Amber Archive Sep 2015: by subject

[AMBER] 12 PhD positions for the Marie Skłodowska-Curie ITN-European MoGglyNet
- Alessandro Contini (Tue Sep 29 2015 - 02:23:46 PDT)
[AMBER] [parmed.py] chemistry.exceptions.AmberParmError loading topology file
- Juan Eiros Zamora (Fri Sep 11 2015 - 04:16:26 PDT)
- Jason Swails (Thu Sep 10 2015 - 05:36:16 PDT)
- Eiros Zamora, Juan (Thu Sep 10 2015 - 03:41:52 PDT)
- Jason Swails (Wed Sep 09 2015 - 18:50:01 PDT)
- Eiros Zamora, Juan (Wed Sep 09 2015 - 10:34:50 PDT)
[AMBER] A question on binding free energy decomposition output
- wliu (Tue Sep 15 2015 - 18:28:58 PDT)
- Jason Swails (Tue Sep 15 2015 - 07:30:30 PDT)
- Sofia Vasilakaki (Tue Sep 15 2015 - 01:01:20 PDT)
- wliu (Mon Sep 14 2015 - 23:22:27 PDT)
[AMBER] Addions Na+
- David A Case (Wed Sep 23 2015 - 06:40:11 PDT)
- Marcelo Andrade Chagas (Tue Sep 22 2015 - 14:20:26 PDT)
- Jason Swails (Tue Sep 22 2015 - 14:17:02 PDT)
- Marcelo Andrade Chagas (Tue Sep 22 2015 - 14:07:47 PDT)
- Bill Ross (Tue Sep 22 2015 - 13:44:35 PDT)
- Jason Swails (Tue Sep 22 2015 - 12:33:44 PDT)
- Kenneth Huang (Tue Sep 22 2015 - 12:26:10 PDT)
- Marcelo Andrade Chagas (Tue Sep 22 2015 - 12:20:08 PDT)
- Bill Ross (Tue Sep 22 2015 - 12:11:10 PDT)
- Marcelo Andrade Chagas (Tue Sep 22 2015 - 11:52:44 PDT)
[AMBER] Addition of single water molecules
- Jason Swails (Fri Sep 11 2015 - 15:40:20 PDT)
- Eric Berquist (Fri Sep 11 2015 - 13:21:06 PDT)
[AMBER] adQMMM multiple solvation regions
- Covington, Cody Lance (Fri Sep 25 2015 - 08:03:31 PDT)
[AMBER] AMBER benchmarks
- Hannes Loeffler (Fri Sep 25 2015 - 03:26:08 PDT)
- Neha Gandhi (Fri Sep 25 2015 - 03:05:55 PDT)
[AMBER] Amber compilation problem
- Jason Swails (Wed Sep 30 2015 - 05:22:06 PDT)
- Theoretical Research (Wed Sep 30 2015 - 05:13:59 PDT)
- Weinzierl, Robert O J (Wed Sep 30 2015 - 04:43:54 PDT)
[AMBER] AMBER Tutorial B1 Backbone atoms
- Aishani Prem (Wed Sep 23 2015 - 18:51:18 PDT)
- Thomas Cheatham (Tue Sep 22 2015 - 13:46:18 PDT)
- Aishani Prem (Tue Sep 22 2015 - 13:32:28 PDT)
[AMBER] Amber14 Update 13 fails.
