Amber Archive Oct 2017: by subject

[AMBER] (no subject)
- Hossein Geraili (Thu Oct 05 2017 - 02:20:22 PDT)
[AMBER] about Paramfit
- Albert (Fri Oct 06 2017 - 23:59:56 PDT)
- Robin Betz (Fri Oct 06 2017 - 14:22:43 PDT)
- Albert (Fri Oct 06 2017 - 14:03:21 PDT)
[AMBER] About paramfit 1-4 scaling
- David Cerutti (Wed Oct 25 2017 - 13:08:09 PDT)
- Arun Srikanth (Tue Oct 24 2017 - 17:47:18 PDT)
[AMBER] About penalty scores
- Arun Srikanth (Tue Oct 24 2017 - 07:29:15 PDT)
- David A Case (Tue Oct 24 2017 - 05:09:55 PDT)
- Arun Srikanth (Mon Oct 23 2017 - 17:02:08 PDT)
[AMBER] AM1-BCC for charge derivation
- Shilpa Gupta (Sun Oct 29 2017 - 12:22:40 PDT)
[AMBER] AMBER
- Chris Moth (Thu Oct 05 2017 - 05:16:11 PDT)
- Hossein Geraili (Thu Oct 05 2017 - 02:44:50 PDT)
[AMBER] Amber16 electric field parameters
- Pengfei Li (Thu Oct 05 2017 - 18:15:47 PDT)
- Pengfei Li (Tue Oct 03 2017 - 19:10:00 PDT)
- Ross Walker (Mon Oct 02 2017 - 06:52:14 PDT)
- David A Case (Mon Oct 02 2017 - 06:46:12 PDT)
- Alessandro Mariani (Mon Oct 02 2017 - 01:18:57 PDT)
[AMBER] AMBER16 parallelisation and fftw3 error
- Shirin Jamshidi (Fri Oct 06 2017 - 14:45:02 PDT)
- Hai Nguyen (Fri Oct 06 2017 - 14:25:32 PDT)
- Shirin Jamshidi (Fri Oct 06 2017 - 06:37:20 PDT)
- David A Case (Fri Oct 06 2017 - 05:08:24 PDT)
- Shirin Jamshidi (Fri Oct 06 2017 - 04:24:57 PDT)
- Hai Nguyen (Thu Oct 05 2017 - 15:57:17 PDT)
- Shirin Jamshidi (Thu Oct 05 2017 - 15:24:08 PDT)
- Hai Nguyen (Thu Oct 05 2017 - 15:20:47 PDT)
- Shirin Jamshidi (Thu Oct 05 2017 - 14:41:57 PDT)
[AMBER] AmberTools17 and shape.h
- Christopher Benjamin Coffey (Fri Oct 06 2017 - 11:01:03 PDT)
- Hai Nguyen (Thu Oct 05 2017 - 17:28:56 PDT)
- Bill Ross (Thu Oct 05 2017 - 16:53:21 PDT)
- Bill Ross (Thu Oct 05 2017 - 16:51:02 PDT)
- Christopher Benjamin Coffey (Thu Oct 05 2017 - 16:26:09 PDT)
- David A Case (Thu Oct 05 2017 - 10:53:04 PDT)
- Christopher Benjamin Coffey (Thu Oct 05 2017 - 07:11:55 PDT)
[AMBER] APR method in CHCl3
- Jian Yin (Fri Oct 20 2017 - 14:02:53 PDT)
- Jian Yin (Wed Oct 18 2017 - 13:51:34 PDT)
- Maura Malinska (Wed Oct 18 2017 - 09:34:01 PDT)
[AMBER] Are RNA with ligand system and a GB neck2 protocol compatible
- Hai Nguyen (Tue Oct 24 2017 - 19:31:20 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Tue Oct 24 2017 - 10:57:29 PDT)
[AMBER] barostat with large coupling constant
- Jason Swails (Wed Oct 04 2017 - 12:58:20 PDT)
- R zu (Wed Oct 04 2017 - 09:16:53 PDT)
- R zu (Wed Oct 04 2017 - 08:49:22 PDT)
- Jason Swails (Sun Oct 01 2017 - 20:37:57 PDT)
[AMBER] Bias Towards the Periodic Boundary
- Timothy Schutt (Wed Oct 18 2017 - 13:11:43 PDT)
- David A Case (Wed Oct 18 2017 - 13:03:02 PDT)
- Adrian Roitberg (Wed Oct 18 2017 - 11:22:01 PDT)
- Timothy Schutt (Wed Oct 18 2017 - 10:37:56 PDT)
[AMBER] Binding affinity of different small molecules to a complex of metal + protein + DNA
- Thomas Cheatham (Fri Oct 27 2017 - 15:20:03 PDT)
- Elvis Martis (Fri Oct 27 2017 - 08:06:07 PDT)
- Alonso Martinez, Diego (Fri Oct 27 2017 - 06:17:57 PDT)
[AMBER] Can we use OPLS force field in AMBER
- Jason Swails (Fri Oct 27 2017 - 04:56:54 PDT)
- Bill Ross (Wed Oct 25 2017 - 00:11:27 PDT)
- Shilpa Gupta (Tue Oct 24 2017 - 21:06:17 PDT)
- Bill Ross (Tue Oct 24 2017 - 07:01:47 PDT)
- Shilpa Gupta (Tue Oct 24 2017 - 06:57:11 PDT)
- David A Case (Tue Oct 24 2017 - 06:34:59 PDT)
- Shilpa Gupta (Tue Oct 24 2017 - 05:35:52 PDT)
[AMBER] Cannot create Ru-ligands bonds using genMetalFF.sh
- Sanaa ALAbbad (Thu Oct 19 2017 - 06:39:47 PDT)
- Sanaa ALAbbad (Wed Oct 18 2017 - 17:14:09 PDT)
- Pengfei Li (Wed Oct 18 2017 - 09:21:34 PDT)
- Pengfei Li (Wed Oct 18 2017 - 09:19:19 PDT)
- Sanaa ALAbbad (Tue Oct 17 2017 - 16:10:44 PDT)
[AMBER] Center of mass restraint on GPU?
