Amber Archive Sep 2021: by author

Aliakbartehrani Zahra
- [AMBER] atom type issue in tleap with ff-nucleic-OL15 (Tue Sep 07 2021 - 03:49:37 PDT)
Alyemni, Saleh
- [AMBER] Lipid21 (Wed Sep 15 2021 - 23:40:10 PDT)
Annabelle Hartt
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 09:19:22 PDT)
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 03:15:00 PDT)
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 01:50:17 PDT)
- [AMBER] Co-ordinates switching in CPPTRAJ output (Fri Sep 24 2021 - 07:37:08 PDT)
ARITRA MITRA
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol (Mon Sep 13 2021 - 09:05:31 PDT)
- [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol (Mon Sep 13 2021 - 08:58:22 PDT)
Carlos Simmerling
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 06:45:28 PDT)
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 03:03:15 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 12:36:42 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 10:22:05 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 09:27:03 PDT)
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Fri Sep 24 2021 - 08:07:42 PDT)
- Re: [AMBER] How to set up a simulation keeping crystal waters in the binding site (Wed Sep 22 2021 - 08:30:28 PDT)
- Re: [AMBER] Zinc is escaping position restraint (Tue Sep 14 2021 - 04:01:50 PDT)
- Re: [AMBER] Positional restraints in thermodynamic integration (Thu Sep 09 2021 - 14:39:35 PDT)
- Re: [AMBER] Positional restraints in thermodynamic integration (Wed Sep 08 2021 - 03:18:00 PDT)
- Re: [AMBER] How to print out implicit solvent charges? (Mon Sep 06 2021 - 02:44:55 PDT)
- Re: [AMBER] REMD using multiple gpus (Sun Sep 05 2021 - 08:58:56 PDT)
Chloe Jaiswal
- [AMBER] Custom Residue frcmod (Fri Sep 24 2021 - 01:38:24 PDT)
- [AMBER] Reduced Units (Tue Sep 21 2021 - 23:10:54 PDT)
Daniel Roe
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 08:35:44 PDT)
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Mon Sep 27 2021 - 07:16:01 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 12:10:21 PDT)
- Re: [AMBER] Co-ordinates switching in CPPTRAJ output (Fri Sep 24 2021 - 08:20:17 PDT)
- Re: [AMBER] cpptraj has stopped working (Mon Sep 20 2021 - 06:28:02 PDT)
- Re: [AMBER] cpptraj has stopped working (Sun Sep 19 2021 - 05:23:57 PDT)
- [AMBER] New In CPPTRAJ (September 2021) (Fri Sep 17 2021 - 13:05:39 PDT)
- Re: [AMBER] Problem with AMBER20 aMD tutorial (Fri Sep 17 2021 - 10:19:19 PDT)
- Re: [AMBER] GIST question (Fri Sep 17 2021 - 10:10:38 PDT)
- Re: [AMBER] how to set distance restraints in amber (Tue Sep 07 2021 - 06:39:45 PDT)
- Re: [AMBER] Esander and multiple topologies (Fri Sep 03 2021 - 13:14:26 PDT)
David A Case
- Re: [AMBER] Error installing amber macOS M1 (Thu Sep 30 2021 - 11:01:36 PDT)
- Re: [AMBER] Problem in installing AMBER 20 Ubantu ; configuring molecules from own data obtained from Gaussian (Wed Sep 29 2021 - 05:58:51 PDT)
- Re: [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system (Wed Sep 29 2021 - 05:47:47 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Tue Sep 28 2021 - 18:40:09 PDT)