- Jason Swails (Wed Sep 02 2015 - 08:22:16 PDT)
- Oliver Grant (Wed Sep 02 2015 - 07:44:51 PDT)
[AMBER] Amber15 compiler error 'undefined reference to `fftw_plan_dft_r2c_3d'' with Cygwin
- Nigel Palmer (Tue Sep 08 2015 - 06:50:24 PDT)
- Jason Swails (Tue Sep 08 2015 - 06:38:51 PDT)
- Nigel Palmer (Tue Sep 08 2015 - 06:16:29 PDT)
[AMBER] ambertools14
- Jason Swails (Sat Sep 19 2015 - 06:04:49 PDT)
- Andrew Bostick (Sat Sep 19 2015 - 04:30:55 PDT)
[AMBER] analysis from mixed amber 12 and amber 14 simulations
- George Green (Wed Sep 23 2015 - 22:27:27 PDT)
- David A Case (Wed Sep 23 2015 - 18:21:59 PDT)
- George Green (Wed Sep 23 2015 - 12:22:24 PDT)
[AMBER] antechamber error
- Atila Petrosian (Fri Sep 18 2015 - 12:57:54 PDT)
- David A Case (Fri Sep 18 2015 - 11:56:07 PDT)
- Atila Petrosian (Fri Sep 18 2015 - 11:04:08 PDT)
- Atila Petrosian (Fri Sep 18 2015 - 10:55:26 PDT)
- David A Case (Fri Sep 18 2015 - 06:02:33 PDT)
- Jason Swails (Fri Sep 18 2015 - 04:34:51 PDT)
- Atila Petrosian (Fri Sep 18 2015 - 04:29:01 PDT)
- Atila Petrosian (Thu Sep 17 2015 - 23:21:22 PDT)
- David A Case (Thu Sep 17 2015 - 11:47:15 PDT)
- Nic Steussy (Thu Sep 17 2015 - 10:35:42 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Sep 17 2015 - 10:29:00 PDT)
- Atila Petrosian (Thu Sep 17 2015 - 08:44:08 PDT)
- David A Case (Thu Sep 17 2015 - 08:29:17 PDT)
- Atila Petrosian (Thu Sep 17 2015 - 06:56:54 PDT)
- Atila Petrosian (Thu Sep 17 2015 - 06:51:03 PDT)
- David A Case (Tue Sep 15 2015 - 14:41:08 PDT)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Tue Sep 15 2015 - 11:38:43 PDT)
[AMBER] Antechamber Flags
- David A Case (Fri Sep 18 2015 - 18:24:45 PDT)
- Robert Molt (Fri Sep 18 2015 - 18:00:04 PDT)
[AMBER] Calculating energy of solute
- Christina Bergonzo (Fri Sep 18 2015 - 14:44:08 PDT)
- Krantzman, Kristin D (Fri Sep 18 2015 - 14:33:10 PDT)
[AMBER] Changing font size with mdout_analyzer.py
- Jason Swails (Wed Sep 09 2015 - 08:47:21 PDT)
- Krantzman, Kristin D (Wed Sep 09 2015 - 08:19:31 PDT)
[AMBER] chirality.c
- Aronica, Pietro (Tue Sep 08 2015 - 07:05:53 PDT)
- David A Case (Sat Sep 05 2015 - 09:13:47 PDT)
- Aronica, Pietro (Fri Sep 04 2015 - 08:20:39 PDT)
[AMBER] closest command in cpptraj
- Daniel Roe (Tue Sep 08 2015 - 08:48:02 PDT)
- Joseph Baker (Mon Sep 07 2015 - 11:22:57 PDT)
[AMBER] clustering in PC subspace
- Daniel Roe (Mon Sep 28 2015 - 20:00:48 PDT)
- filip fratev (Mon Sep 28 2015 - 16:17:14 PDT)
- filip fratev (Mon Sep 28 2015 - 16:10:18 PDT)
- filip fratev (Mon Sep 28 2015 - 15:41:59 PDT)
[AMBER] Command for hbond analysis
- Martina Devi (Wed Sep 23 2015 - 07:08:51 PDT)
- Daniel Roe (Wed Sep 23 2015 - 04:11:57 PDT)
- Martina Devi (Wed Sep 23 2015 - 00:41:35 PDT)
[AMBER] Contact map residues
- Daniel Roe (Wed Sep 16 2015 - 07:40:01 PDT)
- Neha Gandhi (Wed Sep 09 2015 - 00:30:30 PDT)
[AMBER] Cphmd
- Jason Swails (Wed Sep 09 2015 - 08:49:50 PDT)
- Arjun Sharma (Wed Sep 09 2015 - 08:17:13 PDT)
[AMBER] CpHMD for non protein residues
- Rahul Ramesh (Fri Sep 18 2015 - 14:23:02 PDT)
- Jason Swails (Fri Sep 18 2015 - 14:04:09 PDT)
- Rahul Ramesh (Fri Sep 18 2015 - 13:59:29 PDT)
[AMBER] CpHMD of Succinic Acid
- Jason Swails (Sat Sep 12 2015 - 19:56:59 PDT)
- Rahul Ramesh (Fri Sep 11 2015 - 18:02:24 PDT)
[AMBER] cphmd reference energy
- Jason Swails (Wed Sep 16 2015 - 08:16:01 PDT)
- Arjun Sharma (Wed Sep 16 2015 - 07:44:10 PDT)
[AMBER] CpHMD simulation for non protein residues
- Rahul Ramesh (Wed Sep 23 2015 - 10:55:22 PDT)
- Jason Swails (Wed Sep 23 2015 - 10:28:54 PDT)
- Rahul Ramesh (Wed Sep 23 2015 - 09:05:46 PDT)
[AMBER] cpptraj script for average 3D protein structure?