- Lin Song (Fri Oct 20 2017 - 11:39:59 PDT)
- Ross Walker (Fri Oct 20 2017 - 10:28:31 PDT)
- Lin Song (Fri Oct 20 2017 - 08:12:50 PDT)
[AMBER] chamber is unavailable from terminal MacOS
- Hai Nguyen (Fri Oct 06 2017 - 15:31:18 PDT)
- Sundar (Fri Oct 06 2017 - 15:02:47 PDT)
[AMBER] colvar in string methods
- Chunli Yan (Wed Oct 04 2017 - 20:51:16 PDT)
- Feng Pan (Wed Oct 04 2017 - 20:33:26 PDT)
- Chunli Yan (Wed Oct 04 2017 - 19:57:27 PDT)
[AMBER] Constant pH Explicit Solvent
- Pacheco, Sayuri (Wed Oct 04 2017 - 18:22:18 PDT)
[AMBER] Constant temperature is not constant from the beginning
- David Sáez (Tue Oct 31 2017 - 14:31:22 PDT)
- Bill Ross (Mon Oct 30 2017 - 22:16:08 PDT)
- David Sáez (Mon Oct 30 2017 - 21:32:29 PDT)
[AMBER] contributing code
- Holger Kruse (Tue Oct 31 2017 - 06:19:43 PDT)
[AMBER] Converting atom names from NAMD to AMBER
- Bill Ross (Fri Oct 13 2017 - 13:36:55 PDT)
- Daniel Roe (Fri Oct 13 2017 - 10:32:16 PDT)
- Eiros Zamora, Juan (Fri Oct 13 2017 - 10:10:54 PDT)
[AMBER] Cpptraj HBond salt bridge output question
- Amy Rice (Wed Oct 25 2017 - 08:57:15 PDT)
- Daniel Roe (Wed Oct 25 2017 - 08:39:56 PDT)
- Amy Rice (Wed Oct 25 2017 - 08:22:27 PDT)
[AMBER] CUDA 9
- Scott Le Grand (Tue Oct 31 2017 - 12:36:33 PDT)
- Ross Walker (Tue Oct 31 2017 - 10:53:58 PDT)
- Weinzierl, Robert O J (Tue Oct 31 2017 - 10:11:52 PDT)
[AMBER] Current rmsd from reference in targeted MD
- Sonia Ziada (Wed Oct 04 2017 - 08:16:55 PDT)
- Carlos Simmerling (Wed Oct 04 2017 - 06:04:55 PDT)
- Sonia Ziada (Wed Oct 04 2017 - 05:45:34 PDT)
- Carlos Simmerling (Wed Oct 04 2017 - 05:38:13 PDT)
- Sonia Ziada (Wed Oct 04 2017 - 05:25:36 PDT)
- Carlos Simmerling (Wed Oct 04 2017 - 03:30:59 PDT)
- Sonia Ziada (Wed Oct 04 2017 - 00:10:11 PDT)
- Hai Nguyen (Tue Oct 03 2017 - 16:22:38 PDT)
- Sonia Ziada (Tue Oct 03 2017 - 14:05:04 PDT)
- Carlos Simmerling (Tue Oct 03 2017 - 09:44:00 PDT)
- Sonia Ziada (Tue Oct 03 2017 - 04:36:33 PDT)
[AMBER] difficulty reading a frcmod file in amber
- Elvis Martis (Mon Oct 23 2017 - 02:24:27 PDT)
- Eugene Cha (Sun Oct 22 2017 - 23:41:42 PDT)
[AMBER] disulfide bonds braking during MD simulation
- Michael Shokhen (Mon Oct 30 2017 - 05:23:00 PDT)
- Michael Shokhen (Wed Oct 25 2017 - 14:05:50 PDT)
- Carlos Simmerling (Wed Oct 25 2017 - 13:56:03 PDT)
- Bill Ross (Wed Oct 25 2017 - 13:33:06 PDT)
- Adrian Roitberg (Wed Oct 25 2017 - 13:31:58 PDT)
- Michael Shokhen (Wed Oct 25 2017 - 13:26:36 PDT)
- Carlos Simmerling (Wed Oct 25 2017 - 12:59:28 PDT)
- Michael Shokhen (Wed Oct 25 2017 - 12:39:14 PDT)
- Michael Shokhen (Wed Oct 25 2017 - 11:51:29 PDT)
- Carlos Simmerling (Wed Oct 25 2017 - 11:44:55 PDT)
- Michael Shokhen (Wed Oct 25 2017 - 11:37:47 PDT)
- David A Case (Tue Oct 24 2017 - 17:39:09 PDT)
- Michael Shokhen (Tue Oct 24 2017 - 08:50:17 PDT)
- Carlos Simmerling (Tue Oct 24 2017 - 08:07:21 PDT)
- Michael Shokhen (Tue Oct 24 2017 - 07:59:52 PDT)
[AMBER] DPPG lipid bilayer simulation using Lipid17 - too small area per lipid ?
