Amber Archive Dec 2022 by date

99 messages: Starting Thu Dec 01 2022 - 04:00:02 PST, Ending Fri Dec 30 2022 - 14:00:03 PST
This period: Most recent messages
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Thursday, 1 December 2022
- [AMBER] amber- Error: an illegal memory access was encountered launching kernel kClearForces ışılay öztürk via AMBER
Friday, 2 December 2022
- [AMBER] cutoff=8.0 or cutoff=10.0? Téletchéa Stéphane via AMBER
- [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Vlad Cojocaru via AMBER
- [AMBER] Generate top file using tleap without atom reordering Kari Gaalswyk via AMBER
- Re: [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Scott Brozell via AMBER
- [AMBER] one question about setting up amber simulation on negatively charged ligand laura zhang via AMBER
- Re: [AMBER] Generate top file using tleap without atom reordering David A Case via AMBER
- Re: [AMBER] one question about setting up amber simulation on negatively charged ligand David A Case via AMBER
- Re: [AMBER] one question about setting up amber simulation on negatively charged ligand laura zhang via AMBER
- [AMBER] ntave, surpress output? Matthew Guberman-Pfeffer via AMBER
Saturday, 3 December 2022
- [AMBER] H100 & RTX4090 Benchmarks Ross Walker via AMBER
- Re: [AMBER] H100 & RTX4090 Benchmarks James Kress via AMBER
- Re: [AMBER] about setting up a simulation system including multiple protein aishen via AMBER
- Re: [AMBER] {SPAM?} Re: about setting up a simulation system including multiple protein laura zhang via AMBER
- Re: [AMBER] {SPAM?} Re: about setting up a simulation system including multiple protein laura zhang via AMBER
- Re: [AMBER] about setting up a simulation system including multiple protein laura zhang via AMBER
Sunday, 4 December 2022
- Re: [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Vlad Cojocaru via AMBER
- [AMBER] Perform Multi-COARE 3D-RISM Alexis Azucena via AMBER
Monday, 5 December 2022
- Re: [AMBER] H100 & RTX4090 Benchmarks David A Case via AMBER
- Re: [AMBER] H100 & RTX4090 Benchmarks Gould, Ian R via AMBER
- Re: [AMBER] H100 & RTX4090 Benchmarks Ross Walker via AMBER
Tuesday, 6 December 2022
- [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER
- [AMBER] NPT TI only works with CPU version of PMEMD Bruno Falcone via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
- [AMBER] amber installation on linux mint nahoum a via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
- Re: [AMBER] Cpptraj for loops and dataset operations Daniel Roe via AMBER
- [AMBER] AMBER tLEaP Issues Gonzalo R. Vazquez-Jimenez via AMBER
- Re: [AMBER] AMBER tLEaP Issues Suchetana Gupta via AMBER
- Re: [AMBER] amber installation on linux mint David A Case via AMBER
Wednesday, 7 December 2022
- Re: [AMBER] AMBER tLEaP Issues David A Case via AMBER
- Re: [AMBER] Reimaging issues Daniel Roe via AMBER
- Re: [AMBER] tleap for RNA Prithviraj Nandigrami via AMBER
- [AMBER] about running mmgbsa energy calculation on some molecules in the simulation system laura zhang via AMBER
- Re: [AMBER] about running mmgbsa energy calculation on some molecules in the simulation system Bill Miller III via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Stéphane Téletchéa via AMBER
Thursday, 8 December 2022
- Re: [AMBER] about running mmgbsa energy calculation on some molecules in the simulation system David A Case via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
- [AMBER] AM1-BCC without optimization in antechamber? Brian Radak via AMBER
- [AMBER] Amber CUDA implementation Rana Rehan Khalid via AMBER
Friday, 9 December 2022
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Téletchéa Stéphane via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER
- [AMBER] Additional Marsili Gasteiger parameters? Brian Radak via AMBER
- Re: [AMBER] Amber compilation with GCC 11.3.0 + CUDA 11.7.0 Scott Brozell via AMBER
- Re: [AMBER] tleap for RNA Prithviraj Nandigrami via AMBER
Monday, 12 December 2022
- [AMBER] cpptraj normal mode visualization Prithviraj Nandigrami via AMBER
- [AMBER] NMR-based restraints Matthew Guberman-Pfeffer via AMBER