- Michael Shokhen (Thu Sep 10 2015 - 05:53:49 PDT)
- Eiros Zamora, Juan (Thu Sep 10 2015 - 03:37:59 PDT)
- Michael Shokhen (Thu Sep 10 2015 - 03:11:09 PDT)
- Repic Matej (Thu Sep 10 2015 - 02:58:59 PDT)
- Michael Shokhen (Thu Sep 10 2015 - 01:23:13 PDT)
[AMBER] cyclic peptides and bond command in leap
- Anselm Horn (Thu Sep 17 2015 - 00:19:13 PDT)
- David A Case (Tue Sep 15 2015 - 14:50:59 PDT)
- Jonathan Gough (Tue Sep 15 2015 - 12:55:49 PDT)
- Jonathan Gough (Tue Sep 15 2015 - 12:11:29 PDT)
- David A Case (Tue Sep 15 2015 - 12:02:04 PDT)
- Jonathan Gough (Tue Sep 15 2015 - 10:04:18 PDT)
[AMBER] degraded GPU performance
- Ross Walker (Tue Sep 22 2015 - 07:41:47 PDT)
- Alessandro Contini (alessandro.contini) (Tue Sep 22 2015 - 07:22:00 PDT)
[AMBER] Different result before and after AUTOIMAGE from CPPTRAJ?
- Jason Swails (Wed Sep 02 2015 - 13:46:14 PDT)
- Eg eh (Wed Sep 02 2015 - 13:21:50 PDT)
[AMBER] DISAVE does not work on pmemd.cuda / GPU
- David A Case (Wed Sep 16 2015 - 19:42:13 PDT)
- Mykola Dimura (Wed Sep 16 2015 - 09:57:33 PDT)
[AMBER] distance based mask problem
- Daniel Roe (Mon Sep 28 2015 - 08:00:20 PDT)
- Chris (Mon Sep 28 2015 - 05:57:13 PDT)
- Daniel Roe (Thu Sep 24 2015 - 08:19:47 PDT)
- Daniel Roe (Thu Sep 24 2015 - 07:55:32 PDT)
- Chris (Thu Sep 24 2015 - 05:46:10 PDT)
- Jason Swails (Tue Sep 22 2015 - 05:15:26 PDT)
- Chris (Mon Sep 21 2015 - 21:01:19 PDT)
[AMBER] error in GPU during equilibration
- Lara rajam (Wed Sep 02 2015 - 15:35:39 PDT)
- Ross Walker (Wed Sep 02 2015 - 15:30:31 PDT)
- Lara rajam (Wed Sep 02 2015 - 15:17:51 PDT)
- Ross Walker (Wed Sep 02 2015 - 12:09:48 PDT)
- Ross Walker (Wed Sep 02 2015 - 12:04:55 PDT)
- Lara rajam (Wed Sep 02 2015 - 11:51:41 PDT)
- David A Case (Wed Sep 02 2015 - 11:40:14 PDT)
- Lara rajam (Wed Sep 02 2015 - 09:30:26 PDT)
[AMBER] Error: ptraj is needed for MMPBSA
- Jason Swails (Wed Sep 30 2015 - 08:37:45 PDT)
- Ayesha Kanwal (Wed Sep 30 2015 - 07:46:04 PDT)
- Daniel Roe (Tue Sep 29 2015 - 15:52:16 PDT)
- Ayesha Kanwal (Tue Sep 29 2015 - 15:07:43 PDT)
[AMBER] Extracting Information for each Frames Considered for Entropy Calculation by Normal Modes
- anilkumarsahoo.physics.iisc.ernet.in (Mon Sep 21 2015 - 05:17:30 PDT)
- Jason Swails (Sun Sep 20 2015 - 19:09:32 PDT)
- anilkumarsahoo.physics.iisc.ernet.in (Sun Sep 20 2015 - 15:09:22 PDT)
[AMBER] free -COOH at the C-terminus
- Xing (Thu Sep 24 2015 - 13:01:34 PDT)
- Jason Swails (Thu Sep 24 2015 - 12:13:46 PDT)
- Xing (Thu Sep 24 2015 - 12:11:27 PDT)
[AMBER] Freeze atoms to DM
- Marcelo Andrade Chagas (Mon Sep 21 2015 - 12:55:55 PDT)
- Jason Swails (Mon Sep 21 2015 - 12:34:27 PDT)
- Jason Swails (Mon Sep 21 2015 - 12:33:37 PDT)
- Gustavo Seabra (Mon Sep 21 2015 - 12:33:00 PDT)