- Marek Maly (Wed Oct 04 2017 - 16:44:02 PDT)
- Batuhan Kav (Wed Oct 04 2017 - 11:41:43 PDT)
- Marek Maly (Tue Oct 03 2017 - 08:52:41 PDT)
[AMBER] Dr. Nick Riviera
- Junmei Wang (Thu Oct 05 2017 - 08:47:29 PDT)
[AMBER] Dummy Atoms in CP
- Paul Freidhoff (Thu Oct 19 2017 - 06:34:57 PDT)
[AMBER] effect of MPI problem on MD calculations
- Bill Ross (Fri Oct 20 2017 - 10:05:29 PDT)
- David A Case (Fri Oct 20 2017 - 05:21:48 PDT)
- sangita kachhap (Fri Oct 20 2017 - 01:25:20 PDT)
[AMBER] Error Due to Duplicate residues atoms
- Rana Rehan Khalid (Sat Oct 28 2017 - 09:31:48 PDT)
- David A Case (Fri Oct 27 2017 - 12:15:49 PDT)
- Rana Rehan Khalid (Fri Oct 27 2017 - 11:15:16 PDT)
[AMBER] Error in calculating MM-PBSA
- David A Case (Sun Oct 29 2017 - 05:14:01 PDT)
- Elvis Martis (Sun Oct 29 2017 - 03:34:10 PDT)
- Mustafa Alhaji Isa (Sun Oct 29 2017 - 01:11:59 PDT)
[AMBER] Error in preparation of Zn.lib
- Pengfei Li (Fri Oct 06 2017 - 07:45:49 PDT)
- Anton Perera (Fri Oct 06 2017 - 01:12:44 PDT)
[AMBER] Error reading Ruthenium complex residue
- Sanaa ALAbbad (Fri Oct 13 2017 - 06:18:03 PDT)
- Pengfei Li (Thu Oct 12 2017 - 19:47:11 PDT)
- Bill Ross (Thu Oct 12 2017 - 14:57:24 PDT)
- Sanaa ALAbbad (Thu Oct 12 2017 - 09:56:11 PDT)
- Szymon Żaczek (Thu Oct 12 2017 - 09:51:35 PDT)
- Sanaa ALAbbad (Thu Oct 12 2017 - 08:27:17 PDT)
[AMBER] error with restraint distance minimization
- Michael Shokhen (Wed Oct 25 2017 - 09:31:00 PDT)
- Adrian Roitberg (Wed Oct 25 2017 - 09:08:57 PDT)
- Michael Shokhen (Wed Oct 25 2017 - 09:02:52 PDT)
[AMBER] force distribution analysis and Ewald
- David Cerutti (Tue Oct 03 2017 - 19:09:42 PDT)
- Jason Swails (Tue Oct 03 2017 - 12:37:44 PDT)
- Thomas Pochapsky (Tue Oct 03 2017 - 11:57:01 PDT)
[AMBER] Force field parameters for Magnesium and Calcium in Amber
- David A Case (Fri Oct 20 2017 - 05:26:40 PDT)
- Nadine Schwierz-Neumann (Fri Oct 20 2017 - 03:35:06 PDT)
[AMBER] Forecefield error
- Carlos Simmerling (Wed Oct 25 2017 - 03:40:25 PDT)
- Arthi Venkat (Tue Oct 24 2017 - 20:30:39 PDT)
- Hai Nguyen (Tue Oct 24 2017 - 20:20:26 PDT)
- Arthi Venkat (Tue Oct 24 2017 - 20:16:41 PDT)
- Hai Nguyen (Tue Oct 24 2017 - 20:09:53 PDT)
- Arthi Venkat (Tue Oct 24 2017 - 20:05:28 PDT)
[AMBER] frozen atoms.
- Cruzeiro,Vinicius Wilian D (Fri Oct 27 2017 - 12:30:14 PDT)
- David A Case (Fri Oct 27 2017 - 12:23:44 PDT)
- danilo gonzalez (Fri Oct 27 2017 - 11:40:25 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Oct 27 2017 - 09:28:32 PDT)
- danilo gonzalez (Fri Oct 27 2017 - 09:14:30 PDT)
[AMBER] Fwd: Error with AMBER/Charmm-GUI output
- Mac Kevin Braza (Mon Oct 09 2017 - 22:57:59 PDT)
- Mac Kevin Braza (Mon Oct 09 2017 - 22:57:33 PDT)
[AMBER] Generating a dimer starting from monomers using MD
- jacob wick (Thu Oct 05 2017 - 05:47:40 PDT)
- Karl Kirschner (Thu Oct 05 2017 - 03:57:46 PDT)
- jacob wick (Thu Oct 05 2017 - 02:26:48 PDT)
[AMBER] getting MC barostat to print less
- Smith, Louis (Thu Oct 12 2017 - 22:14:25 PDT)
- Jason Swails (Thu Oct 12 2017 - 19:36:26 PDT)
- Smith, Louis (Wed Oct 11 2017 - 21:36:58 PDT)
[AMBER] help for the installation of Ambertools 17 on Mac
- Andrew Schaub (Mon Oct 16 2017 - 14:42:49 PDT)
- David A Case (Fri Oct 13 2017 - 05:08:18 PDT)
- huangwc8 (Thu Oct 12 2017 - 22:40:50 PDT)
[AMBER] How to add the deprotonated SER residue to the ff14SB leap library?
