Amber Archive Jul 2022: by author

accuratefreeenergy--- via AMBER
- Re: [AMBER] [amber.ambermd.org: Amber22 test suite results on a cray with AMD cores and A100 GPUs] (Thu Jul 21 2022 - 05:45:16 PDT)
Adrian Roitberg via AMBER
- Re: [AMBER] Constant pH MD Simulation (Fri Jul 29 2022 - 08:50:37 PDT)
Ali Morshedi via AMBER
- [AMBER] Different prmtop with reordered mol2 file (Tue Jul 19 2022 - 10:45:47 PDT)
Ali Morshedifard via AMBER
- Re: [AMBER] Different prmtop with reordered mol2 file (Wed Jul 20 2022 - 09:33:09 PDT)
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 (Fri Jul 22 2022 - 01:46:35 PDT)
- [AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag (Thu Jul 21 2022 - 03:38:52 PDT)
Carlos Simmerling via AMBER
- Re: [AMBER] Regarding increase in size of combine trajectory (Fri Jul 29 2022 - 04:45:34 PDT)
- Re: [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges (Thu Jul 28 2022 - 02:48:19 PDT)
- Re: [AMBER] restraint definitions (Fri Jul 22 2022 - 09:39:51 PDT)
- Re: [AMBER] Amber minimization with packmol failing with segmentation fault (Wed Jul 20 2022 - 14:35:15 PDT)
- Re: [AMBER] Amber minimization with packmol failing with segmentation fault (Wed Jul 20 2022 - 14:03:10 PDT)
- Re: [AMBER] No PDB space group specified (Tue Jul 19 2022 - 06:02:36 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file (Mon Jul 18 2022 - 07:34:26 PDT)
- Re: [AMBER] Fwd: Constant pH Molecular Dynamics Simulation (Mon Jul 18 2022 - 02:30:16 PDT)
- Re: [AMBER] atomic chaos in the equilibration trajectory (Sat Jul 02 2022 - 05:39:37 PDT)
Charlotta Lebedenko via AMBER
- [AMBER] Problems with Antechamber leading to failed minimization (Sun Jul 31 2022 - 13:16:15 PDT)
Christian Seitz via AMBER
- [AMBER] Amber minimization with packmol failing with segmentation fault (Wed Jul 20 2022 - 13:52:23 PDT)
Cianna Calia via AMBER
- [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj (Mon Jul 25 2022 - 05:57:56 PDT)
Daniel Roe via AMBER
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj (Sun Jul 31 2022 - 07:54:14 PDT)
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj (Fri Jul 29 2022 - 12:51:13 PDT)
- Re: [AMBER] Unwrapping in MSD calculations with pytraj/cpptraj (Fri Jul 29 2022 - 12:49:55 PDT)
- Re: [AMBER] Job Opening in the Laboratory of Computational Biology, NIH (Fri Jul 29 2022 - 09:31:39 PDT)
- Re: [AMBER] Regarding increase in size of combine trajectory (Fri Jul 29 2022 - 06:06:21 PDT)
- [AMBER] Job Opening in the Laboratory of Computational Biology, NIH (Thu Jul 28 2022 - 05:45:26 PDT)
- Re: [AMBER] {SPAM?} Re: CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 15:50:59 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:41:37 PDT)
- Re: [AMBER] error opening OpenFabrics device (Fri Jul 22 2022 - 11:05:20 PDT)
- Re: [AMBER] error opening OpenFabrics device (Fri Jul 22 2022 - 07:37:16 PDT)
- Re: [AMBER] how to convert the eigenvector projection to a free energy landscape plotting (Fri Jul 22 2022 - 07:32:39 PDT)
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file (Fri Jul 22 2022 - 07:25:46 PDT)
- Re: [AMBER] RDF vs, Coordination numbers (Fri Jul 22 2022 - 07:16:51 PDT)
- Re: [AMBER] No PDB space group specified (Wed Jul 20 2022 - 08:06:05 PDT)
David A Case via AMBER
- Re: [AMBER] How to avoid SHAKE on a specific QM hydrogen atom in QM/MM simulations without compromising qmshake=1 flag (Thu Jul 21 2022 - 05:27:48 PDT)
- Re: [AMBER] No PDB space group specified (Wed Jul 20 2022 - 07:34:50 PDT)
- Re: [AMBER] build with GPU issue (Wed Jul 20 2022 - 07:18:34 PDT)
- Re: [AMBER] AmberTools installation issue (Tue Jul 19 2022 - 05:48:27 PDT)
- Re: [AMBER] Advice on applying restraints (Mon Jul 18 2022 - 05:20:45 PDT)
- Re: [AMBER] atomic chaos in the equilibration trajectory (Mon Jul 04 2022 - 04:36:00 PDT)
Deepshikha Ghosh 19310001 via AMBER
- [AMBER] regarding "watershell" command of cpptraj (Sun Jul 03 2022 - 22:09:35 PDT)
Domenico Marson via AMBER
- Re: [AMBER] how to use Amber patched with Plumed (Tue Jul 19 2022 - 03:02:09 PDT)
Dr. Anselm Horn via AMBER
- Re: [AMBER] what is hx atomtype? (Tue Jul 26 2022 - 00:26:27 PDT)
- Re: [AMBER] Constant pH MD Simulation (Wed Jul 20 2022 - 01:14:39 PDT)
- Re: [AMBER] appending to existing files (Mon Jul 18 2022 - 08:19:21 PDT)
- Re: [AMBER] Multiple cpu with Sander (Mon Jul 18 2022 - 06:02:52 PDT)
- Re: [AMBER] atomic chaos in the equilibration trajectory (Mon Jul 04 2022 - 04:28:58 PDT)
Dulal Mondal via AMBER
- [AMBER] Constant pH MD Simulation (Fri Jul 29 2022 - 00:28:41 PDT)
- [AMBER] Constant pH MD Simulation (Tue Jul 19 2022 - 23:38:40 PDT)
- [AMBER] Fwd: Constant pH Molecular Dynamics Simulation (Sun Jul 17 2022 - 22:21:17 PDT)
- [AMBER] Constant pH Molecular Dynamics Simulation (Sat Jul 16 2022 - 00:31:07 PDT)
Enrico Martinez via AMBER
- [AMBER] tleap: position of the ligand in the input pdb for protein-ligand complex (Mon Jul 25 2022 - 01:43:06 PDT)
