Amber Archive Sep 2022: by date

Thursday, 1 September 2022
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest David A Case via AMBER
- [AMBER] Calculation of dihedral angle using cpptraj in CpHMD simulation Dulal Mondal via AMBER
- Re: [AMBER] Calculation of dihedral angle using cpptraj in CpHMD simulation Daniel Roe via AMBER
- Re: [AMBER] Calculation of dihedral angle using cpptraj in CpHMD simulation Carlos Simmerling via AMBER
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest Christian Seitz via AMBER
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest Daniel Roe via AMBER
- Re: [AMBER] Question about NAB package usage in AMBER David A Case via AMBER
- [AMBER] Problem with TI minimization Matthew Guberman-Pfeffer via AMBER
Friday, 2 September 2022
- [AMBER] crash o the pmemd.cuda Enrico Martinez via AMBER
- [AMBER] Nanodisk preparation with Packmol-memgen? Gustavo Seabra via AMBER
- [AMBER] problem of the protonation of the ligand Enrico Martinez via AMBER
- Re: [AMBER] Problem with TI minimization David A Case via AMBER
- Re: [AMBER] Problem with TI minimization David Case via AMBER
- Re: [AMBER] {SPAM?} Re: Problem with TI minimization Matthew Guberman-Pfeffer via AMBER
Saturday, 3 September 2022
- [AMBER] Fwd: CPPTRAJ: sign convention for dihedral angles!! Cenk Andac via AMBER
- [AMBER] Fwd: CPPTRAJ: sign convention for dihedral angles!! Cenk Andac via AMBER
- [AMBER] AMBER 22 installation with CUDA support SATYAJIT KHATUA via AMBER
- [AMBER] Histidine tautomer state and pKa? Liao via AMBER
- Re: [AMBER] Histidine tautomer state and pKa? Carlos Simmerling via AMBER
Sunday, 4 September 2022
- [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide Jiaan Zhu via AMBER
- Re: [AMBER] AMBER 22 installation with CUDA support SATYAJIT KHATUA via AMBER
- Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide David A Case via AMBER
- Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide Jiaan Zhu via AMBER
- [AMBER] Fwd: Failed TI heating simulation (RBFE) using Amber22 Pengfei Li via AMBER
- [AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1? He, Amy via AMBER
Monday, 5 September 2022
- Re: [AMBER] problem of the protonation of the ligand Enrico Martinez via AMBER
- Re: [AMBER] crash o the pmemd.cuda Enrico Martinez via AMBER
- Re: [AMBER] problem of the protonation of the ligand Enrico Martinez via AMBER
- [AMBER] Test result of amber22 installation Dulal Mondal via AMBER
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1? David A Case via AMBER
- [AMBER] Fwd: AMBER 22 installation with CUDA support SATYAJIT KHATUA via AMBER
- Re: [AMBER] Fwd: AMBER 22 installation with CUDA support SATYAJIT KHATUA via AMBER
- Re: [AMBER] Fwd: AMBER 22 installation with CUDA support SATYAJIT KHATUA via AMBER
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1? He, Amy via AMBER
Tuesday, 6 September 2022
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
- [AMBER] paramfit and EQM - EVDW-ELE(MM) energy difference Cenk Andac via AMBER
- Re: [AMBER] problem of the protonation of the ligand Enrico Martinez via AMBER
- Re: [AMBER] problem of the protonation of the ligand sribone via AMBER
- Re: [AMBER] problem of the protonation of the ligand Enrico Martinez via AMBER
- [AMBER] AMBER22 INSTALLING Edivaldo Rodrigues via AMBER
- Re: [AMBER] AMBER22 INSTALLING David A Case via AMBER
- Re: [AMBER] Test result of amber22 installation David A Case via AMBER
- Re: [AMBER] AMBER22 INSTALLING Edivaldo Rodrigues via AMBER
