Amber Archive Dec 2022: by thread

[AMBER] amber- Error: an illegal memory access was encountered launching kernel kClearForces ışılay öztürk via AMBER (Thu Dec 01 2022 - 03:57:51 PST)
[AMBER] cutoff=8.0 or cutoff=10.0? Téletchéa Stéphane via AMBER (Fri Dec 02 2022 - 01:56:11 PST)
[AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Vlad Cojocaru via AMBER (Fri Dec 02 2022 - 04:16:37 PST)
- Re: [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Scott Brozell via AMBER (Fri Dec 02 2022 - 12:27:58 PST)
  - Re: [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Vlad Cojocaru via AMBER (Sun Dec 04 2022 - 07:16:05 PST)
    - Re: [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Scott Brozell via AMBER (Fri Dec 09 2022 - 14:11:26 PST)
[AMBER] Generate top file using tleap without atom reordering Kari Gaalswyk via AMBER (Fri Dec 02 2022 - 10:46:49 PST)
- Re: [AMBER] Generate top file using tleap without atom reordering David A Case via AMBER (Fri Dec 02 2022 - 13:44:02 PST)
[AMBER] one question about setting up amber simulation on negatively charged ligand laura zhang via AMBER (Fri Dec 02 2022 - 12:34:33 PST)
- Re: [AMBER] one question about setting up amber simulation on negatively charged ligand David A Case via AMBER (Fri Dec 02 2022 - 13:45:47 PST)
  - Re: [AMBER] one question about setting up amber simulation on negatively charged ligand laura zhang via AMBER (Fri Dec 02 2022 - 17:57:34 PST)
[AMBER] ntave, surpress output? Matthew Guberman-Pfeffer via AMBER (Fri Dec 02 2022 - 22:31:28 PST)
[AMBER] H100 & RTX4090 Benchmarks Ross Walker via AMBER (Sat Dec 03 2022 - 05:31:33 PST)
- Re: [AMBER] H100 & RTX4090 Benchmarks James Kress via AMBER (Sat Dec 03 2022 - 11:49:56 PST)
  - Re: [AMBER] H100 & RTX4090 Benchmarks David A Case via AMBER (Mon Dec 05 2022 - 06:13:23 PST)
    - Re: [AMBER] H100 & RTX4090 Benchmarks Gould, Ian R via AMBER (Mon Dec 05 2022 - 06:33:15 PST)
    - Re: [AMBER] H100 & RTX4090 Benchmarks Ross Walker via AMBER (Mon Dec 05 2022 - 07:12:02 PST)
Re: [AMBER] about setting up a simulation system including multiple protein aishen via AMBER (Sat Dec 03 2022 - 17:06:01 PST)
- Re: [AMBER] about setting up a simulation system including multiple protein laura zhang via AMBER (Sat Dec 03 2022 - 17:38:18 PST)
Re: [AMBER] {SPAM?} Re: about setting up a simulation system including multiple protein laura zhang via AMBER (Sat Dec 03 2022 - 17:44:11 PST)
- Re: [AMBER] {SPAM?} Re: about setting up a simulation system including multiple protein laura zhang via AMBER (Sat Dec 03 2022 - 17:53:29 PST)
[AMBER] Perform Multi-COARE 3D-RISM Alexis Azucena via AMBER (Sun Dec 04 2022 - 23:11:31 PST)
- Re: [AMBER] Perform Multi-COARE 3D-RISM David A Case via AMBER (Wed Dec 21 2022 - 06:14:51 PST)
[AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER (Tue Dec 06 2022 - 02:31:57 PST)
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Tue Dec 06 2022 - 05:26:33 PST)
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Tue Dec 06 2022 - 07:43:14 PST)
  - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER (Thu Dec 08 2022 - 05:50:59 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Thu Dec 08 2022 - 07:17:15 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Fri Dec 09 2022 - 05:56:28 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER (Fri Dec 09 2022 - 07:10:28 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Tue Dec 13 2022 - 09:14:11 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER (Wed Dec 14 2022 - 01:43:49 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Fri Dec 16 2022 - 10:00:15 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER (Mon Dec 19 2022 - 12:52:04 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Tue Dec 20 2022 - 10:44:07 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER (Wed Dec 21 2022 - 00:13:11 PST)