- Marcelo Andrade Chagas (Mon Sep 21 2015 - 12:21:27 PDT)
[AMBER] Fwd: ISC-2015-3BS-09
- Sushi Shilpa (Sat Sep 26 2015 - 03:39:40 PDT)
[AMBER] Fwd: Mail ceased to work in the last 72 hours
- George Tzotzos (Tue Sep 15 2015 - 19:01:37 PDT)
[AMBER] Fwd: q4md FF with two "small" molecules
- Francesco Pietra (Mon Sep 21 2015 - 09:38:44 PDT)
- Jason Swails (Mon Sep 21 2015 - 04:23:50 PDT)
- Francesco Pietra (Mon Sep 21 2015 - 03:11:00 PDT)
[AMBER] glycam parameter file
- Batuhan Kav (Mon Sep 21 2015 - 07:27:50 PDT)
- Lachele Foley (Mon Sep 21 2015 - 06:55:32 PDT)
- Jason Swails (Mon Sep 21 2015 - 06:35:01 PDT)
- Batuhan Kav (Mon Sep 21 2015 - 05:45:09 PDT)
- Jason Swails (Mon Sep 21 2015 - 04:18:01 PDT)
- Batuhan Kav (Mon Sep 21 2015 - 03:23:39 PDT)
[AMBER] gpu run
- Jason Swails (Sun Sep 06 2015 - 10:26:03 PDT)
- Lara rajam (Sun Sep 06 2015 - 09:41:55 PDT)
- Ross Walker (Sun Sep 06 2015 - 09:14:12 PDT)
- Kenneth Huang (Sat Sep 05 2015 - 18:12:05 PDT)
- Lara rajam (Sat Sep 05 2015 - 16:32:13 PDT)
[AMBER] Halogen bond force field in AMBER
- Mahmoud A. A. Ibrahim (Wed Sep 23 2015 - 02:00:00 PDT)
- Thomas Cheatham (Tue Sep 22 2015 - 16:04:56 PDT)
- psu4.uic.edu (Tue Sep 22 2015 - 15:49:39 PDT)
[AMBER] Has anyone tried VMD in the second step of tutorial A1?
- Xing (Tue Sep 15 2015 - 08:52:33 PDT)
[AMBER] HELP in Emperical Valence bond model (EVB)
- bijyalaxmi athokpam (Thu Sep 24 2015 - 08:19:59 PDT)
- David A Case (Wed Sep 23 2015 - 12:16:13 PDT)
- bijyalaxmi athokpam (Wed Sep 23 2015 - 01:55:54 PDT)
[AMBER] help in parallel run
- David A Case (Wed Sep 16 2015 - 05:58:37 PDT)
- Jason Swails (Wed Sep 16 2015 - 05:41:05 PDT)
- Robin Jain (Wed Sep 16 2015 - 02:36:36 PDT)
[AMBER] help in RDF
- Tom Kurtzman (Tue Sep 22 2015 - 07:26:38 PDT)
- Jason Swails (Tue Sep 22 2015 - 05:20:01 PDT)
- Robin Jain (Tue Sep 22 2015 - 01:18:57 PDT)
[AMBER] Hoogsteen-Watson Base pair
- David A Case (Wed Sep 23 2015 - 12:21:33 PDT)
- Martina Devi (Wed Sep 23 2015 - 08:02:01 PDT)
[AMBER] HPC
- Sofia Vasilakaki (Thu Sep 10 2015 - 13:32:38 PDT)
- Ross Walker (Thu Sep 10 2015 - 12:33:48 PDT)
- Sofia Vasilakaki (Thu Sep 10 2015 - 12:17:43 PDT)
[AMBER] hpc error
- Jason Swails (Mon Sep 28 2015 - 14:41:14 PDT)
- Duke, Robert E Jr (Sun Sep 27 2015 - 13:24:25 PDT)
- Jason Swails (Sun Sep 27 2015 - 12:43:14 PDT)
- Damiano Spadoni (Sun Sep 27 2015 - 10:23:53 PDT)
- Duke, Robert E Jr (Thu Sep 24 2015 - 09:12:33 PDT)
- Jason Swails (Thu Sep 24 2015 - 06:23:39 PDT)
- David A Case (Thu Sep 24 2015 - 05:48:22 PDT)
- Jason Swails (Thu Sep 24 2015 - 05:18:50 PDT)
- Damiano Spadoni (Thu Sep 24 2015 - 03:55:45 PDT)
- Jason Swails (Thu Sep 03 2015 - 05:25:58 PDT)
- Damiano Spadoni (Thu Sep 03 2015 - 03:16:19 PDT)
[AMBER] Implementation of GBSA in AMBER.
