Amber Archive Jul 2022: by date

Thursday, 30 June 2022
- Re: [AMBER] acetonitrile Kshatresh Dutta Dubey via AMBER
- [AMBER] What is the compatible versions of the MKL for Amber22? Gao Zhenting via AMBER
Saturday, 2 July 2022
- [AMBER] atomic chaos in the equilibration trajectory 王展峰 via AMBER
- Re: [AMBER] atomic chaos in the equilibration trajectory Carlos Simmerling via AMBER
- Re: [AMBER] atomic chaos in the equilibration trajectory James Kress via AMBER
- Re: [AMBER] atomic chaos in the equilibration trajectory 王展峰 via AMBER
- Re: [AMBER] What is the compatible versions of the MKL for Amber22? Gao Zhenting via AMBER
Sunday, 3 July 2022
- [AMBER] regarding "watershell" command of cpptraj Deepshikha Ghosh 19310001 via AMBER
Monday, 4 July 2022
- Re: [AMBER] atomic chaos in the equilibration trajectory Dr. Anselm Horn via AMBER
- Re: [AMBER] atomic chaos in the equilibration trajectory David A Case via AMBER
- Re: [AMBER] atomic chaos in the equilibration trajectory 王展峰 via AMBER
Thursday, 14 July 2022
- [AMBER] cpptraj selection mask syntax issue during clustering Liao via AMBER
- Re: [AMBER] cpptraj selection mask syntax issue during clustering Liao via AMBER
Friday, 15 July 2022
- [AMBER] Conversion NETCDF trajectory to other formats Enrico Martinez via AMBER
- [AMBER] Fwd: MOPAC Gustavo Seabra via AMBER
Saturday, 16 July 2022
- [AMBER] Constant pH Molecular Dynamics Simulation Dulal Mondal via AMBER
- Re: [AMBER] Constant pH Molecular Dynamics Simulation Vinicius Wilian Cruzeiro via AMBER
- [AMBER] Advice on applying restraints Matthew Guberman-Pfeffer via AMBER
Sunday, 17 July 2022
- Re: [AMBER] AmberTools installation issue Rybenkov, Valentin V. via AMBER
- [AMBER] Fwd: Constant pH Molecular Dynamics Simulation Dulal Mondal via AMBER
Monday, 18 July 2022
- Re: [AMBER] Fwd: Constant pH Molecular Dynamics Simulation Carlos Simmerling via AMBER
- [AMBER] Multiple cpu with Sander Enrico Martinez via AMBER
- Re: [AMBER] Advice on applying restraints David A Case via AMBER
- Re: [AMBER] Multiple cpu with Sander Dr. Anselm Horn via AMBER
- [AMBER] appending to existing files Giulia Sormani via AMBER
- Re: [AMBER] appending to existing files Suchetana Gupta via AMBER
- Re: [AMBER] appending to existing files Suchetana Gupta via AMBER
- [AMBER] Number of atoms in the coordinate file does not match the parm file Saranya vasudevan via AMBER
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file Carlos Simmerling via AMBER
- Re: [AMBER] appending to existing files Dr. Anselm Horn via AMBER
Tuesday, 19 July 2022
- Re: [AMBER] Multiple cpu with Sander Enrico Martinez via AMBER
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file Sruthi Sudhakar via AMBER
- [AMBER] how to use Amber patched with Plumed Giulia Sormani via AMBER
- Re: [AMBER] how to use Amber patched with Plumed Domenico Marson via AMBER
- Re: [AMBER] AmberTools installation issue David A Case via AMBER
- Re: [AMBER] No PDB space group specified Saranya vasudevan via AMBER
- [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- Re: [AMBER] Multiple cpu with Sander Enrico Martinez via AMBER
- Re: [AMBER] No PDB space group specified Carlos Simmerling via AMBER
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 Enrico Martinez via AMBER
- Re: [AMBER] AmberTools installation issue Rybenkov, Valentin V. via AMBER
- Re: [AMBER] AmberTools installation issue Rybenkov, Valentin V. via AMBER
- [AMBER] Different prmtop with reordered mol2 file Ali Morshedi via AMBER
- Re: [AMBER] Loading external basis sets with Gaussian to use in QMMM James Kress via AMBER
- Re: [AMBER] Loading external basis sets with Gaussian to use in QMMM Kung, Ryan via AMBER
- [AMBER] how to convert the eigenvector projection to a free energy landscape plotting ning via AMBER
- [AMBER] Constant pH MD Simulation Dulal Mondal via AMBER
Wednesday, 20 July 2022
- Re: [AMBER] Constant pH MD Simulation Dr. Anselm Horn via AMBER
- [AMBER] Fw: Average number of water molecules per GIST group Miroslav Dikov via AMBER
- Re: [AMBER] Fw: Average number of water molecules per GIST group Franz Waibl via AMBER
- [AMBER] build with GPU issue Matthew Phanchana via AMBER
- Re: [AMBER] build with GPU issue David A Case via AMBER
- Re: [AMBER] No PDB space group specified David A Case via AMBER
- Re: [AMBER] No PDB space group specified Daniel Roe via AMBER
- Re: [AMBER] Different prmtop with reordered mol2 file Ali Morshedifard via AMBER
- [AMBER] Amber minimization with packmol failing with segmentation fault Christian Seitz via AMBER