- Re: [AMBER] installing CUDA driver with ubuntu 20.04 (Tue Jul 19 2022 - 07:39:30 PDT)
- Re: [AMBER] Multiple cpu with Sander (Tue Jul 19 2022 - 05:54:14 PDT)
- [AMBER] installing CUDA driver with ubuntu 20.04 (Tue Jul 19 2022 - 05:48:15 PDT)
- Re: [AMBER] Multiple cpu with Sander (Tue Jul 19 2022 - 01:19:58 PDT)
- [AMBER] Multiple cpu with Sander (Mon Jul 18 2022 - 02:43:47 PDT)
- [AMBER] Conversion NETCDF trajectory to other formats (Fri Jul 15 2022 - 04:33:59 PDT)
Erdem Yeler via AMBER
- [AMBER] AMBER22 pmemd.cuda installation ERROR (Sat Jul 30 2022 - 03:23:33 PDT)
Franz Waibl via AMBER
- Re: [AMBER] Fw: Average number of water molecules per GIST group (Thu Jul 21 2022 - 03:12:44 PDT)
- Re: [AMBER] Fw: Average number of water molecules per GIST group (Wed Jul 20 2022 - 05:27:18 PDT)
Gao Zhenting via AMBER
- Re: [AMBER] What is the compatible versions of the MKL for Amber22? (Sat Jul 02 2022 - 19:09:34 PDT)
- [AMBER] What is the compatible versions of the MKL for Amber22? (Thu Jun 30 2022 - 17:45:37 PDT)
Gert Kruger via AMBER
- Re: [AMBER] Ambertools21 installation problems (Fri Jul 22 2022 - 01:52:45 PDT)
- [AMBER] Ambertools21 installation problems (Fri Jul 22 2022 - 01:09:14 PDT)
Giulia Sormani via AMBER
- [AMBER] how to use Amber patched with Plumed (Tue Jul 19 2022 - 02:34:58 PDT)
- [AMBER] appending to existing files (Mon Jul 18 2022 - 06:50:00 PDT)
Gustavo Seabra via AMBER
- [AMBER] Fwd: MOPAC (Fri Jul 15 2022 - 08:21:04 PDT)
James Kress via AMBER
- Re: [AMBER] Loading external basis sets with Gaussian to use in QMMM (Tue Jul 19 2022 - 12:46:13 PDT)
- Re: [AMBER] atomic chaos in the equilibration trajectory (Sat Jul 02 2022 - 10:20:29 PDT)
Jordi Bujons via AMBER
- [AMBER] restraint definitions (Fri Jul 22 2022 - 09:38:15 PDT)
King Wu via AMBER
- [AMBER] atom charge from MD trajectory (Wed Jul 20 2022 - 15:44:38 PDT)
Kshatresh Dutta Dubey via AMBER
- Re: [AMBER] acetonitrile (Thu Jun 30 2022 - 13:30:32 PDT)
Kung, Ryan via AMBER
- Re: [AMBER] Loading external basis sets with Gaussian to use in QMMM (Tue Jul 19 2022 - 13:03:46 PDT)
Liao via AMBER
- Re: [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges (Wed Jul 27 2022 - 17:05:50 PDT)
- [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges (Wed Jul 27 2022 - 13:45:03 PDT)
- Re: [AMBER] Fwd: Entropy value in MM/GBSA calculation (Sun Jul 24 2022 - 06:45:19 PDT)
- Re: [AMBER] cpptraj selection mask syntax issue during clustering (Thu Jul 14 2022 - 21:10:20 PDT)
- [AMBER] cpptraj selection mask syntax issue during clustering (Thu Jul 14 2022 - 20:35:23 PDT)
Marie Brut via AMBER
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 13:14:08 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:45 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:55 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:20 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:52 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:21 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:51 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:02 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:12 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:26 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:55 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:48 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:12 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:02 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:11 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:18 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:52 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:25 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:44 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:44 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:13 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:26 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:26 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:10 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:11 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:37 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:32 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:00 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:55 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:52 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:56 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:43 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:00 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:55 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:37 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:25 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:56 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:45 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:22 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:32 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:43 