Amber Archive Aug 2022: by date

Monday, 1 August 2022
- [AMBER] Amber 20 - error with PI parallel install Gert Kruger via AMBER
- Re: [AMBER] Problems with Antechamber leading to failed minimization David A Case via AMBER
- Re: [AMBER] Amber 20 - error with PI parallel install David A Case via AMBER
- Re: [AMBER] Amber22 installation David A Case via AMBER
- [AMBER] Amber21: rism3d.periodic/1ahoa test fails for number of CPUs > 2 Vlad via AMBER
Tuesday, 2 August 2022
- Re: [AMBER] Amber21: rism3d.periodic/1ahoa test fails for number of CPUs > 2 tluchko via AMBER
Wednesday, 3 August 2022
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 David A Case via AMBER
- [AMBER] Inquiry regarding pmemd and gem.pmemd Jiaqiao Zhou via AMBER
- Re: [AMBER] Inquiry regarding pmemd and gem.pmemd Elvis Martis via AMBER
- Re: [AMBER] AMBER NME caps not recognized Dr. Anselm Horn via AMBER
Thursday, 4 August 2022
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- Re: [AMBER] AMBER NME caps not recognized Valentin Hörschinger via AMBER
- [AMBER] Software announcement: Release of PUPIL 4.0 Juan Torras Costa via AMBER
- [AMBER] running pmemd.cuda with 2 GPUs Enrico Martinez via AMBER
- Re: [AMBER] running pmemd.cuda with 2 GPUs Enrico Martinez via AMBER
- Re: [AMBER] AMBER NME caps not recognized Kellon Belfon via AMBER
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- [AMBER] Restraints with replica exchange MD Juliette Newell via AMBER
- Re: [AMBER] Restraints with replica exchange MD Carlos Simmerling via AMBER
- [AMBER] How can I install AmberTools22? 清川慎介 via AMBER
- Re: [AMBER] AMBER NME caps not recognized Debarati DasGupta via AMBER
- [AMBER] any ideas on this? Debarati DasGupta via AMBER
- [AMBER] pmemd.cuda crash Enrico Martinez via AMBER
- Re: [AMBER] AMBER NME caps not recognized David A Case via AMBER
- Re: [AMBER] AMBER NME caps not recognized Dr. Anselm Horn via AMBER
- Re: [AMBER] How can I install AmberTools22? David A Case via AMBER
- Re: [AMBER] AMBER NME caps not recognized Carlos Simmerling via AMBER
- Re: [AMBER] AMBER NME caps not recognized Carlos Simmerling via AMBER
Friday, 5 August 2022
- Re: [AMBER] pmemd.cuda crash Enrico Martinez via AMBER
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- Re: [AMBER] pmemd.cuda crash Enrico Martinez via AMBER
- [AMBER] problem with MMPBSA.py.mpi Enrico Martinez via AMBER
- [AMBER] method to change residue numbering for amber masks after production Murray, Makay via AMBER
- [AMBER] AMBER to LAMMPS Conversion Cianna Calia via AMBER
Monday, 8 August 2022
- [AMBER] question about run TI with REMD (amber20) 费俊文 via AMBER
- Re: [AMBER] problem with MMPBSA.py.mpi Enrico Martinez via AMBER
- Re: [AMBER] Conversion NETCDF trajectory to other formats Daniel Roe via AMBER
- Re: [AMBER] method to change residue numbering for amber masks after production Daniel Roe via AMBER
- Re: [AMBER] method to change residue numbering for amber masks after production Daniel Roe via AMBER
- Re: [AMBER] problem with MMPBSA.py.mpi Enrico Martinez via AMBER
- Re: [AMBER] Conversion NETCDF trajectory to other formats Daniel Roe via AMBER
- Re: [AMBER] Creating rst7 file with CHARMM-GUI generated parm7 and pdb files (Charmm36 force field) Daniel Roe via AMBER
- [AMBER] Fwd: Extracting residue number from a given resname - Pytraj Carlos Navarro via AMBER
- Re: [AMBER] tleap: position of the ligand in the input pdb for protein-ligand complex Daniel Roe via AMBER
