Amber Archive Nov 2024: by thread

Re: [AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21) David A Case via AMBER (Sat Nov 02 2024 - 09:29:11 PDT)
- Re: [AMBER] How to Derive missing parameters for modified nucleosides (OL15/OL21) Carlos Simmerling via AMBER (Sat Nov 02 2024 - 13:41:57 PDT)
Re: [AMBER] Installing Amber24 and AmberTools24 David A Case via AMBER (Sat Nov 02 2024 - 09:31:41 PDT)
- Re: [AMBER] Installing Amber24 and AmberTools24 Gerald Monard via AMBER (Tue Nov 05 2024 - 07:54:16 PST)
Re: [AMBER] BZIP2 Error when building Amber24 Li, Zhen via AMBER (Mon Nov 04 2024 - 05:59:52 PST)
[AMBER] BZIP2 Error when building Amber24 Patricio Barletta via AMBER (Mon Nov 04 2024 - 13:14:19 PST)
- Re: [AMBER] BZIP2 Error when building Amber24 Li, Zhen via AMBER (Mon Nov 04 2024 - 14:21:54 PST)
  - Re: [AMBER] BZIP2 Error when building Amber24 Téletchéa Stéphane via AMBER (Fri Nov 08 2024 - 01:22:22 PST)
[AMBER] Guidance on WHAM PMF graph Frederico Henrique Ferreira via AMBER (Mon Nov 04 2024 - 15:32:25 PST)
[AMBER] Question about cpptraj for PBC removal Enrico Martinez via AMBER (Thu Nov 07 2024 - 00:36:46 PST)
- Re: [AMBER] Question about cpptraj for PBC removal Téletchéa Stéphane via AMBER (Fri Nov 08 2024 - 00:59:25 PST)
  - Re: [AMBER] Question about cpptraj for PBC removal Enrico Martinez via AMBER (Fri Nov 08 2024 - 01:08:51 PST)
- Re: [AMBER] Question about cpptraj for PBC removal Enrico Martinez via AMBER (Fri Nov 08 2024 - 01:19:47 PST)
Re: [AMBER] Atommap doesn't change atom names Daniel Roe via AMBER (Thu Nov 07 2024 - 05:44:12 PST)
Re: [AMBER] AMBER Digest, Vol 4547, Issue 1 袁浩亮 via AMBER (Thu Nov 07 2024 - 17:54:37 PST)
- Re: [AMBER] Installation of Amber on Ubuntu 22.04 David A Case via AMBER (Thu Nov 07 2024 - 20:01:37 PST)
[AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Maciej Spiegel via AMBER (Fri Nov 08 2024 - 00:43:15 PST)
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. David A Case via AMBER (Fri Nov 08 2024 - 15:55:47 PST)
- Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Maciej Spiegel via AMBER (Sat Nov 09 2024 - 03:40:20 PST)
  - Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Carlos Simmerling via AMBER (Sat Nov 09 2024 - 03:50:17 PST)
    - Re: [AMBER] ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values. Maciej Spiegel via AMBER (Sat Nov 09 2024 - 04:03:11 PST)
[AMBER] md simulations running very slow Rosa Teijeiro Juiz via AMBER (Fri Nov 08 2024 - 05:54:14 PST)
- Re: [AMBER] md simulations running very slow David A Case via AMBER (Fri Nov 08 2024 - 16:02:39 PST)
[AMBER] FF for Amino Acid side chains analogs mish via AMBER (Fri Nov 08 2024 - 12:39:59 PST)
- Re: [AMBER] FF for Amino Acid side chains analogs Dr. Anselm Horn via AMBER (Tue Nov 12 2024 - 02:18:19 PST)
  - Re: [AMBER] FF for Amino Acid side chains analogs mish via AMBER (Tue Nov 12 2024 - 06:52:51 PST)
[AMBER] AMBER24 install Error: nvcc fatal : Unsupported gpu architecture 'compute_30' Md Fulbabu Sk via AMBER (Sat Nov 09 2024 - 20:24:47 PST)
- Re: [AMBER] AMBER24 install Error: nvcc fatal : Unsupported gpu architecture 'compute_30' Goetz, Andreas via AMBER (Sun Nov 10 2024 - 16:47:49 PST)