- Re: [AMBER] Amber minimization with packmol failing with segmentation fault Carlos Simmerling via AMBER
- Re: [AMBER] Amber minimization with packmol failing with segmentation fault Carlos Simmerling via AMBER
- [AMBER] atom charge from MD trajectory King Wu via AMBER
Thursday, 21 July 2022
- Re: [AMBER] Fw: Average number of water molecules per GIST group Miroslav Dikov via AMBER
- Re: [AMBER] Fw: Average number of water molecules per GIST group Franz Waibl via AMBER
- Re: [AMBER] Fw: Average number of water molecules per GIST group Miroslav Dikov via AMBER
- [AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag Amit, Amit \(amit.amit--- via AMBER
- Re: [AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag David A Case via AMBER
- Re: [AMBER] [amber.ambermd.org: Amber22 test suite results on a cray with AMD cores and A100 GPUs] accuratefreeenergy--- via AMBER
Friday, 22 July 2022
- [AMBER] Ambertools21 installation problems Gert Kruger via AMBER
- Re: [AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag Amit, Amit \(amit.amit--- via AMBER
- Re: [AMBER] Ambertools21 installation problems Gert Kruger via AMBER
- [AMBER] error opening OpenFabrics device Rybenkov, Valentin V. via AMBER
- Re: [AMBER] RDF vs, Coordination numbers Daniel Roe via AMBER
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file Daniel Roe via AMBER
- Re: [AMBER] how to convert the eigenvector projection to a free energy landscape plotting Daniel Roe via AMBER
- Re: [AMBER] error opening OpenFabrics device Daniel Roe via AMBER
- [AMBER] restraint definitions Jordi Bujons via AMBER
- Re: [AMBER] restraint definitions Carlos Simmerling via AMBER
- [AMBER] pairwise MMPBSA calculations Rana Rehan Khalid via AMBER
- Re: [AMBER] error opening OpenFabrics device Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- [AMBER] One building error with MPI option ning via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
Saturday, 23 July 2022
- [AMBER] Entropy value in MM/GBSA calculation SATYAJIT KHATUA via AMBER
Friday, 22 July 2022
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] {SPAM?} Re: CPPTRAJ, Total H-Bond Count Question Daniel Roe via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question Marie Brut via AMBER
Saturday, 23 July 2022
- [AMBER] Fwd: Entropy value in MM/GBSA calculation SATYAJIT KHATUA via AMBER
Sunday, 24 July 2022
- [AMBER] Errors in test results for AMBER and AMBER.CUDA Matthew Phanchana via AMBER
- Re: [AMBER] Fwd: Entropy value in MM/GBSA calculation Liao via AMBER
Monday, 25 July 2022
- [AMBER] tleap: position of the ligand in the input pdb for protein-ligand complex Enrico Martinez via AMBER
- [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Cianna Calia via AMBER
- [AMBER] what is hx atomtype? Ranajit Saha via AMBER
Tuesday, 26 July 2022
- Re: [AMBER] what is hx atomtype? Dr. Anselm Horn via AMBER
- [AMBER] Creating rst7 file with CHARMM-GUI generated parm7 and pdb files (Charmm36 force field) Prathit Chatterjee via AMBER
Wednesday, 27 July 2022
- [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges Liao via AMBER
- Re: [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges Shiji Zhao via AMBER
- Re: [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges Liao via AMBER
Thursday, 28 July 2022
- Re: [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges Carlos Simmerling via AMBER
- [AMBER] Job Opening in the Laboratory of Computational Biology, NIH Daniel Roe via AMBER
- [AMBER] AMBER20 GPU error Prithviraj Nandigrami via AMBER
Friday, 29 July 2022
- [AMBER] Constant pH MD Simulation Dulal Mondal via AMBER
- [AMBER] Regarding increase in size of combine trajectory Rajarshi Roy via AMBER
- Re: [AMBER] Regarding increase in size of combine trajectory Carlos Simmerling via AMBER
- Re: [AMBER] Regarding increase in size of combine trajectory Daniel Roe via AMBER
- Re: [AMBER] Constant pH MD Simulation Adrian Roitberg via AMBER
- Re: [AMBER] Job Opening in the Laboratory of Computational Biology, NIH Daniel Roe via AMBER
- [AMBER] Asking about any upcoming workshop Suchetana Gupta 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
Saturday, 30 July 2022
- [AMBER] AMBER22 pmemd.cuda installation ERROR Erdem Yeler via AMBER
Sunday, 31 July 2022
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj Daniel Roe via AMBER
- [AMBER] Problems with Antechamber leading to failed minimization Charlotta Lebedenko via AMBER

Last message date: Thu Aug 04 2022 - 13:37:49 PDT
Archived on: Wed Apr 24 2024 - 05:56:09 PDT

Amber Archive Jul 2022 by date