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Stéphane Téletchéa via AMBER (Wed Dec 07 2022 - 16:00:54 PST)
  - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER (Thu Dec 08 2022 - 07:14:37 PST)
    - Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Téletchéa Stéphane via AMBER (Fri Dec 09 2022 - 03:37:44 PST)
[AMBER] NPT TI only works with CPU version of PMEMD Bruno Falcone via AMBER (Tue Dec 06 2022 - 04:54:56 PST)
[AMBER] amber installation on linux mint nahoum a via AMBER (Tue Dec 06 2022 - 06:52:22 PST)
- Re: [AMBER] amber installation on linux mint David A Case via AMBER (Tue Dec 06 2022 - 13:17:36 PST)
Re: [AMBER] Cpptraj for loops and dataset operations Daniel Roe via AMBER (Tue Dec 06 2022 - 08:03:50 PST)
[AMBER] AMBER tLEaP Issues Gonzalo R. Vazquez-Jimenez via AMBER (Tue Dec 06 2022 - 09:52:18 PST)
- Re: [AMBER] AMBER tLEaP Issues Suchetana Gupta via AMBER (Tue Dec 06 2022 - 10:09:41 PST)
- Re: [AMBER] AMBER tLEaP Issues David A Case via AMBER (Wed Dec 07 2022 - 06:56:04 PST)
Re: [AMBER] Reimaging issues Daniel Roe via AMBER (Wed Dec 07 2022 - 07:44:57 PST)
Re: [AMBER] tleap for RNA Prithviraj Nandigrami via AMBER (Wed Dec 07 2022 - 13:00:30 PST)
- Re: [AMBER] tleap for RNA Prithviraj Nandigrami via AMBER (Fri Dec 09 2022 - 14:54:25 PST)
[AMBER] about running mmgbsa energy calculation on some molecules in the simulation system laura zhang via AMBER (Wed Dec 07 2022 - 14:11:09 PST)
- Re: [AMBER] about running mmgbsa energy calculation on some molecules in the simulation system Bill Miller III via AMBER (Wed Dec 07 2022 - 14:53:08 PST)
- Re: [AMBER] about running mmgbsa energy calculation on some molecules in the simulation system David A Case via AMBER (Thu Dec 08 2022 - 05:24:21 PST)
[AMBER] AM1-BCC without optimization in antechamber? Brian Radak via AMBER (Thu Dec 08 2022 - 12:11:18 PST)
[AMBER] Amber CUDA implementation Rana Rehan Khalid via AMBER (Thu Dec 08 2022 - 13:15:55 PST)
[AMBER] Additional Marsili Gasteiger parameters? Brian Radak via AMBER (Fri Dec 09 2022 - 08:16:20 PST)
[AMBER] cpptraj normal mode visualization Prithviraj Nandigrami via AMBER (Mon Dec 12 2022 - 07:51:28 PST)
- Re: [AMBER] cpptraj normal mode visualization Prithviraj Nandigrami via AMBER (Thu Dec 15 2022 - 14:41:49 PST)
[AMBER] NMR-based restraints Matthew Guberman-Pfeffer via AMBER (Mon Dec 12 2022 - 18:29:08 PST)
- Re: [AMBER] NMR-based restraints David A Case via AMBER (Tue Dec 13 2022 - 08:36:34 PST)
[AMBER] Improper torsion term cavallaro.mattia via AMBER (Tue Dec 13 2022 - 04:16:51 PST)
- Re: [AMBER] Improper torsion term David A Case via AMBER (Tue Dec 13 2022 - 08:37:40 PST)
[AMBER] R: Reimaging issues Damiano Spadoni via AMBER (Tue Dec 13 2022 - 12:22:09 PST)
[AMBER] Amber20 build/install errors Masshardt, Eric via AMBER (Tue Dec 13 2022 - 13:37:27 PST)
- Re: [AMBER] Amber20 build/install errors David A Case via AMBER (Wed Dec 14 2022 - 06:29:52 PST)
[AMBER] Analysis of protein-ligand hydrogen bonds for dimer system Enrico Martinez via AMBER (Wed Dec 14 2022 - 06:58:31 PST)
- Re: [AMBER] Analysis of protein-ligand hydrogen bonds for dimer system Enrico Martinez via AMBER (Wed Dec 14 2022 - 07:19:25 PST)