- Michael Shokhen (Mon Oct 23 2017 - 06:51:58 PDT)
- David A Case (Thu Oct 19 2017 - 09:06:36 PDT)
- Cruzeiro,Vinicius Wilian D (Thu Oct 19 2017 - 07:28:38 PDT)
- Michael Shokhen (Thu Oct 19 2017 - 07:27:17 PDT)
- Carlos Simmerling (Thu Oct 19 2017 - 06:46:13 PDT)
- Pietro Aronica (Thu Oct 19 2017 - 06:44:17 PDT)
- Michael Shokhen (Thu Oct 19 2017 - 05:42:38 PDT)
[AMBER] how to generated data for plot?
- Albert (Wed Oct 25 2017 - 11:50:18 PDT)
- Daniel Roe (Fri Oct 20 2017 - 06:39:31 PDT)
- Albert (Fri Oct 20 2017 - 04:17:17 PDT)
[AMBER] How to put anchor_position for RMSD collective variable Value in string methods
- Chunli Yan (Fri Oct 13 2017 - 09:37:00 PDT)
- Feng Pan (Fri Oct 13 2017 - 09:06:52 PDT)
- Chunli Yan (Mon Oct 09 2017 - 05:45:01 PDT)
[AMBER] How to save reimaged trajectory file during MD?
- Daniel Roe (Mon Oct 02 2017 - 06:05:16 PDT)
[AMBER] How to show double bond connection between N=O2
- Bill Ross (Sat Oct 14 2017 - 15:47:40 PDT)
- Rana Rehan Khalid (Sat Oct 14 2017 - 07:31:29 PDT)
[AMBER] how we can visualized the bonds after saving on of the MD frame into pdb file.
- Bill Ross (Thu Oct 19 2017 - 12:06:43 PDT)
- Rana Rehan Khalid (Thu Oct 19 2017 - 11:22:46 PDT)
- Carlos Simmerling (Thu Oct 19 2017 - 11:19:00 PDT)
- Rana Rehan Khalid (Thu Oct 19 2017 - 11:16:51 PDT)
[AMBER] Hydrogen Bond
- Daniel Roe (Tue Oct 10 2017 - 12:16:35 PDT)
- ATUL KUMAR (Mon Oct 09 2017 - 05:48:23 PDT)
- ATUL KUMAR (Mon Oct 09 2017 - 04:54:07 PDT)
[AMBER] hydrogenbond calculations
- Hai Nguyen (Sun Oct 22 2017 - 21:53:36 PDT)
- megha vaishnavi (Sun Oct 22 2017 - 20:11:44 PDT)
[AMBER] identiy the step of interaction from an entire trajectory
- Daniel Roe (Mon Oct 02 2017 - 05:55:48 PDT)
[AMBER] Independent MD runs
- Chris Neale (Wed Oct 04 2017 - 22:30:01 PDT)
- Elvis Martis (Wed Oct 04 2017 - 21:58:33 PDT)
- colvin (Wed Oct 04 2017 - 20:11:19 PDT)
[AMBER] Independent production runs
- Lizelle Lubbe (Fri Oct 20 2017 - 05:44:53 PDT)
- Carlos Simmerling (Fri Oct 20 2017 - 05:08:22 PDT)
- Lizelle Lubbe (Fri Oct 20 2017 - 04:28:34 PDT)
[AMBER] Is it possible to simulate Indium (coupled with sulpher and copper) nano material in amber?