- Re: [AMBER] Atom type of NO does not shown up in PARMCHK.DAT (Tue Sep 28 2021 - 13:09:58 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Tue Sep 28 2021 - 13:00:53 PDT)
- Re: [AMBER] Amber20 installation (Mon Sep 27 2021 - 05:08:05 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Fri Sep 24 2021 - 18:04:22 PDT)
- Re: [AMBER] Custom Residue frcmod (Fri Sep 24 2021 - 04:35:37 PDT)
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? (Thu Sep 23 2021 - 18:52:39 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Thu Sep 23 2021 - 18:07:35 PDT)
- Re: [AMBER] Reduced Units (Wed Sep 22 2021 - 04:39:37 PDT)
- Re: [AMBER] cpptraj has stopped working (Sun Sep 19 2021 - 05:23:02 PDT)
- Re: [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 (Sun Sep 19 2021 - 05:18:19 PDT)
- Re: [AMBER] Non-integer pbsa surface charge? (Sat Sep 18 2021 - 05:01:26 PDT)
- Re: [AMBER] Is AMBER multithreaded? (Fri Sep 17 2021 - 18:13:53 PDT)
- Re: [AMBER] Error while running make install (Fri Sep 17 2021 - 11:08:02 PDT)
- Re: [AMBER] Error while running make install (Fri Sep 17 2021 - 05:15:33 PDT)
- Re: [AMBER] Non-integer pbsa surface charge? (Thu Sep 16 2021 - 05:18:51 PDT)
- Re: [AMBER] ambermd.org SSL Certificate (Wed Sep 15 2021 - 09:44:27 PDT)
- Re: [AMBER] Amber20 installation, Amber.pip file broken (Mon Sep 13 2021 - 12:32:25 PDT)
- Re: [AMBER] cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol (Mon Sep 13 2021 - 12:22:41 PDT)
- Re: [AMBER] Amber20 installation, Amber.pip file broken (Mon Sep 13 2021 - 05:41:28 PDT)
- Re: [AMBER] [Amber] gbnsr6 doesn't calculate VDWAALS (Mon Sep 13 2021 - 05:35:51 PDT)
- Re: [AMBER] guv output file format (Fri Sep 10 2021 - 04:52:49 PDT)
- Re: [AMBER] ModuleNotFoundError: No module named 'alamdcrd' (Thu Sep 09 2021 - 10:34:19 PDT)
- Re: [AMBER] Restart (Thu Sep 09 2021 - 08:54:30 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Thu Sep 09 2021 - 05:53:25 PDT)
- Re: [AMBER] atom type issue in tleap with ff-nucleic-OL15 (Wed Sep 08 2021 - 05:02:23 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Wed Sep 08 2021 - 04:49:53 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Mon Sep 06 2021 - 13:27:50 PDT)
- Re: [AMBER] How to print out implicit solvent charges? (Mon Sep 06 2021 - 05:52:51 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Sat Sep 04 2021 - 04:57:34 PDT)
Debarati DasGupta
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? (Fri Sep 24 2021 - 12:40:34 PDT)
- Re: [AMBER] How to compute pairwise interaction between masks (Mon Sep 13 2021 - 04:50:53 PDT)
- [AMBER] GIST with cosolvents like acetonitrile, ethanol instead of water (Wed Sep 01 2021 - 07:37:52 PDT)
Debostuti Ghoshdastidar
- [AMBER] Zinc is escaping position restraint (Tue Sep 14 2021 - 02:45:47 PDT)
Delwakkada Liyanage, Senal Dinuka
- [AMBER] TI simulation for ligand vanishing (Thu Sep 09 2021 - 09:45:30 PDT)
Dr. Anselm Horn
- Re: [AMBER] Use Amber12 with cuda (Fri Sep 17 2021 - 02:05:30 PDT)
- Re: [AMBER] How to compute pairwise interaction between masks (Mon Sep 13 2021 - 06:31:15 PDT)
- Re: [AMBER] How to compute pairwise interaction between masks (Mon Sep 13 2021 - 06:19:43 PDT)
- Re: [AMBER] How to compute pairwise interaction between masks (Mon Sep 13 2021 - 02:11:46 PDT)