  - Re: [AMBER] Analysis of protein-ligand hydrogen bonds for dimer system Enrico Martinez via AMBER (Wed Dec 14 2022 - 08:12:58 PST)
[AMBER] MCPB.py tutorial output Reed, Carly \(creed\) via AMBER (Thu Dec 15 2022 - 09:09:11 PST)
[AMBER] Post-Doctoral Offer Téletchéa Stéphane via AMBER (Thu Dec 15 2022 - 10:29:04 PST)
[AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors Ursula Perez-Salas via AMBER (Thu Dec 15 2022 - 15:09:30 PST)
- Re: [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors David A Case via AMBER (Fri Dec 16 2022 - 05:56:40 PST)
  - Re: [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors Ursula Perez-Salas via AMBER (Fri Dec 16 2022 - 08:36:41 PST)
- Re: [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors Ursula Perez-Salas via AMBER (Mon Dec 19 2022 - 17:47:08 PST)
[AMBER] Regarding unusual free energy value Kapil Ursal via AMBER (Thu Dec 15 2022 - 21:26:57 PST)
- Re: [AMBER] Regarding unusual free energy value David A Case via AMBER (Wed Dec 21 2022 - 06:10:30 PST)
Re: [AMBER] MMPBSA Pairwise per-residue error Bill Miller III via AMBER (Fri Dec 16 2022 - 04:25:26 PST)
[AMBER] How to build the charmmgen program Kotaro TANAKA via AMBER (Sun Dec 18 2022 - 17:46:25 PST)
- Re: [AMBER] How to build the charmmgen program Kotaro TANAKA via AMBER (Mon Dec 19 2022 - 23:29:14 PST)
[AMBER] Help - NADPH's parameterization Bruna Schuck de Azevedo via AMBER (Tue Dec 20 2022 - 07:45:53 PST)
- Re: [AMBER] Help - NADPH's parameterization Dr. Anselm Horn via AMBER (Wed Dec 21 2022 - 05:42:59 PST)
- Re: [AMBER] Help - NADPH's parameterization David A Case via AMBER (Wed Dec 21 2022 - 05:59:43 PST)
Re: [AMBER] query about 2-forms of a cofactor in MCPB.py Vaibhav Dixit via AMBER (Wed Dec 21 2022 - 06:20:46 PST)
Re: [AMBER] {SPAM?} Re: query about 2-forms of a cofactor in MCPB.py Vaibhav Dixit via AMBER (Wed Dec 21 2022 - 06:49:23 PST)
[AMBER] Using filter command to select frames from the RDF Swapnil Singh via AMBER (Wed Dec 21 2022 - 18:10:51 PST)
- Re: [AMBER] Using filter command to select frames from the RDF Daniel Roe via AMBER (Thu Dec 22 2022 - 07:06:45 PST)
[AMBER] How can I use GRF as Long range electrostatic calculcation Dulal Mondal via AMBER (Wed Dec 21 2022 - 22:50:31 PST)
- Re: [AMBER] How can I use GRF as Long range electrostatic calculcation David A Case via AMBER (Thu Dec 22 2022 - 06:40:14 PST)
[AMBER] hbond criteria Umesh Roy via AMBER (Sun Dec 25 2022 - 21:20:27 PST)
[AMBER] Potential energy calculation Dulal Mondal via AMBER (Mon Dec 26 2022 - 04:39:53 PST)
- Re: [AMBER] Potential energy calculation Carlos Simmerling via AMBER (Mon Dec 26 2022 - 07:29:33 PST)
[AMBER] MCPB.py output Reed, Carly \(creed\) via AMBER (Wed Dec 28 2022 - 18:35:39 PST)
- Re: [AMBER] MCPB.py output David A Case via AMBER (Thu Dec 29 2022 - 05:54:58 PST)
[AMBER] installation windows.h no file found Ryan Woltz via AMBER (Thu Dec 29 2022 - 14:45:31 PST)
- Re: [AMBER] installation windows.h no file found David A Case via AMBER (Thu Dec 29 2022 - 19:09:51 PST)
  - Re: [AMBER] installation windows.h no file found Scott Brozell via AMBER (Thu Dec 29 2022 - 22:26:47 PST)
  - Re: [AMBER] installation windows.h no file found Ryan Woltz via AMBER (Thu Dec 29 2022 - 23:56:11 PST)
[AMBER] Determination of percentage population Dulal Mondal via AMBER (Thu Dec 29 2022 - 22:10:41 PST)
[AMBER] parmed FileNotFoundError: parm7 does not exist İmren Bayıl via AMBER (Fri Dec 30 2022 - 07:15:26 PST)
- Re: [AMBER] parmed FileNotFoundError: parm7 does not exist David A Case via AMBER (Fri Dec 30 2022 - 13:52:22 PST)

Amber Archive Dec 2022 by thread