- Re: [AMBER] ATOMIC NUMBER section in prmtop file - sulfur atom in ligand is -1? He, Amy via AMBER
- [AMBER] AMBER22 INSTALLATION Edivaldo Rodrigues via AMBER
- [AMBER] AMBER22 INSTALLATION Edivaldo Rodrigues via AMBER
- Re: [AMBER] Test result of amber22 installation Yeng-Tseng Wang via AMBER
Wednesday, 7 September 2022
- [AMBER] Amber patched with Plumed, units conversion Giulia Sormani via AMBER
- Re: [AMBER] paramfit and EQM - EVDW-ELE(MM) energy difference Cenk Andac via AMBER
- Re: [AMBER] paramfit and EQM - EVDW-ELE(MM) energy difference Cenk Andac via AMBER
Thursday, 8 September 2022
- Re: [AMBER] Test result of amber22 installation Yeng-Tseng Wang via AMBER
- [AMBER] Raw RDF exceeds total number of waters? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Raw RDF exceeds total number of waters? Daniel Roe via AMBER
Friday, 9 September 2022
- [AMBER] How to determine the optimal number of cluster in cpptraj or other something ning via AMBER
- Re: [AMBER] How to determine the optimal number of cluster in cpptraj or other something Rybenkov, Valentin V. via AMBER
- Re: [AMBER] How to determine the optimal number of cluster in cpptraj or other something Carlos Simmerling via AMBER
- Re: [AMBER] How to determine the optimal number of cluster in cpptraj or other something SATYAJIT KHATUA via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
Saturday, 10 September 2022
- Re: [AMBER] [amber.ambermd.org: Fwd: Failed TI heating simulation (RBFE) using Amber22] accuratefreeenergy--- via AMBER
Sunday, 11 September 2022
- [AMBER] Autocorrelation time He, Amy via AMBER
- Re: [AMBER] Autocorrelation time Charo del Genio via AMBER
Monday, 12 September 2022
- [AMBER] Error in calculation of Binding free energy ! angad sharma via AMBER
- [AMBER] On the skipping of first frames in mmpbsa calculations Enrico Martinez via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
Tuesday, 13 September 2022
- Re: [AMBER] {SPAM?} Re: Raw RDF exceeds total number of waters? Daniel Roe via AMBER
Thursday, 15 September 2022
- [AMBER] interpreting paramfit results Cenk Andac via AMBER
- [AMBER] Force field parameters for non canonical amino acids Suchetana Gupta via AMBER
- Re: [AMBER] Force field parameters for non canonical amino acids Suchetana Gupta via AMBER
Friday, 16 September 2022
- [AMBER] Normal mode analysis for entropy calculation in MM/GBSA He, Amy via AMBER
- Re: [AMBER] interpreting paramfit results David A Case via AMBER
- [AMBER] Bump "Distance restraint and periodic boundary conditions" Demian Riccardi via AMBER
Sunday, 18 September 2022
- Re: [AMBER] interpreting paramfit results Cenk Andac via AMBER
- Re: [AMBER] interpreting paramfit results Cenk Andac via AMBER
- [AMBER] MMPBSA.py.MPI not bulit in Amber20 amirhossein taghavi via AMBER
Monday, 19 September 2022
- Re: [AMBER] interpreting paramfit results David A Case via AMBER
- Re: [AMBER] MMPBSA.py.MPI not bulit in Amber20 Adrian Roitberg via AMBER
- [AMBER] What to use to build nanodisc system? Gustavo Seabra via AMBER
Tuesday, 20 September 2022
- [AMBER] Possible memory leaks in Amber22 Franz Waibl via AMBER
- Re: [AMBER] MMPBSA.py.MPI not bulit in Amber20 Yoshitaka Moriwaki via AMBER
Wednesday, 21 September 2022
- [AMBER] FATAL Error Issue Tamsila Parveen via AMBER
- Re: [AMBER] interpreting paramfit results Barış KURT via AMBER
- Re: [AMBER] FATAL Error Issue David A Case via AMBER
- [AMBER] [NEB] Convergence criteria Madhur Aggarwal via AMBER
- [AMBER] problems in using autoimage Giulia Sormani via AMBER