- David A Case (Tue Oct 03 2017 - 10:15:49 PDT)
- Charles Mariasoosai (Tue Oct 03 2017 - 09:33:25 PDT)
[AMBER] leaprc.constph and ff14sb
- Jason Swails (Sun Oct 01 2017 - 20:29:41 PDT)
[AMBER] making 6M GDMCl box
- Bill Ross (Thu Oct 12 2017 - 12:06:25 PDT)
- ATUL KUMAR (Thu Oct 12 2017 - 03:34:07 PDT)
- Bill Ross (Thu Oct 12 2017 - 03:02:03 PDT)
- ATUL KUMAR (Thu Oct 12 2017 - 02:58:08 PDT)
[AMBER] MCPB.py issue - add_bonded_pairs
- Pengfei Li (Thu Oct 12 2017 - 19:53:18 PDT)
- Szymon Żaczek (Mon Oct 09 2017 - 13:00:18 PDT)
- Miha Purg (Mon Oct 09 2017 - 10:53:04 PDT)
- Szymon Żaczek (Mon Oct 09 2017 - 08:37:38 PDT)
[AMBER] mdfrc for a single ion in vacuum
- David A Case (Fri Oct 13 2017 - 13:43:55 PDT)
- William Marquardt (Fri Oct 13 2017 - 11:24:46 PDT)
[AMBER] Metal site hybrid bonded model
- Lizelle Lubbe (Fri Oct 13 2017 - 05:45:30 PDT)
[AMBER] MM-PBSA calculation
- Elvis Martis (Fri Oct 27 2017 - 08:53:02 PDT)
- Mustafa Alhaji Isa (Fri Oct 27 2017 - 08:22:33 PDT)
[AMBER] MM/PBSA or MM/GBSA
- Alessandro Contini (Wed Oct 25 2017 - 00:03:03 PDT)
- sangita kachhap (Tue Oct 24 2017 - 12:46:57 PDT)
- Alessandro Contini (Tue Oct 24 2017 - 08:06:50 PDT)
- sangita kachhap (Tue Oct 24 2017 - 07:00:07 PDT)
- Carlos Simmerling (Tue Oct 24 2017 - 06:51:48 PDT)
- sangita kachhap (Tue Oct 24 2017 - 06:47:21 PDT)
[AMBER] MMPBSA error
- Ray Luo (Wed Oct 11 2017 - 07:58:55 PDT)
- sangita kachhap (Wed Oct 11 2017 - 03:37:25 PDT)
- Ray Luo (Mon Oct 09 2017 - 20:20:37 PDT)
- sangita kachhap (Mon Oct 09 2017 - 07:27:26 PDT)
[AMBER] net charge problem of Amber Lipid14 Force Field
- Bill Ross (Thu Oct 05 2017 - 16:08:48 PDT)
- Bill Ross (Thu Oct 05 2017 - 15:56:08 PDT)
- Xibing He (Thu Oct 05 2017 - 15:03:47 PDT)
[AMBER] output file .out file deleted mistakenly
- Daniel Roe (Thu Oct 12 2017 - 06:02:55 PDT)
- Bill Ross (Wed Oct 11 2017 - 11:15:25 PDT)
- Rana Rehan Khalid (Wed Oct 11 2017 - 11:13:49 PDT)
- Bill Ross (Wed Oct 11 2017 - 11:06:30 PDT)
- Bill Ross (Wed Oct 11 2017 - 11:04:25 PDT)
- Rana Rehan Khalid (Wed Oct 11 2017 - 10:35:48 PDT)
[AMBER] parmed.py and xparmed.py problem
- Michael Shokhen (Fri Oct 27 2017 - 06:40:18 PDT)
- mirzo (Fri Oct 27 2017 - 06:36:29 PDT)
- Hai Nguyen (Fri Oct 27 2017 - 06:06:06 PDT)
- Michael Shokhen (Fri Oct 27 2017 - 05:58:50 PDT)
[AMBER] parmstrip with cpptraj in Ambertools 17
- Daniel Roe (Fri Oct 13 2017 - 09:54:59 PDT)
- Li, Wen (Fri Oct 13 2017 - 08:48:54 PDT)
- Daniel Roe (Fri Oct 13 2017 - 07:25:43 PDT)
- Daniel Roe (Thu Oct 12 2017 - 17:35:39 PDT)
- Li, Wen (Thu Oct 12 2017 - 10:12:37 PDT)
[AMBER] PB Bomb in pb_aaradi()
- Urszula Uciechowska (Tue Oct 31 2017 - 06:41:15 PDT)
[AMBER] pdb4amber bug - incorrect "CONECT" between chains
- Hai Nguyen (Tue Oct 31 2017 - 06:12:11 PDT)
- Daniel Roe (Tue Oct 31 2017 - 06:07:05 PDT)
- Hai Nguyen (Tue Oct 31 2017 - 05:39:30 PDT)
- David A Case (Tue Oct 31 2017 - 05:12:23 PDT)
- Hai Nguyen (Mon Oct 30 2017 - 20:21:27 PDT)
- Hai Nguyen (Mon Oct 30 2017 - 19:46:32 PDT)
- Diego Gomes (Mon Oct 30 2017 - 10:49:33 PDT)
[AMBER] pmemd.cuda and rigid CH2Cl2
- David A Case (Sat Oct 14 2017 - 06:35:17 PDT)
- Alain Chaumont (Tue Oct 10 2017 - 04:31:12 PDT)
[AMBER] positional restraint to optimize crystal structure
- M P (Mon Oct 30 2017 - 04:12:40 PDT)
[AMBER] positive electrostatic energy
- Sharon D. Morris (Mon Oct 30 2017 - 03:35:18 PDT)
[AMBER] Possible concerns regarding future availability of cost effective NVIDIA GPU systems for running AMBER
- Scott Le Grand (Tue Oct 31 2017 - 08:30:51 PDT)
- Marek Maly (Mon Oct 30 2017 - 18:15:10 PDT)
- Dow Hurst (Mon Oct 30 2017 - 16:10:34 PDT)
- Bill Ross (Mon Oct 30 2017 - 14:57:33 PDT)
- Gerald Monard (Mon Oct 30 2017 - 14:29:33 PDT)
- Bill Ross (Mon Oct 30 2017 - 14:10:45 PDT)
- David Cerutti (Mon Oct 30 2017 - 13:21:06 PDT)
- Robert Molt (Mon Oct 30 2017 - 12:59:43 PDT)
- Scott Le Grand (Mon Oct 30 2017 - 12:29:30 PDT)
- Ross Walker (Mon Oct 30 2017 - 11:57:47 PDT)
[AMBER] problem with AMBER TUTORIAL A1
