re: [AMBER] question about steered MD Carlos Simmerling via AMBER
Monday, 25 November 2024
- [AMBER] query reg QM/MM-MD with metalloprotein to simulate TS and estimate barrier Vaibhav Dixit via AMBER
- [AMBER] Help regarding 5'-phosphate added Uridine structure Sruthi Sudhakar via AMBER
- [AMBER] Question about vectors Jing Qu via AMBER
- [AMBER] Build DNA with 5-methylcytosine James Kress via AMBER
- Re: [AMBER] Build DNA with 5-methylcytosine Carlos Simmerling via AMBER
- Re: [AMBER] ERROR: PMEMD does not support single H residues! Carlos Simmerling via AMBER
Tuesday, 26 November 2024
- Re: [AMBER] Build DNA with 5-methylcytosine David A Case via AMBER
- [AMBER] Info on xparmed installation Andrea Piserchia \(E4\) via AMBER
- [AMBER] Generating GAFF for Conformational Polymorphs Pradip Si via AMBER
Wednesday, 27 November 2024
- Re: [AMBER] Generating GAFF for Conformational Polymorphs Dr. Anselm Horn via AMBER
- Re: [AMBER] Question about vectors Daniel Roe via AMBER
- Re: [AMBER] Question about vectors David A Case via AMBER

Last message date: Wed Nov 27 2024 - 08:00:02 PST
Archived on: Mon Nov 03 2025 - 05:56:20 PST