- Re: [AMBER] problems in using autoimage Daniel Roe via AMBER
- Re: [AMBER] problems in using autoimage David A Case via AMBER
Thursday, 22 September 2022
- Re: [AMBER] problems in using autoimage Daniel Roe via AMBER
- Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide Jiaan Zhu via AMBER
- [AMBER] MM-PBSA calculations Marcelo Andrade Chagas via AMBER
- [AMBER] any parameter settings in paramfit for a short restrained minimization before fitting? Cenk Andac via AMBER
- [AMBER] any parameter settings in paramfit for a short restrained minimization before fitting? Cenk Andac via AMBER
- Re: [AMBER] any parameter settings in paramfit for a short restrained minimization before fitting? Cenk Andac via AMBER
- [AMBER] Data set math gives "size is 0" Chunsheng Lin via AMBER
- Re: [AMBER] Data set math gives "size is 0" Rodrigo Galindo-Murillo via AMBER
Friday, 23 September 2022
- Re: [AMBER] problems in using autoimage David A Case via AMBER
- [AMBER] Amber22, no DV/DL value with option gti_lam_sch Domenico Marson via AMBER
- [AMBER] Use of parmed to generate modified prmtop file Sruthi Sudhakar via AMBER
Saturday, 24 September 2022
- Re: [AMBER] Normal mode analysis for entropy calculation in MM/GBSA David A Case via AMBER
- Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide David A Case via AMBER
- Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide Jiaan Zhu via AMBER
Sunday, 25 September 2022
- Re: [AMBER] Segmentation fault when starting parmchk2 for an artificial nucleotide Jiaan Zhu via AMBER
Monday, 26 September 2022
- Re: [AMBER] FATAL Error Issue Tamsila Parveen via AMBER
- Re: [AMBER] FATAL Error Issue Amara Jabeen via AMBER
- Re: [AMBER] FATAL Error Issue Carlos Simmerling via AMBER
- Re: [AMBER] Using CHARMM-GUI FF Convert from CHARMM to Amber With Ligand David A Case via AMBER
- Re: [AMBER] Using CHARMM-GUI FF Convert from CHARMM to Amber With Ligand Collin Nisler via AMBER
- [AMBER] Can restraints on protein substitute membrane? Rafał Madaj via AMBER
Tuesday, 27 September 2022
- Re: [AMBER] Amber22, no DV/DL value with option gti_lam_sch Domenico Marson via AMBER
- [AMBER] Amber 22 Installation Nagar, Hemant via AMBER
- Re: [AMBER] Amber 22 Installation Scott Brozell via AMBER
Wednesday, 28 September 2022
- Re: [AMBER] problems in using autoimage Giulia Sormani via AMBER
- [AMBER] Warning in free energy output file Sayan Poddar via AMBER
- Re: [AMBER] Warning in free energy output file Carlos Simmerling via AMBER
- [AMBER] Which molecule should the environment feel, in TI simulations? Liao via AMBER
Thursday, 29 September 2022
- [AMBER] Define angle between planes of monomers in a hexamer Rosellen, Martin via AMBER
- Re: [AMBER] Which molecule should the environment feel, in TI simulations? David A Case via AMBER
- Re: [AMBER] Define angle between planes of monomers in a hexamer David A Case via AMBER
- Re: [AMBER] Amber22, no DV/DL value with option gti_lam_sch Domenico Marson via AMBER
- [AMBER] NUMEXTRA Error Qi Wang via AMBER
Friday, 30 September 2022
- Re: [AMBER] NUMEXTRA Error David A Case via AMBER
- Re: [AMBER] any parameter settings in paramfit for a short restrained minimization before fitting? Cenk Andac via AMBER
- [AMBER] Modifying Parameters in parm7 Collin Nisler via AMBER
- Re: [AMBER] Modifying Parameters in parm7 David A Case via AMBER

Last message date: Fri Sep 30 2022 - 18:00:03 PDT
Archived on: Sun Nov 17 2024 - 05:56:10 PST

Amber Archive Sep 2022 by date