- David A Case (Sat Oct 14 2017 - 06:31:18 PDT)
- Michael Shokhen (Fri Oct 13 2017 - 05:27:12 PDT)
[AMBER] Problem with charges - Unable to recover LYS charges from AmberFF
- Nicolas Cheron (Mon Oct 16 2017 - 00:50:46 PDT)
- David A Case (Wed Oct 11 2017 - 05:38:32 PDT)
- Nicolas Cheron (Wed Oct 11 2017 - 03:13:59 PDT)
[AMBER] problem with TUTORAL C5: Hydrogen Bond Analysis with CPPTRAJ
- Setyanto Md (Mon Oct 30 2017 - 07:07:55 PDT)
- Rodrigo Galindo-Murillo (Mon Oct 30 2017 - 06:25:58 PDT)
- Setyanto Md (Mon Oct 30 2017 - 05:16:23 PDT)
[AMBER] Protein drift from solvent box
- Daniel Roe (Fri Oct 20 2017 - 11:43:08 PDT)
- Lizelle Lubbe (Fri Oct 20 2017 - 01:13:38 PDT)
- Lizelle Lubbe (Thu Oct 19 2017 - 09:14:32 PDT)
- David A Case (Thu Oct 19 2017 - 09:11:11 PDT)
- Lizelle Lubbe (Thu Oct 19 2017 - 07:58:51 PDT)
- Bill Ross (Thu Oct 19 2017 - 07:29:39 PDT)
- Thakur, Abhishek (Thu Oct 19 2017 - 07:06:42 PDT)
- Lizelle Lubbe (Thu Oct 19 2017 - 05:44:48 PDT)
[AMBER] PyRed
- FyD (Mon Oct 02 2017 - 23:10:11 PDT)
[AMBER] query regarding the restart file of molecular dynamics simulation
- David A Case (Mon Oct 16 2017 - 05:03:23 PDT)
- Leena Aggarwal (Mon Oct 16 2017 - 03:50:44 PDT)
- Bill Ross (Sun Oct 15 2017 - 23:25:21 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 23:23:08 PDT)
- Bill Ross (Sun Oct 15 2017 - 23:18:32 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 23:15:29 PDT)
- Bill Ross (Sun Oct 15 2017 - 23:11:06 PDT)
- Bill Ross (Sun Oct 15 2017 - 23:09:37 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 23:08:20 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 23:07:56 PDT)
- Bill Ross (Sun Oct 15 2017 - 22:48:17 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 22:46:11 PDT)
- Bill Ross (Sun Oct 15 2017 - 22:38:23 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 22:37:01 PDT)
- Bill Ross (Sun Oct 15 2017 - 22:29:02 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 22:26:53 PDT)
- Bill Ross (Sun Oct 15 2017 - 22:12:03 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 22:06:56 PDT)
- Bill Ross (Sun Oct 15 2017 - 21:41:18 PDT)
- Leena Aggarwal (Sun Oct 15 2017 - 21:38:15 PDT)
- Elvis Martis (Fri Oct 13 2017 - 01:01:54 PDT)
- Bill Ross (Thu Oct 12 2017 - 22:52:13 PDT)
- Leena Aggarwal (Thu Oct 12 2017 - 22:49:18 PDT)
- Elvis Martis (Thu Oct 12 2017 - 06:59:13 PDT)
- Leena Aggarwal (Thu Oct 12 2017 - 05:12:51 PDT)
- Bill Ross (Thu Oct 12 2017 - 02:11:08 PDT)
- Leena Aggarwal (Thu Oct 12 2017 - 02:00:28 PDT)
- Bill Ross (Wed Oct 11 2017 - 21:27:32 PDT)
- Leena Aggarwal (Wed Oct 11 2017 - 21:24:17 PDT)
- Bill Ross (Wed Oct 11 2017 - 10:31:45 PDT)
- Elvis Martis (Wed Oct 11 2017 - 02:25:21 PDT)
- Leena Aggarwal (Wed Oct 11 2017 - 01:04:09 PDT)
- Elvis Martis (Wed Oct 11 2017 - 00:33:43 PDT)
- Leena Aggarwal (Wed Oct 11 2017 - 00:11:12 PDT)
- Leena Aggarwal (Wed Oct 11 2017 - 00:09:08 PDT)
- Bill Ross (Wed Oct 11 2017 - 00:05:25 PDT)
- Leena Aggarwal (Wed Oct 11 2017 - 00:03:36 PDT)
- Bill Ross (Tue Oct 10 2017 - 23:05:47 PDT)
- Leena Aggarwal (Tue Oct 10 2017 - 21:17:59 PDT)
- Bill Ross (Tue Oct 10 2017 - 08:05:03 PDT)
- David A Case (Tue Oct 10 2017 - 06:55:29 PDT)
- Leena Aggarwal (Tue Oct 10 2017 - 06:47:19 PDT)
- Elvis Martis (Tue Oct 10 2017 - 06:09:39 PDT)
- Leena Aggarwal (Tue Oct 10 2017 - 05:40:03 PDT)
[AMBER] Question on GPUs and OS
- George Tzotzos (Mon Oct 16 2017 - 11:28:00 PDT)
- Hai Nguyen (Mon Oct 16 2017 - 11:20:50 PDT)
- George Tzotzos (Mon Oct 16 2017 - 11:15:38 PDT)
[AMBER] Question regarding protonated CP in pH dependent REMD
- Paul Freidhoff (Mon Oct 09 2017 - 09:04:09 PDT)
[AMBER] reference for long-range van der Waals interactions
- Wook Lee (Thu Oct 26 2017 - 08:16:06 PDT)
[AMBER] REMD job failed
- Daniel Roe (Tue Oct 10 2017 - 10:15:37 PDT)
- Albert (Tue Oct 10 2017 - 07:44:56 PDT)
- Cruzeiro,Vinicius Wilian D (Tue Oct 10 2017 - 07:41:03 PDT)
- Albert (Tue Oct 10 2017 - 07:34:32 PDT)
[AMBER] RESP charges for a peptide-bound probe with R.E.D.