- Re: [AMBER] Restart (Mon Sep 06 2021 - 08:10:00 PDT)
- Re: [AMBER] how to change residue number of several residues in AMBER trajectories (Thu Sep 02 2021 - 01:23:27 PDT)
Elvis A F Martis
- Re: [AMBER] Zinc is escaping position restraint (Tue Sep 14 2021 - 18:14:57 PDT)
Franz Waibl
- Re: [AMBER] GIST question (Tue Sep 14 2021 - 10:03:01 PDT)
- Re: [AMBER] GIST question (Thu Sep 09 2021 - 01:46:05 PDT)
Henry Green
- [AMBER] Restart (Mon Sep 06 2021 - 20:08:17 PDT)
- Re: [AMBER] Restart (Mon Sep 06 2021 - 06:45:34 PDT)
- [AMBER] Restart (Sun Sep 05 2021 - 23:21:31 PDT)
- [AMBER] Restart (Sun Sep 05 2021 - 22:58:33 PDT)
- [AMBER] Restart (Sun Sep 05 2021 - 22:52:20 PDT)
- [AMBER] Restart (Sun Sep 05 2021 - 22:35:11 PDT)
jamal kazazi
- Re: [AMBER] zero torsion in DUMPAVE file in a sander run (Mon Sep 27 2021 - 09:18:17 PDT)
- [AMBER] zero torsion in DUMPAVE file in a sander run (Sun Sep 26 2021 - 23:16:46 PDT)
James Kress
- [AMBER] Is AMBER multithreaded? (Fri Sep 17 2021 - 14:44:42 PDT)
Jason Swails
- Re: [AMBER] parmed for 12-6-4 LJ (Geng Dong) (Mon Sep 27 2021 - 11:28:19 PDT)
- Re: [AMBER] PARMED Charmber User Warning Quesiton (Tue Sep 14 2021 - 13:49:39 PDT)
jinfeng liu
- [AMBER] REMD using multiple gpus (Sun Sep 05 2021 - 06:56:07 PDT)
Kevin Hauser
- [AMBER] NVIDIA RTX3080s or 3090s for servers? (Mon Sep 20 2021 - 08:20:07 PDT)
Lennart Gundelach
- [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P (Wed Sep 08 2021 - 04:33:36 PDT)
LEO LIM
- Re: [AMBER] Positional restraints in thermodynamic integration (Fri Sep 10 2021 - 04:58:53 PDT)
- [AMBER] Positional restraints in thermodynamic integration (Wed Sep 08 2021 - 01:40:48 PDT)
Liao
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? (Thu Sep 23 2021 - 20:19:00 PDT)
- Re: [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? (Thu Sep 23 2021 - 20:05:19 PDT)
- [AMBER] Question regarding LIE calculations vs explicit solvent enthalpy calculations? (Thu Sep 23 2021 - 12:36:55 PDT)
Matthew Guberman-Pfeffer
- [AMBER] Seeking advice on computing interaction energies (Mon Sep 27 2021 - 15:42:19 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 11:33:15 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 11:18:37 PDT)
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 09:28:33 PDT)
- [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 09:09:30 PDT)
- Re: [AMBER] Non-integer pbsa surface charge? (Thu Sep 16 2021 - 11:56:13 PDT)
- [AMBER] Non-integer pbsa surface charge? (Thu Sep 16 2021 - 01:14:16 PDT)
- Re: [AMBER] PARMED Charmber User Warning Quesiton (Tue Sep 14 2021 - 16:31:10 PDT)
- Re: [AMBER] How to compute pairwise interaction between masks (Mon Sep 13 2021 - 17:54:37 PDT)
- [AMBER] PARMED Charmber User Warning Quesiton (Mon Sep 13 2021 - 04:18:00 PDT)
- Re: [AMBER] How to compute pairwise interaction between masks (Mon Sep 13 2021 - 02:26:15 PDT)
- [AMBER] How to compute pairwise interaction between masks (Fri Sep 10 2021 - 14:26:27 PDT)
- Re: [AMBER] How to print out implicit solvent charges? (Wed Sep 08 2021 - 10:59:34 PDT)
- Re: [AMBER] How to print out implicit solvent charges? (Mon Sep 06 2021 - 02:53:29 PDT)