  - Re: [AMBER] AMBER24 install Error: nvcc fatal : Unsupported gpu architecture 'compute_30' Md Fulbabu Sk via AMBER (Mon Nov 11 2024 - 08:50:17 PST)
[AMBER] Automatic cation an anion detection for GAFF Husak Michal via AMBER (Sun Nov 10 2024 - 09:37:13 PST)
- Re: [AMBER] [Sender Not Verified] Automatic cation an anion detection for GAFF Steinbrecher, Thomas via AMBER (Sun Nov 10 2024 - 23:44:42 PST)
[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 (Sun Nov 10 2024 - 17:57:59 PST)
- 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 (Sun Nov 10 2024 - 18:34:42 PST)
  - 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 (Sun Nov 10 2024 - 18:55:23 PST)
[AMBER] CPPTRAJ, unit cell not X-aligned? Guberman-Pfeffer, Matthew via AMBER (Sun Nov 10 2024 - 20:45:20 PST)
- Re: [AMBER] [Sender Not Verified] CPPTRAJ, unit cell not X-aligned? Steinbrecher, Thomas via AMBER (Sun Nov 10 2024 - 23:16:51 PST)
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER (Mon Nov 11 2024 - 06:04:19 PST)
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER (Thu Nov 14 2024 - 06:26:32 PST)
  - Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER (Thu Nov 14 2024 - 07:10:38 PST)
- Re: [AMBER] CPPTRAJ, unit cell not X-aligned? Daniel Roe via AMBER (Thu Nov 14 2024 - 08:12:06 PST)
[AMBER] Cpptraj: is it possible to perform 2D RMSD analysis from average data of several simulations? Nikolay Kuzmich via AMBER (Mon Nov 11 2024 - 02:31:17 PST)
- Re: [AMBER] Cpptraj: is it possible to perform 2D RMSD analysis from average data of several simulations? Carlos Simmerling via AMBER (Mon Nov 11 2024 - 03:21:22 PST)
- Re: [AMBER] Cpptraj: is it possible to perform 2D RMSD analysis from average data of several simulations? Carlos Simmerling via AMBER (Mon Nov 18 2024 - 04:55:50 PST)
[AMBER] extraction of ph specific trajectory from constant ph replica exchange Dulal Mondal via AMBER (Mon Nov 11 2024 - 05:21:18 PST)
- Re: [AMBER] extraction of ph specific trajectory from constant ph replica exchange Dulal Mondal via AMBER (Wed Nov 13 2024 - 22:25:33 PST)
- Re: [AMBER] extraction of ph specific trajectory from constant ph replica exchange Daniel Roe via AMBER (Thu Nov 14 2024 - 06:23:58 PST)
[AMBER] How to compile with SANDER API Guberman-Pfeffer, Matthew via AMBER (Tue Nov 12 2024 - 06:34:22 PST)
- Re: [AMBER] How to compile with SANDER API David A Case via AMBER (Tue Nov 12 2024 - 10:57:38 PST)
[AMBER] Download for Amber 22? Loris Bennett via AMBER (Fri Nov 15 2024 - 01:03:11 PST)
[AMBER] Swapping the use of gms or Gaussian for ORCA in the MCPB.py example YESID ARMANDO ARISTIZABAL SALAZAR via AMBER (Sat Nov 16 2024 - 12:10:02 PST)
[AMBER] Question about restrainmask Enrico Martinez via AMBER (Mon Nov 18 2024 - 04:43:10 PST)
[AMBER] PeptidoGlycans Angelo Gallo via AMBER (Mon Nov 18 2024 - 15:31:30 PST)
- Re: [AMBER] PeptidoGlycans Warren, Kyle Benjamin via AMBER (Tue Nov 19 2024 - 08:31:04 PST)
[AMBER] Help with Bad atom type error in MMPBSA Osman, Roman via AMBER (Wed Nov 20 2024 - 07:20:30 PST)