- Seth Axen (Tue Oct 17 2017 - 08:54:39 PDT)
- Andrew Schaub (Mon Oct 16 2017 - 17:15:44 PDT)
- Seth Axen (Mon Oct 16 2017 - 16:00:30 PDT)
[AMBER] Restarting pH-REMD simulations after abnormal termination
- Eric Lang (Fri Oct 13 2017 - 09:11:32 PDT)
- Cruzeiro,Vinicius Wilian D (Fri Oct 13 2017 - 07:07:18 PDT)
- Eric Lang (Thu Oct 12 2017 - 06:55:28 PDT)
[AMBER] Restarting REMD
- Andreas Tosstorff (Fri Oct 13 2017 - 03:43:02 PDT)
- Carlos Simmerling (Fri Oct 13 2017 - 03:34:15 PDT)
- Andreas Tosstorff (Fri Oct 13 2017 - 01:17:37 PDT)
- Andreas Tosstorff (Fri Oct 13 2017 - 01:13:54 PDT)
[AMBER] restraint_wt applied to wrong atoms
- sangita kachhap (Mon Oct 30 2017 - 06:02:50 PDT)
- Carlos Simmerling (Mon Oct 30 2017 - 05:22:20 PDT)
- sangita kachhap (Mon Oct 30 2017 - 05:14:11 PDT)
[AMBER] RNA with ligand - a follow-up ANTECHAMBER question
- Junmei Wang (Thu Oct 26 2017 - 08:51:43 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Thu Oct 26 2017 - 08:10:22 PDT)
- David A Case (Wed Oct 25 2017 - 19:35:50 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 25 2017 - 14:00:06 PDT)
[AMBER] Running Explicit pH MD
- Cruzeiro,Vinicius Wilian D (Mon Oct 30 2017 - 08:24:00 PDT)
- Pacheco, Sayuri (Mon Oct 30 2017 - 08:20:52 PDT)
- Cruzeiro,Vinicius Wilian D (Mon Oct 30 2017 - 08:14:03 PDT)
- Pacheco, Sayuri (Mon Oct 30 2017 - 07:31:36 PDT)
- Pacheco, Sayuri (Tue Oct 24 2017 - 21:54:54 PDT)
- Adrian Roitberg (Mon Oct 16 2017 - 08:31:03 PDT)
- Pacheco, Sayuri (Mon Oct 16 2017 - 08:26:33 PDT)
[AMBER] Ruthenium complex MD simulation ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not supported!
- Carlos Simmerling (Mon Oct 09 2017 - 16:54:47 PDT)
- Sanaa ALAbbad (Mon Oct 09 2017 - 16:52:01 PDT)
- Adrian Roitberg (Mon Oct 09 2017 - 16:48:50 PDT)
- Sanaa ALAbbad (Mon Oct 09 2017 - 16:44:24 PDT)
[AMBER] SCC-DFTB for iron
- Goetz, Andreas (Tue Oct 31 2017 - 14:20:21 PDT)
- Àngels González Lafont (Tue Oct 31 2017 - 09:04:43 PDT)
[AMBER] SCEE incorrectly set for certain dihedral parameter comments
- Niel Henriksen (Fri Oct 13 2017 - 12:05:00 PDT)
[AMBER] Specify amount of memory
- David A Case (Sun Oct 15 2017 - 10:28:45 PDT)
- Bill Ross (Sun Oct 15 2017 - 01:39:11 PDT)
- David Sáez (Sun Oct 15 2017 - 00:20:44 PDT)
[AMBER] STOP PMEMD Terminated Abnormally!
