Amber Archive Sep 2021: by subject

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

Amber Archive Sep 2021 by subject