- Re: [AMBER] Help with Bad atom type error in MMPBSA Carlos Simmerling via AMBER (Wed Nov 20 2024 - 08:25:01 PST)
[AMBER] GOLD ions Enrico Martinez via AMBER (Thu Nov 21 2024 - 02:59:48 PST)
- Re: [AMBER] GOLD ions Enrico Martinez via AMBER (Fri Nov 22 2024 - 08:38:07 PST)
[AMBER] ERROR: PMEMD does not support single H residues! Christian Seitz via AMBER (Fri Nov 22 2024 - 13:35:40 PST)
- Re: [AMBER] ERROR: PMEMD does not support single H residues! Carlos Simmerling via AMBER (Fri Nov 22 2024 - 13:44:37 PST)
- Re: [AMBER] ERROR: PMEMD does not support single H residues! Carlos Simmerling via AMBER (Mon Nov 25 2024 - 14:58:43 PST)
[AMBER] question about steered MD Ramdhan,Peter A via AMBER (Fri Nov 22 2024 - 16:08:44 PST)
- Re: [AMBER] question about steered MD Carlos Simmerling via AMBER (Fri Nov 22 2024 - 16:23:12 PST)
- Re: [AMBER] question about steered MD Carlos Simmerling via AMBER (Fri Nov 22 2024 - 17:45:02 PST)
- Re: [AMBER] question about steered MD Carlos Simmerling via AMBER (Sun Nov 24 2024 - 08:23:30 PST)
[AMBER] Regarding PBC correction issue for trimeric complex: Kankana Bhattacharjee via AMBER (Fri Nov 22 2024 - 20:50:14 PST)
- Re: [AMBER] Regarding PBC correction issue for trimeric complex: Carlos Simmerling via AMBER (Sat Nov 23 2024 - 06:17:21 PST)
- Re: [AMBER] Regarding PBC correction issue for trimeric complex: Carlos Simmerling via AMBER (Sat Nov 23 2024 - 06:26:50 PST)
[AMBER] Accelerating microsecond-scale simulations on GPUs Maciej Spiegel via AMBER (Sun Nov 24 2024 - 03:49:16 PST)
- Re: [AMBER] Accelerating microsecond-scale simulations on GPUs Carlos Simmerling via AMBER (Sun Nov 24 2024 - 04:32:22 PST)
- Re: [AMBER] Accelerating microsecond-scale simulations on GPUs Carlos Simmerling via AMBER (Sun Nov 24 2024 - 05:51:44 PST)
- Re: [AMBER] Accelerating microsecond-scale simulations on GPUs Carlos Simmerling via AMBER (Sun Nov 24 2024 - 06:25:46 PST)
[AMBER] query reg QM/MM-MD with metalloprotein to simulate TS and estimate barrier Vaibhav Dixit via AMBER (Mon Nov 25 2024 - 02:45:12 PST)
[AMBER] Help regarding 5'-phosphate added Uridine structure Sruthi Sudhakar via AMBER (Mon Nov 25 2024 - 04:21:36 PST)
[AMBER] Question about vectors Jing Qu via AMBER (Mon Nov 25 2024 - 13:08:06 PST)
- [AMBER] Build DNA with 5-methylcytosine James Kress via AMBER (Mon Nov 25 2024 - 13:54:50 PST)
  - Re: [AMBER] Build DNA with 5-methylcytosine Carlos Simmerling via AMBER (Mon Nov 25 2024 - 13:58:23 PST)
  - Re: [AMBER] Build DNA with 5-methylcytosine David A Case via AMBER (Tue Nov 26 2024 - 08:35:40 PST)
- Re: [AMBER] Question about vectors Daniel Roe via AMBER (Wed Nov 27 2024 - 05:49:12 PST)
  - Re: [AMBER] Question about vectors David A Case via AMBER (Wed Nov 27 2024 - 07:56:50 PST)
[AMBER] Info on xparmed installation Andrea Piserchia \(E4\) via AMBER (Tue Nov 26 2024 - 08:59:30 PST)
[AMBER] Generating GAFF for Conformational Polymorphs Pradip Si via AMBER (Tue Nov 26 2024 - 09:34:53 PST)
- Re: [AMBER] Generating GAFF for Conformational Polymorphs Dr. Anselm Horn via AMBER (Wed Nov 27 2024 - 01:41:19 PST)

Amber Archive Nov 2024 by thread