Tuesday, 13 December 2022
- [AMBER] Improper torsion term cavallaro.mattia via AMBER
- Re: [AMBER] NMR-based restraints David A Case via AMBER
- Re: [AMBER] Improper torsion term David A Case via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
- [AMBER] R: Reimaging issues Damiano Spadoni via AMBER
- [AMBER] Amber20 build/install errors Masshardt, Eric via AMBER
Wednesday, 14 December 2022
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER
- Re: [AMBER] Amber20 build/install errors David A Case via AMBER
- [AMBER] Analysis of protein-ligand hydrogen bonds for dimer system Enrico Martinez via AMBER
- Re: [AMBER] Analysis of protein-ligand hydrogen bonds for dimer system Enrico Martinez via AMBER
- Re: [AMBER] Analysis of protein-ligand hydrogen bonds for dimer system Enrico Martinez via AMBER
Thursday, 15 December 2022
- [AMBER] MCPB.py tutorial output Reed, Carly \(creed\) via AMBER
- [AMBER] Post-Doctoral Offer Téletchéa Stéphane via AMBER
- Re: [AMBER] cpptraj normal mode visualization Prithviraj Nandigrami via AMBER
- [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors Ursula Perez-Salas via AMBER
- [AMBER] Regarding unusual free energy value Kapil Ursal via AMBER
Friday, 16 December 2022
- Re: [AMBER] MMPBSA Pairwise per-residue error Bill Miller III via AMBER
- Re: [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors David A Case via AMBER
- Re: [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors Ursula Perez-Salas via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
Sunday, 18 December 2022
- [AMBER] How to build the charmmgen program Kotaro TANAKA via AMBER
Monday, 19 December 2022
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER
- Re: [AMBER] Amber22 installation: "source /home/xxxx/amber22/amber.sh" and "make test.serial" errors Ursula Perez-Salas via AMBER
- Re: [AMBER] How to build the charmmgen program Kotaro TANAKA via AMBER
Tuesday, 20 December 2022
- [AMBER] Help - NADPH's parameterization Bruna Schuck de Azevedo via AMBER
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Daniel Roe via AMBER
Wednesday, 21 December 2022
- Re: [AMBER] possible bug - SIGSEGV in cpptraj called from MMPBSA.py Andrzej Dorobisz via AMBER
- Re: [AMBER] Help - NADPH's parameterization Dr. Anselm Horn via AMBER
- Re: [AMBER] Help - NADPH's parameterization David A Case via AMBER
- Re: [AMBER] Regarding unusual free energy value David A Case via AMBER
- Re: [AMBER] Perform Multi-COARE 3D-RISM David A Case via AMBER
- Re: [AMBER] query about 2-forms of a cofactor in MCPB.py Vaibhav Dixit via AMBER
- Re: [AMBER] {SPAM?} Re: query about 2-forms of a cofactor in MCPB.py Vaibhav Dixit via AMBER
- [AMBER] Using filter command to select frames from the RDF Swapnil Singh via AMBER
- [AMBER] How can I use GRF as Long range electrostatic calculcation Dulal Mondal via AMBER
Thursday, 22 December 2022
- Re: [AMBER] How can I use GRF as Long range electrostatic calculcation David A Case via AMBER
- Re: [AMBER] Using filter command to select frames from the RDF Daniel Roe via AMBER
Sunday, 25 December 2022
- [AMBER] hbond criteria Umesh Roy via AMBER
Monday, 26 December 2022
- [AMBER] Potential energy calculation Dulal Mondal via AMBER
- Re: [AMBER] Potential energy calculation Carlos Simmerling via AMBER
Wednesday, 28 December 2022
- [AMBER] MCPB.py output Reed, Carly \(creed\) via AMBER
Thursday, 29 December 2022
- Re: [AMBER] MCPB.py output David A Case via AMBER
- [AMBER] installation windows.h no file found Ryan Woltz via AMBER
- Re: [AMBER] installation windows.h no file found David A Case via AMBER
- [AMBER] Determination of percentage population Dulal Mondal via AMBER
- Re: [AMBER] installation windows.h no file found Scott Brozell via AMBER
- Re: [AMBER] installation windows.h no file found Ryan Woltz via AMBER
Friday, 30 December 2022
- [AMBER] parmed FileNotFoundError: parm7 does not exist İmren Bayıl via AMBER
- Re: [AMBER] parmed FileNotFoundError: parm7 does not exist David A Case via AMBER

Last message date: Fri Dec 30 2022 - 14:00:03 PST
Archived on: Mon Apr 15 2024 - 05:56:08 PDT