- Jason Swails (Wed Sep 23 2015 - 06:31:37 PDT)
- Abhilash J (Tue Sep 22 2015 - 23:26:03 PDT)
- Hai Nguyen (Tue Sep 22 2015 - 22:32:11 PDT)
- Abhilash J (Tue Sep 22 2015 - 22:14:07 PDT)
[AMBER] index and sort order in prmtop
- Jason Swails (Tue Sep 08 2015 - 13:19:29 PDT)
- Hannes Loeffler (Tue Sep 08 2015 - 07:55:06 PDT)
[AMBER] Installing AMBER
- David A Case (Tue Sep 22 2015 - 05:17:06 PDT)
- Hector A. Baldoni (Tue Sep 22 2015 - 04:12:37 PDT)
- Wong Li Zhe (Mon Sep 21 2015 - 20:19:54 PDT)
[AMBER] Issues with gaff cd=cc atom type
- Francesco Pietra (Sat Sep 19 2015 - 00:21:33 PDT)
- Robert Molt (Fri Sep 18 2015 - 17:52:24 PDT)
- Francesco Pietra (Fri Sep 18 2015 - 13:39:46 PDT)
- Jason Swails (Fri Sep 18 2015 - 10:47:57 PDT)
- Francesco Pietra (Fri Sep 18 2015 - 09:57:12 PDT)
- Jason Swails (Fri Sep 18 2015 - 04:36:52 PDT)
- Francesco Pietra (Fri Sep 18 2015 - 00:46:20 PDT)
[AMBER] jfastw=4 and vlimit exceeded
- Ruth Helena Tichauer (Fri Sep 25 2015 - 08:45:08 PDT)
- Jason Swails (Fri Sep 25 2015 - 08:24:32 PDT)
- Ruth Helena Tichauer (Fri Sep 25 2015 - 08:08:38 PDT)
- Jason Swails (Fri Sep 25 2015 - 07:27:43 PDT)
- Ruth Helena Tichauer (Fri Sep 25 2015 - 06:46:06 PDT)
[AMBER] job submission in RED
- FyD (Thu Sep 03 2015 - 02:12:10 PDT)
[AMBER] keep residue numbering?
- David A Case (Fri Sep 11 2015 - 08:06:09 PDT)
- Albert (Fri Sep 11 2015 - 00:12:24 PDT)
[AMBER] KeyError: 4018
- Pengfei Li (Wed Sep 02 2015 - 18:35:15 PDT)
- Sushi Shilpa (Tue Sep 01 2015 - 20:42:09 PDT)
[AMBER] Leap Connection of Covalent Unit Continued
- David A Case (Wed Sep 16 2015 - 19:27:48 PDT)
- Robert Molt (Wed Sep 16 2015 - 18:30:45 PDT)
[AMBER] lifetime analysis
- loic etheve (Wed Sep 02 2015 - 07:14:27 PDT)
- Daniel Roe (Wed Sep 02 2015 - 07:10:26 PDT)
- loic etheve (Wed Sep 02 2015 - 06:47:39 PDT)
- Daniel Roe (Wed Sep 02 2015 - 06:43:53 PDT)
- loic etheve (Wed Sep 02 2015 - 06:41:46 PDT)
- loic etheve (Wed Sep 02 2015 - 06:37:45 PDT)
[AMBER] limit exceeded and high temperature
- Ruth Helena Tichauer (Mon Sep 14 2015 - 02:56:46 PDT)
- Ruth Helena Tichauer (Fri Sep 11 2015 - 09:06:21 PDT)
- Ross Walker (Fri Sep 11 2015 - 08:48:30 PDT)
- Ruth Helena Tichauer (Fri Sep 11 2015 - 08:40:13 PDT)
- Jason Swails (Fri Sep 11 2015 - 08:26:17 PDT)
- Ruth Helena Tichauer (Fri Sep 11 2015 - 07:52:05 PDT)
[AMBER] MCPB problem
- Pengfei Li (Mon Sep 14 2015 - 14:28:42 PDT)
- Kshatresh Dutta Dubey (Mon Sep 14 2015 - 10:42:01 PDT)
- Pengfei Li (Mon Sep 14 2015 - 09:15:29 PDT)
- Kshatresh Dutta Dubey (Sat Sep 12 2015 - 20:05:24 PDT)
- Kshatresh Dutta Dubey (Sat Sep 12 2015 - 19:11:10 PDT)
- Pengfei Li (Sat Sep 12 2015 - 16:30:02 PDT)