- Carlos Simmerling (Thu Oct 26 2017 - 05:23:44 PDT)
- Jeyaram R A (Thu Oct 26 2017 - 05:01:21 PDT)
[AMBER] striping correctly with ante-MMPBSA.py
- Sundar (Mon Oct 09 2017 - 01:24:38 PDT)
[AMBER] System preparation for protein with Multiple Zn-CCCC
- Pengfei Li (Thu Oct 12 2017 - 19:59:28 PDT)
- Bill Ross (Sat Oct 07 2017 - 16:37:08 PDT)
- Parthiban Marimuthu (Sat Oct 07 2017 - 13:58:49 PDT)
- Amani Eshtiwi (Fri Oct 06 2017 - 19:59:06 PDT)
- Parthiban Marimuthu (Fri Oct 06 2017 - 09:16:07 PDT)
[AMBER] Test failed after installing Amber Tools 17
- David A Case (Tue Oct 31 2017 - 17:36:14 PDT)
- Crystal Vander Zanden (Tue Oct 31 2017 - 13:18:24 PDT)
[AMBER] Thermodynamic Integration with pmemd, for explicit solvent models
- Roma Mukhopadhyay (Sun Oct 01 2017 - 16:54:40 PDT)
- David A Case (Sun Oct 01 2017 - 13:08:25 PDT)
- Roma Mukhopadhyay (Sat Sep 30 2017 - 19:48:47 PDT)
[AMBER] Thermodynamic integration/switch off/on cloumbic and vdw interactions
- Daniel Mermelstein (Mon Oct 09 2017 - 10:40:02 PDT)
- Khabiri, Morteza (Fri Oct 06 2017 - 11:05:54 PDT)
[AMBER] TI calculations using pmemd
- Roma Mukhopadhyay (Wed Oct 04 2017 - 13:00:22 PDT)
[AMBER] TImask command for PMEMD
- David A Case (Mon Oct 02 2017 - 14:26:26 PDT)
- Roma Mukhopadhyay (Mon Oct 02 2017 - 10:01:12 PDT)
[AMBER] total frames for hbond
- Elvis Martis (Sun Oct 01 2017 - 20:30:15 PDT)
- Thakur, Abhishek (Sun Oct 01 2017 - 12:16:42 PDT)
[AMBER] trajout format with cpptraj in Ambertools 17
- Li, Wen (Tue Oct 17 2017 - 10:57:26 PDT)
- Li, Wen (Tue Oct 17 2017 - 08:54:53 PDT)
- Elvis Martis (Tue Oct 17 2017 - 08:53:16 PDT)
- Daniel Roe (Tue Oct 17 2017 - 08:52:07 PDT)
- Li, Wen (Tue Oct 17 2017 - 08:40:28 PDT)
[AMBER] trajout last x frames cpptraj
- Hughes, Travis (Mon Oct 02 2017 - 07:16:01 PDT)
- Daniel Roe (Mon Oct 02 2017 - 05:31:23 PDT)
[AMBER] Use of pmemd for minimisation and equilibration
- Carlos Simmerling (Fri Oct 27 2017 - 09:06:47 PDT)
- David A Case (Fri Oct 27 2017 - 09:01:35 PDT)
- Ross Walker (Fri Oct 27 2017 - 08:06:34 PDT)
- David A Case (Fri Oct 27 2017 - 07:09:14 PDT)
- Elvis Martis (Fri Oct 27 2017 - 07:05:49 PDT)
- Suchetana Gupta (Fri Oct 27 2017 - 05:52:56 PDT)
[AMBER] vague error when running constant ph simulations
- Andrew Schaub (Wed Oct 11 2017 - 13:06:45 PDT)
- Andrew Schaub (Wed Oct 11 2017 - 12:24:13 PDT)
- David A Case (Wed Oct 04 2017 - 05:44:57 PDT)
- Andrew Schaub (Tue Oct 03 2017 - 21:08:01 PDT)
[AMBER] Vector command in cpptraj
- Pietro Aronica (Mon Oct 16 2017 - 20:39:44 PDT)
- Daniel Roe (Mon Oct 16 2017 - 06:23:37 PDT)
- Pietro Aronica (Sun Oct 15 2017 - 21:14:22 PDT)
[AMBER] Vector math: a couple of questions
- George Tzotzos (Wed Oct 04 2017 - 09:56:04 PDT)
- Daniel Roe (Wed Oct 04 2017 - 09:54:11 PDT)
- George Tzotzos (Wed Oct 04 2017 - 09:43:20 PDT)
- Daniel Roe (Wed Oct 04 2017 - 09:30:02 PDT)
- George Tzotzos (Tue Oct 03 2017 - 11:42:09 PDT)
[AMBER] warning Close contact
- David A Case (Mon Oct 30 2017 - 05:02:26 PDT)
- Shilpa Gupta (Mon Oct 30 2017 - 03:56:13 PDT)
[AMBER] Wham analysis
- diego.soler.uam.es (Sat Oct 14 2017 - 12:42:13 PDT)
- Thakur, Abhishek (Fri Oct 13 2017 - 07:32:40 PDT)
- Thakur, Abhishek (Thu Oct 12 2017 - 14:02:35 PDT)
[AMBER] WHAM, DHAM, MBAR, BAR, TI...
- Niel Henriksen (Thu Oct 19 2017 - 12:24:19 PDT)
- Andreas Tosstorff (Thu Oct 19 2017 - 09:04:22 PDT)
[AMBER] Wrong connectivity after antechamber/Gaussian16
- Junmei Wang (Sat Oct 28 2017 - 18:02:13 PDT)
- David A Case (Sat Oct 28 2017 - 17:31:21 PDT)
- Andreas Tosstorff (Sat Oct 28 2017 - 13:47:33 PDT)
- Junmei Wang (Sat Oct 28 2017 - 06:23:26 PDT)
- David A Case (Sat Oct 28 2017 - 05:16:25 PDT)
- Andreas Tosstorff (Sat Oct 28 2017 - 02:24:57 PDT)
- David A Case (Fri Oct 27 2017 - 12:20:59 PDT)
- Andreas Tosstorff (Fri Oct 27 2017 - 11:19:04 PDT)

Amber Archive Oct 2017 by subject