- Re: [AMBER] pmemd.cuda crash Enrico Martinez via AMBER
- [AMBER] Questions about MMPBSA.py Enrico Martinez via AMBER
- Re: [AMBER] Fwd: MOPAC Gustavo Seabra via AMBER
Tuesday, 9 August 2022
- Re: [AMBER] Questions about MMPBSA.py Enrico Martinez via AMBER
- [AMBER] Question about cpptraj analysis Enrico Martinez via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
- Re: [AMBER] Questions about MMPBSA.py Enrico Martinez via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
Wednesday, 10 August 2022
- Re: [AMBER] Questions about MMPBSA.py Enrico Martinez via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
Thursday, 11 August 2022
- [AMBER] Some basic questions about cpptraj Enrico Martinez via AMBER
Friday, 12 August 2022
- [AMBER] How to extract last snapshot from the trajectory with re imaging? Enrico Martinez via AMBER
- Re: [AMBER] how to convert the eigenvector projection to a free energy landscape plotting Daniel Roe via AMBER
- [AMBER] nvcc fatal : Unsupported gpu architecture 'compute_75' Erdem Yeler via AMBER
- [AMBER] MMPBSA with implicit radii error King Wu via AMBER
- Re: [AMBER] MMPBSA with implicit radii error King Wu via AMBER
- Re: [AMBER] Extracting residue number from a given resname - Pytraj Hai Nguyen via AMBER
Monday, 15 August 2022
- [AMBER] gremd_acyc keyword for H-REMD Zhuoran Long via AMBER
- Re: [AMBER] gremd_acyc keyword for H-REMD Adrian Roitberg via AMBER
- Re: [AMBER] gremd_acyc keyword for H-REMD Zhuoran Long via AMBER
- [AMBER] AMBER/ORCA for QM/MM 许茂峰 via AMBER
Tuesday, 16 August 2022
- Re: [AMBER] How to extract last snapshot from the trajectory with re imaging? Enrico Martinez via AMBER
- [AMBER] How to do multiple 'watershell' analysis in cpptraj XP Chen via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
- Re: [AMBER] How to do multiple 'watershell' analysis in cpptraj Daniel Roe via AMBER
- [AMBER] Bridge hydrogen bonds Umesh Roy via AMBER
- Re: [AMBER] gremd_acyc keyword for H-REMD Adrian Roitberg via AMBER
- Re: [AMBER] gremd_acyc keyword for H-REMD Brian Radak via AMBER
- [AMBER] Question about histograms analysis with multiple values Suchetana Gupta via AMBER
- Re: [AMBER] gremd_acyc keyword for H-REMD accuratefreeenergy--- via AMBER
Wednesday, 17 August 2022
- [AMBER] Backbone decomposition values all zero upon successful MMPBSA.py run Miroslav Suruzhon via AMBER
- Re: [AMBER] nvcc fatal : Unsupported gpu architecture 'compute_75' Erdem Yeler via AMBER
- [AMBER] The file contained 6 atoms not in residue templates Sneha Kandapal via AMBER
- Re: [AMBER] The file contained 6 atoms not in residue templates Rodrigo Galindo-Murillo via AMBER
- Re: [AMBER] AMBER/ORCA for QM/MM James Kress via AMBER
- Re: [AMBER] AMBER/ORCA for QM/MM Adrian Roitberg via AMBER
Thursday, 18 August 2022
- Re: [AMBER] Questions about MMPBSA.py Enrico Martinez via AMBER
- [AMBER] Amber22 incompatible CUDA version - how to solve this? Markowska
- [AMBER] Query about Constant pH MD simulation Dulal Mondal via AMBER
- [AMBER] TiMerge doesn't work, or what am I doing wrong? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] Backbone decomposition values all zero upon successful MMPBSA.py run Bill Miller III via AMBER
Friday, 19 August 2022
- [AMBER] CPPTRAJ: sign convention for dihedral angles!! Cenk Andac via AMBER
- Re: [AMBER] Backbone decomposition values all zero upon successful MMPBSA.py run Miroslav Suruzhon via AMBER