- [AMBER] How to print out implicit solvent charges? (Mon Sep 06 2021 - 00:33:02 PDT)
- [AMBER] Esander and multiple topologies (Thu Sep 02 2021 - 10:07:16 PDT)
- Re: [AMBER] Does AmberTools21 have parameters for I atom? (Wed Sep 01 2021 - 19:49:18 PDT)
- Re: [AMBER] Does AmberTools21 have parameters for I atom? (Wed Sep 01 2021 - 17:17:37 PDT)
Michael Shokhen
- Re: [AMBER] Problem with AMBER20 aMD tutorial (Wed Sep 22 2021 - 05:28:47 PDT)
- [AMBER] Problem with AMBER20 aMD tutorial (Wed Sep 15 2021 - 05:33:08 PDT)
Mike Mazanetz
- [AMBER] cpptraj has stopped working (Sun Sep 19 2021 - 13:57:17 PDT)
- Re: [AMBER] cpptraj has stopped working (Sun Sep 19 2021 - 00:39:15 PDT)
Ming Tang
- [AMBER] how to change residue number of several residues in AMBER trajectories (Thu Sep 02 2021 - 00:25:16 PDT)
- Re: [AMBER] Does AmberTools21 have parameters for I atom? (Wed Sep 01 2021 - 20:44:19 PDT)
- Re: [AMBER] Does AmberTools21 have parameters for I atom? (Wed Sep 01 2021 - 18:21:38 PDT)
- [AMBER] Does AmberTools21 have parameters for I atom? (Wed Sep 01 2021 - 17:05:07 PDT)
neildancer
- Re: [AMBER] How to set a replusive force between two drug molecules or two atoms. (Tue Sep 07 2021 - 02:23:09 PDT)
neildancer.sina.com
- [AMBER] How to combine the coordinate and parm7 files of the glycolipid into a protein complex system (Tue Sep 28 2021 - 20:47:14 PDT)
- [AMBER] 回复：Re: problem about the absolutely binding free energy calculation (Tue Sep 28 2021 - 20:21:27 PDT)
- [AMBER] problem about the absolutely binding free energy calculation (Mon Sep 27 2021 - 22:39:51 PDT)
Oscar Conchillo-Solé
- Re: [AMBER] Amber20 installation, Amber.pip file broken (Tue Sep 14 2021 - 05:08:08 PDT)
- Re: [AMBER] Amber20 installation, Amber.pip file broken (Mon Sep 13 2021 - 10:56:37 PDT)
- Re: [AMBER] Amber20 installation, Amber.pip file broken (Mon Sep 13 2021 - 04:53:52 PDT)
- Re: [AMBER] Amber20 installation, Amber.pip file broken (Mon Sep 13 2021 - 03:51:57 PDT)
Pengfei Li
- Re: [AMBER] How to set a replusive force between two drug molecules or two atoms. (Mon Sep 06 2021 - 16:14:05 PDT)
- Re: [AMBER] Maximum coordination exceeded (Mon Sep 06 2021 - 15:56:44 PDT)
- Re: [AMBER] how to set distance restraints in amber (Mon Sep 06 2021 - 15:48:17 PDT)
- Re: [AMBER] Suggestions for Mn3O4 (Mon Sep 06 2021 - 15:33:51 PDT)
- Re: [AMBER] iron-sulfur clusters parameters (Mon Sep 06 2021 - 15:29:47 PDT)
- Re: [AMBER] Problem with metalpdb2mol2.py script (Mon Sep 06 2021 - 15:18:34 PDT)
Priya Dey
- [AMBER] guv output file format (Fri Sep 10 2021 - 00:28:36 PDT)
Rafał Madaj
- [AMBER] TI in membrane system (Mon Sep 27 2021 - 01:22:36 PDT)
- [AMBER] Restart/Reference file for targeted MD (Tue Sep 21 2021 - 05:16:27 PDT)
Rana Rehan Khalid
- [AMBER] Use Amber12 with cuda (Thu Sep 16 2021 - 20:01:43 PDT)
Ray Luo
- Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P (Wed Sep 08 2021 - 08:31:04 PDT)
Reyes Nuñez Franco
- Re: [AMBER] GIST question (Thu Sep 23 2021 - 03:34:24 PDT)
- Re: [AMBER] GIST question (Wed Sep 15 2021 - 05:59:09 PDT)
- Re: [AMBER] GIST question (Mon Sep 13 2021 - 03:23:59 PDT)
- [AMBER] GIST question (Wed Sep 08 2021 - 09:24:25 PDT)