- Kshatresh Dutta Dubey (Sat Sep 12 2015 - 07:45:29 PDT)
- Kshatresh Dutta Dubey (Fri Sep 11 2015 - 09:50:41 PDT)
- Pengfei Li (Fri Sep 11 2015 - 09:19:52 PDT)
- Kshatresh Dutta Dubey (Fri Sep 11 2015 - 09:15:19 PDT)
- Pengfei Li (Fri Sep 11 2015 - 08:56:14 PDT)
- Kshatresh Dutta Dubey (Thu Sep 10 2015 - 13:25:00 PDT)
[AMBER] Membrane simulation without a membrane, only lipophilic solvent (membranemimetic)
- sridhar ganesan (Thu Sep 24 2015 - 20:10:43 PDT)
- Marawan Hussien (Thu Sep 24 2015 - 19:11:03 PDT)
- Marawan Hussien (Thu Sep 24 2015 - 18:10:50 PDT)
[AMBER] MG ions being misplaced
- David A Case (Fri Sep 18 2015 - 11:43:27 PDT)
- Kalenkiewicz, Andrew (NIH/NICHD) [F] (Fri Sep 18 2015 - 09:44:27 PDT)
[AMBER] Michaelis complex
- Carlos Simmerling (Thu Sep 17 2015 - 11:07:49 PDT)
- Jason Swails (Thu Sep 17 2015 - 10:57:03 PDT)
- Hector A. Baldoni (Thu Sep 17 2015 - 10:35:48 PDT)
- Carlos Simmerling (Thu Sep 17 2015 - 08:34:12 PDT)
- Jason Swails (Thu Sep 17 2015 - 08:20:50 PDT)
- Jason Swails (Thu Sep 17 2015 - 08:16:59 PDT)
- Carlos Simmerling (Thu Sep 17 2015 - 06:48:33 PDT)
- Hector A. Baldoni (Thu Sep 17 2015 - 06:44:18 PDT)
- Jason Swails (Thu Sep 17 2015 - 04:25:44 PDT)
- Hector A. Baldoni (Wed Sep 16 2015 - 13:11:06 PDT)
[AMBER] Minimization
- Bill Ross (Sat Sep 19 2015 - 18:04:36 PDT)
- Marcelo Andrade Chagas (Fri Sep 18 2015 - 14:13:25 PDT)
[AMBER] Minimization of steps
- David A Case (Fri Sep 25 2015 - 17:53:34 PDT)
- Marcelo Andrade Chagas (Fri Sep 25 2015 - 11:26:39 PDT)
[AMBER] mmpbsa error
- Jason Swails (Tue Sep 15 2015 - 10:25:48 PDT)
- Lara rajam (Tue Sep 15 2015 - 09:50:37 PDT)
- Jason Swails (Tue Sep 15 2015 - 07:27:42 PDT)
- Lara rajam (Mon Sep 14 2015 - 18:40:49 PDT)
- Jason Swails (Fri Sep 04 2015 - 04:24:01 PDT)
- sunita gupta (Fri Sep 04 2015 - 00:12:49 PDT)
[AMBER] MMPBSA error - start frame (1) > total frames (0)
- Daniel Roe (Tue Sep 01 2015 - 10:48:06 PDT)
- Sangeetha B (Tue Sep 01 2015 - 08:39:44 PDT)
[AMBER] MMPBSA is not performing
- asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 07:25:37 PDT)
- Jason Swails (Tue Sep 08 2015 - 06:36:07 PDT)
- asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 05:07:23 PDT)
- Aleksandra Skoric (Tue Sep 08 2015 - 03:59:04 PDT)
- Asma Abro 28-FBAS/MSBI/F09 (Tue Sep 08 2015 - 03:02:38 PDT)
- Aleksandra Skoric (Tue Sep 08 2015 - 02:46:24 PDT)
- Asma Abro 28-FBAS/MSBI/F09 (Tue Sep 08 2015 - 02:13:29 PDT)
- asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 01:35:42 PDT)
- Aleksandra Skoric (Tue Sep 08 2015 - 01:30:12 PDT)
- asma.msbi28.iiu.edu.pk (Tue Sep 08 2015 - 01:08:33 PDT)