- Re: [AMBER] Question about cpptraj analysis Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ: sign convention for dihedral angles!! Daniel Roe via AMBER
- [AMBER] error with parmed in MCPB and pdb4amber Nishad Ankita Rudal via AMBER
Sunday, 21 August 2022
- [AMBER] one question about setting up scmask and timask laura zhang via AMBER
- [AMBER] TI and periodic boundaries? Matthew Guberman-Pfeffer via AMBER
- [AMBER] Thermodynamic integration for covalently bound ligands Ali Morshedifard via AMBER
Monday, 22 August 2022
- [AMBER] How to generate PCA and porcupine analysis for crystal structure from X-ray study using AMBER 16 priya murugan via AMBER
- Re: [AMBER] Question about histograms analysis with multiple values Suchetana Gupta via AMBER
- Re: [AMBER] one question about setting up scmask and timask laura zhang via AMBER
- [AMBER] Amber22 installation Rybenkov, Valentin V. via AMBER
- [AMBER] Thermodynamic Integration simulation in pmemd.cuda Suguna Sakkiah via AMBER
Tuesday, 23 August 2022
- [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest Christian Seitz via AMBER
- Re: [AMBER] Amber22 installation David A Case via AMBER
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest David A Case via AMBER
- [AMBER] problem: TIP3P model with tleap in Amber22 王怡文 via AMBER
- Re: [AMBER] problem: TIP3P model with tleap in Amber22 Carlos Simmerling via AMBER
- [AMBER] idecomp in PMEMD? Matthew Guberman-Pfeffer via AMBER
Wednesday, 24 August 2022
- [AMBER] How to convert the dihedral dataset into a probability mass function plotting ning via AMBER
- Re: [AMBER] How to convert the dihedral dataset into a probability mass function plotting Carlos Simmerling via AMBER
- Re: [AMBER] How to convert the dihedral dataset into a probability mass function plotting Daniel Roe via AMBER
- [AMBER] AMBER22 failed during installation on CUDA and centos 7.9 Hamza, Adel via AMBER
- Re: [AMBER] AMBER22 failed during installation on CUDA and centos 7.9 David A Case via AMBER
- Re: [AMBER] AMBER22 failed during installation on CUDA and centos 7.9 Rybenkov, Valentin V. via AMBER
- [AMBER] [AmberTools22 installation] I installed AmberTools22 on my Windows WSL2 but there is no sander.MPI 이동언 via AMBER
Thursday, 25 August 2022
- [AMBER] Query regarding glycoprotein RMSD calculation Sayan Poddar via AMBER
- Re: [AMBER] Query regarding glycoprotein RMSD calculation Carlos Simmerling via AMBER
- Re: [AMBER] problem: TIP3P model with tleap in Amber22 David A Case via AMBER
- Re: [AMBER] idecomp in PMEMD? David A Case via AMBER
- Re: [AMBER] idecomp in PMEMD? Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] [AmberTools22 installation] I installed AmberTools22 on my Windows WSL2 but there is no sander.MPI David A Case via AMBER
- Re: [AMBER] TiMerge doesn't work, or what am I doing wrong? Josiah Bones via AMBER
- [AMBER] Does Parmed tiMerge accept all ambmasks? Wong, Sergio E. via AMBER
- Re: [AMBER] TiMerge doesn't work, or what am I doing wrong? Matthew Guberman-Pfeffer via AMBER
- [AMBER] pmemd.mpi crashes Rybenkov, Valentin V. via AMBER
Friday, 26 August 2022
- [AMBER] Dumping different trajectories at time angad sharma via AMBER
- [AMBER] Automatic glycan bonds in tleap? Dr. Anselm Horn via AMBER
- Re: [AMBER] pmemd.mpi crashes David A Case via AMBER
- Re: [AMBER] Automatic glycan bonds in tleap? Daniel Roe via AMBER