Reza Esmaeeli
- Re: [AMBER] Atom type of NO does not shown up in PARMCHK.DAT (Wed Sep 29 2021 - 10:26:57 PDT)
- [AMBER] Atom type of NO does not shown up in PARMCHK.DAT (Tue Sep 28 2021 - 11:38:31 PDT)
Rodrigo da Silva Bitzer
- Re: [AMBER] Error installing amber macOS M1 (Thu Sep 30 2021 - 14:06:08 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Thu Sep 30 2021 - 10:16:56 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Tue Sep 28 2021 - 13:39:17 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Tue Sep 28 2021 - 10:55:55 PDT)
- Re: [AMBER] Error installing amber macOS M1 (Fri Sep 24 2021 - 15:33:19 PDT)
- [AMBER] Error installing amber macOS M1 (Thu Sep 23 2021 - 12:50:29 PDT)
- Re: [AMBER] Error while running make install (Fri Sep 17 2021 - 05:23:31 PDT)
- [AMBER] Error while running make install (Thu Sep 16 2021 - 15:50:50 PDT)
Rohanizeidanlou, Sahar
- [AMBER] [Amber] gbnsr6 doesn't calculate VDWAALS (Sun Sep 12 2021 - 12:57:44 PDT)
Ryan Novosielski
- Re: [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 (Sun Sep 19 2021 - 13:19:05 PDT)
- Re: [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 (Sun Sep 19 2021 - 12:39:10 PDT)
- [AMBER] Setting compiler flags w/cmake build? Amber20/AmberTools21 (Sat Sep 18 2021 - 16:41:49 PDT)
- [AMBER] ambermd.org SSL Certificate (Wed Sep 15 2021 - 08:44:58 PDT)
Sadaf Rani
- [AMBER] How to set up a simulation keeping crystal waters in the binding site (Wed Sep 22 2021 - 08:00:12 PDT)
- [AMBER] ModuleNotFoundError: No module named 'alamdcrd' (Thu Sep 09 2021 - 07:13:43 PDT)
Satya Pal Singh
- [AMBER] Problem in installing AMBER 20 Ubantu ; configuring molecules from own data obtained from Gaussian (Tue Sep 28 2021 - 22:18:11 PDT)
Song, Lin
- Re: [AMBER] problem about the absolutely binding free energy calculation (Tue Sep 28 2021 - 12:43:33 PDT)
Stephan Schott
- Re: [AMBER] Lipid21 (Thu Sep 16 2021 - 01:09:52 PDT)
Thomas Cheatham
- Re: [AMBER] Can a PDB be loaded directly into cpptraj without a topology? (Sat Sep 25 2021 - 11:23:30 PDT)
Veenis, Andrew Jay
- [AMBER] Cpptraj hbond criteria (Wed Sep 22 2021 - 11:03:40 PDT)
vivek rabha
- [AMBER] Amber20 installation (Mon Sep 27 2021 - 03:33:28 PDT)
wangwei1669
- [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Sat Sep 04 2021 - 01:03:23 PDT)
wangwei1669
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Wed Sep 08 2021 - 17:56:42 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Tue Sep 07 2021 - 20:44:06 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Sun Sep 05 2021 - 06:39:05 PDT)
- Re: [AMBER] A problem about periodic box dimensions happens to Tutorial 1.7 (Sun Sep 05 2021 - 01:49:14 PDT)
yinchaofan
- [AMBER] antechamber raises Segmetation fault (Wed Sep 08 2021 - 04:42:12 PDT)
东庚
- [AMBER] parmed for 12-6-4 LJ (Geng Dong) (Tue Sep 28 2021 - 02:07:03 PDT)
- [AMBER] parmed for 12-6-4 LJ (Geng Dong) (Sun Sep 26 2021 - 02:28:46 PDT)
库米尔
- [AMBER] Hydrogen atoms with negative RESP charges from Antechamber (Thu Sep 02 2021 - 08:23:24 PDT)
임호철
- [AMBER] Positional restraints in thermodynamic integration (Tue Sep 07 2021 - 06:35:53 PDT)

Amber Archive Sep 2021 by author