- Aleksandra Skoric (Tue Sep 08 2015 - 00:59:21 PDT)
- Asma Abro 28-FBAS/MSBI/F09 (Tue Sep 08 2015 - 00:21:10 PDT)
- Jason Swails (Mon Sep 07 2015 - 05:31:07 PDT)
- Asma Abro 28-FBAS/MSBI/F09 (Sun Sep 06 2015 - 22:03:23 PDT)
[AMBER] mmpbsa with Iodine problems
- Kenneth Huang (Sat Sep 05 2015 - 17:18:17 PDT)
- 21428087.zju.edu.cn (Fri Sep 04 2015 - 21:48:29 PDT)
[AMBER] Molecular Dynamics for Porphyrin
- David A Case (Fri Sep 18 2015 - 11:48:09 PDT)
- Jason Swails (Fri Sep 18 2015 - 09:55:28 PDT)
- Amber Maharaj (Fri Sep 18 2015 - 09:45:47 PDT)
[AMBER] Multiplicity in QM/MM calculations
- Jason Swails (Mon Sep 07 2015 - 10:45:38 PDT)
- Kshatresh Dutta Dubey (Mon Sep 07 2015 - 10:13:38 PDT)
[AMBER] Need help regarding references
- Gustavo Seabra (Wed Sep 30 2015 - 07:20:07 PDT)
- Carlos Simmerling (Wed Sep 30 2015 - 06:45:14 PDT)
- Saikat Dutta chowdhury (Wed Sep 30 2015 - 06:28:59 PDT)
- Carlos Simmerling (Wed Sep 30 2015 - 05:50:30 PDT)
- Saikat Dutta chowdhury (Wed Sep 30 2015 - 05:42:07 PDT)
[AMBER] No output
- Jason Swails (Mon Sep 14 2015 - 06:04:19 PDT)
- Damiano Spadoni (Mon Sep 14 2015 - 05:50:12 PDT)
- Jason Swails (Sat Sep 12 2015 - 20:12:29 PDT)
- Ross Walker (Sat Sep 12 2015 - 14:02:09 PDT)
[AMBER] Non-equilibrium pulling with plane-point restraints
- achim.sandmann.chemie.stud.uni-erlangen.de (Tue Sep 01 2015 - 05:42:07 PDT)
[AMBER] on MD and Ramachandran outlier
- Carlos Simmerling (Sun Sep 20 2015 - 05:04:31 PDT)
- Brett (Sun Sep 20 2015 - 04:49:12 PDT)
[AMBER] OpenMM
- Jason Swails (Wed Sep 23 2015 - 06:23:38 PDT)
- Hai Nguyen (Tue Sep 22 2015 - 18:32:39 PDT)
- Sofia Vasilakaki (Tue Sep 22 2015 - 17:26:45 PDT)
[AMBER] Oxygen parameters for AMBER99SB-ILDN
- Ebert Maximilian (Wed Sep 30 2015 - 10:42:45 PDT)
- Jason Swails (Wed Sep 30 2015 - 10:20:59 PDT)
- Ebert Maximilian (Wed Sep 30 2015 - 10:04:27 PDT)
[AMBER] Parameterization empirical method
- Marcelo Andrade Chagas (Fri Sep 11 2015 - 11:40:41 PDT)
[AMBER] Parameters for benzene sulfonamide
- Karl Kirschner (Tue Sep 08 2015 - 01:24:30 PDT)
- Jovanovic, Srdan (Mon Sep 07 2015 - 10:16:55 PDT)
[AMBER] Paramfit issues
- Robin Betz (Mon Sep 14 2015 - 14:53:44 PDT)
- David Poole (Mon Sep 14 2015 - 03:31:57 PDT)
[AMBER] Parmed crash
- Jason Swails (Mon Sep 14 2015 - 09:44:40 PDT)
- Mykola Dimura (Mon Sep 14 2015 - 09:23:14 PDT)
- Jason Swails (Mon Sep 14 2015 - 09:04:23 PDT)
- Mykola Dimura (Mon Sep 14 2015 - 08:50:12 PDT)
[AMBER] ParmEd problem: LJ12_6_4Error: Could not find parameters for ATOM_TYPE CX
- Karolina Markowska (Wed Sep 09 2015 - 12:21:53 PDT)
- Jason Swails (Wed Sep 09 2015 - 08:27:54 PDT)
- Karolina Markowska (Tue Sep 08 2015 - 14:41:10 PDT)