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:12 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:26 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:45 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:25 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:25 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:45 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:51 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:43 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:26 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:47:44 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:23 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:26 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:48:17 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 13:13:48 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:46:11 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:52 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:51 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:48 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:47 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:47 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:25 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:25 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:24 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:24 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:07 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:06 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:06 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:45:06 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:44:43 PDT)
- Re: [AMBER] CPPTRAJ, Total H-Bond Count Question (Fri Jul 22 2022 - 12:44:41 PDT)
Matthew Guberman-Pfeffer via AMBER
- [AMBER] Advice on applying restraints (Sat Jul 16 2022 - 12:48:01 PDT)
Matthew Phanchana via AMBER
- [AMBER] Errors in test results for AMBER and AMBER.CUDA (Sun Jul 24 2022 - 02:39:24 PDT)
- [AMBER] build with GPU issue (Wed Jul 20 2022 - 06:32:19 PDT)
Miroslav Dikov via AMBER
- Re: [AMBER] Fw: Average number of water molecules per GIST group (Thu Jul 21 2022 - 03:18:32 PDT)
- Re: [AMBER] Fw: Average number of water molecules per GIST group (Thu Jul 21 2022 - 03:03:52 PDT)
- [AMBER] Fw: Average number of water molecules per GIST group (Wed Jul 20 2022 - 03:52:23 PDT)
ning via AMBER
- [AMBER] One building error with MPI option (Fri Jul 22 2022 - 14:42:33 PDT)
- [AMBER] how to convert the eigenvector projection to a free energy landscape plotting (Tue Jul 19 2022 - 20:24:22 PDT)
Prathit Chatterjee via AMBER
- [AMBER] Creating rst7 file with CHARMM-GUI generated parm7 and pdb files (Charmm36 force field) (Tue Jul 26 2022 - 07:32:52 PDT)
Prithviraj Nandigrami via AMBER
- [AMBER] AMBER20 GPU error (Thu Jul 28 2022 - 14:47:32 PDT)
Rajarshi Roy via AMBER
- [AMBER] Regarding increase in size of combine trajectory (Fri Jul 29 2022 - 04:20:11 PDT)
Rana Rehan Khalid via AMBER
- [AMBER] pairwise MMPBSA calculations (Fri Jul 22 2022 - 09:42:23 PDT)
Ranajit Saha via AMBER
- [AMBER] what is hx atomtype? (Mon Jul 25 2022 - 18:41:31 PDT)
Rybenkov, Valentin V. via AMBER
- [AMBER] error opening OpenFabrics device (Fri Jul 22 2022 - 06:45:58 PDT)
- Re: [AMBER] AmberTools installation issue (Tue Jul 19 2022 - 10:28:01 PDT)
- Re: [AMBER] AmberTools installation issue (Tue Jul 19 2022 - 08:51:00 PDT)
- Re: [AMBER] AmberTools installation issue (Sun Jul 17 2022 - 16:15:15 PDT)
Saranya vasudevan via AMBER
- Re: [AMBER] No PDB space group specified (Tue Jul 19 2022 - 05:53:08 PDT)
- [AMBER] Number of atoms in the coordinate file does not match the parm file (Mon Jul 18 2022 - 07:21:00 PDT)
SATYAJIT KHATUA via AMBER
- [AMBER] Fwd: Entropy value in MM/GBSA calculation (Sat Jul 23 2022 - 23:28:01 PDT)
- [AMBER] Entropy value in MM/GBSA calculation (Sat Jul 23 2022 - 01:15:50 PDT)
Shiji Zhao via AMBER
- Re: [AMBER] Partial charge discrepancy between AM1-BCC small molecule charge and FF library charges (Wed Jul 27 2022 - 14:24:43 PDT)
Sruthi Sudhakar via AMBER
- Re: [AMBER] Number of atoms in the coordinate file does not match the parm file (Tue Jul 19 2022 - 02:26:26 PDT)
Suchetana Gupta via AMBER
- [AMBER] Asking about any upcoming workshop (Fri Jul 29 2022 - 11:46:21 PDT)
- Re: [AMBER] appending to existing files (Mon Jul 18 2022 - 06:52:59 PDT)
- Re: [AMBER] appending to existing files (Mon Jul 18 2022 - 06:51:25 PDT)
Vinicius Wilian Cruzeiro via AMBER
- Re: [AMBER] Constant pH Molecular Dynamics Simulation (Sat Jul 16 2022 - 00:44:39 PDT)
王展峰 via AMBER
- Re: [AMBER] atomic chaos in the equilibration trajectory (Mon Jul 04 2022 - 04:41:23 PDT)
- Re: [AMBER] atomic chaos in the equilibration trajectory (Sat Jul 02 2022 - 18:49:40 PDT)
- [AMBER] atomic chaos in the equilibration trajectory (Sat Jul 02 2022 - 05:27:40 PDT)

Amber Archive Jul 2022 by author