- Re: [AMBER] [EXTERNAL] Re: AMBER22 failed during installation on CUDA and centos 7.9 Hamza, Adel via AMBER
- Re: [AMBER] Automatic glycan bonds in tleap? Dr. Anselm Horn via AMBER
- Re: [AMBER] Automatic glycan bonds in tleap? Daniel Roe via AMBER
- Re: [AMBER] Automatic glycan bonds in tleap? Dr. Anselm Horn via AMBER
- [AMBER] Timelagged Independent Component plots with Amber? Suchetana Gupta via AMBER
- [AMBER] Confusion of difference EPB value of me and tutorial of MMPBSA.py Dongxiao Yue \(LHS, 220059036\) via AMBER
Saturday, 27 August 2022
- Re: [AMBER] Confusion of difference EPB value of me and tutorial of MMPBSA.py Ray Luo via AMBER
- [AMBER] Dealing with DU atom types in parmchk2 He, Amy via AMBER
Monday, 29 August 2022
- [AMBER] Hydrogen bonding ! angad sharma via AMBER
- [AMBER] MD simulation of complexes with Ag+ ions in Chimera 幅田揚一 via AMBER
- Re: [AMBER] MD simulation of complexes with Ag+ ions in Chimera Dr. Anselm Horn via AMBER
- [AMBER] AMBER tutorial 5.4 original publication? Michael Shokhen via AMBER
- Re: [AMBER] AMBER tutorial 5.4 original publication? Maria Nagan via AMBER
- [AMBER] Bond energy discrepancy between amber simulated results and cpptraj Ruihan Zhou via AMBER
- Re: [AMBER] Bond energy discrepancy between amber simulated results and cpptraj Carlos Simmerling via AMBER
- [AMBER] CpHMD Dulal Mondal via AMBER
- [AMBER] timask vs. scmask question Matthew Guberman-Pfeffer via AMBER
- [AMBER] Frames are zero for prmtop file Sneha Kandapal via AMBER
- Re: [AMBER] Frames are zero for prmtop file Carlos Simmerling via AMBER
- Re: [AMBER] CpHMD Adrian Roitberg via AMBER
- Re: [AMBER] MD simulation of complexes with Ag+ ions in Chimera David A Case via AMBER
- Re: [AMBER] CpHMD David A Case via AMBER
- Re: [AMBER] timask vs. scmask question David A Case via AMBER
- Re: [AMBER] timask vs. scmask question Matthew Guberman-Pfeffer via AMBER
- Re: [AMBER] {SPAM?} Re: timask vs. scmask question Matthew Guberman-Pfeffer via AMBER
Tuesday, 30 August 2022
- Re: [AMBER] Bond energy discrepancy between amber simulated results and cpptraj Daniel Roe via AMBER
- [AMBER] Query regarding calculation of peptide-peptide hydrogen bond lifetime RIMJHIM MORAL via AMBER
- Re: [AMBER] Query regarding calculation of peptide-peptide hydrogen bond lifetime Daniel Roe via AMBER
- Re: [AMBER] Timelagged Independent Component plots with Amber? Suchetana Gupta via AMBER
- [AMBER] makeANG_RST Osman, Roman via AMBER
- Re: [AMBER] {SPAM?} Re: timask vs. scmask question David A Case via AMBER
- Re: [AMBER] makeANG_RST David A Case via AMBER
- Re: [AMBER] {SPAM?} Re: timask vs. scmask question Ali Morshedifard via AMBER
- Re: [AMBER] Question about NAB package usage in AMBER Qinsi Xiong via AMBER
- [AMBER] one error from MMPBSA.py laura zhang via AMBER
Wednesday, 31 August 2022
- Re: [AMBER] Timelagged Independent Component plots with Amber? Valentin Hörschinger via AMBER
- Re: [AMBER] one error from MMPBSA.py David A Case via AMBER
- [AMBER] analysis of the Hydrogen bonds Enrico Martinez via AMBER
- Re: [AMBER] Timelagged Independent Component plots with Amber? Suchetana Gupta via AMBER
- Re: [AMBER] Error: an illegal memory access was encountered launching kernel kNLSkinTest Christian Seitz via AMBER
- Re: [AMBER] Timelagged Independent Component plots with Amber? Suchetana Gupta via AMBER

Last message date: Wed Aug 31 2022 - 12:00:06 PDT
Archived on: Mon Apr 15 2024 - 05:56:06 PDT

Amber Archive Aug 2022 by date