[AMBER] parmed.py
- Jason Swails (Fri Sep 18 2015 - 04:40:43 PDT)
- Urszula Uciechowska (Fri Sep 18 2015 - 03:31:15 PDT)
[AMBER] pca
- Daniel Roe (Wed Sep 16 2015 - 08:04:23 PDT)
- Lara rajam (Thu Sep 10 2015 - 08:30:44 PDT)
[AMBER] per residue decomposition MMPBSA
- Jason Swails (Fri Sep 18 2015 - 10:49:43 PDT)
- Lara rajam (Fri Sep 18 2015 - 10:03:29 PDT)
[AMBER] Prepgen
- David A Case (Tue Sep 22 2015 - 05:10:35 PDT)
- Robert Molt (Mon Sep 21 2015 - 18:36:43 PDT)
[AMBER] Problem compiling cpptraj with openmp
- Marc van der Kamp (Tue Sep 08 2015 - 09:05:48 PDT)
- Hannes Loeffler (Tue Sep 08 2015 - 08:46:08 PDT)
- Daniel Roe (Tue Sep 08 2015 - 08:43:50 PDT)
- Marc van der Kamp (Tue Sep 08 2015 - 08:32:51 PDT)
[AMBER] Problem In Performing MMPBSA Calculation for System containing Ligand and Protein
- Ray Luo, Ph.D. (Tue Sep 22 2015 - 11:28:45 PDT)
- 杨川 (Mon Sep 21 2015 - 19:15:12 PDT)
- Jason Swails (Mon Sep 21 2015 - 04:19:50 PDT)
- 杨川 (Sun Sep 20 2015 - 21:30:38 PDT)
[AMBER] problem in plotting secondary structure graph
- Daniel Roe (Wed Sep 16 2015 - 08:09:40 PDT)
- Sehrish Naz (Tue Sep 15 2015 - 21:11:19 PDT)
[AMBER] Problem with saving parameters for a complex having Heme group
- 杨川 (Tue Sep 29 2015 - 20:25:36 PDT)
- David A Case (Mon Sep 28 2015 - 05:28:53 PDT)
- Jason Swails (Mon Sep 28 2015 - 05:22:29 PDT)
- 杨川 (Sun Sep 27 2015 - 21:29:35 PDT)
[AMBER] Problems with the Amber-14 compilation and using MMPBSA.py with ubuntu
- David A Case (Wed Sep 16 2015 - 05:53:49 PDT)
- Jason Swails (Wed Sep 16 2015 - 05:25:34 PDT)
- ayesha kanwal (Tue Sep 15 2015 - 23:10:16 PDT)
[AMBER] Proper Insertion of Covalently Bound Unit in Helical Structure
- David A Case (Mon Sep 14 2015 - 15:04:13 PDT)
- Robert Molt (Mon Sep 14 2015 - 13:58:22 PDT)
- Dr. Robert Molt Jr. (Mon Sep 14 2015 - 11:29:22 PDT)
- David A Case (Sun Sep 13 2015 - 21:01:02 PDT)
- Robert Molt (Sun Sep 13 2015 - 17:06:36 PDT)
[AMBER] Prospective research areas of AMBER
- Sabyasachi Sahoo (Tue Sep 22 2015 - 02:40:10 PDT)
- David A Case (Mon Sep 21 2015 - 11:34:58 PDT)
- Sabyasachi Sahoo (Mon Sep 21 2015 - 10:25:23 PDT)
[AMBER] Protein - RNA modelling
- David A Case (Wed Sep 23 2015 - 18:21:52 PDT)
- Brian Radak (Tue Sep 22 2015 - 11:45:53 PDT)
- Sidhu, Khushwant (Dr.) (Tue Sep 22 2015 - 06:50:01 PDT)
[AMBER] q4md FF with two "small" molecules
- Francesco Pietra (Sun Sep 20 2015 - 07:47:22 PDT)
- David A Case (Sun Sep 20 2015 - 05:40:16 PDT)
- Francesco Pietra (Sun Sep 20 2015 - 02:01:08 PDT)
[AMBER] QM&Lipid14
- Ross Walker (Mon Sep 21 2015 - 00:19:30 PDT)
- Sofia Vasilakaki (Sun Sep 20 2015 - 16:58:28 PDT)
[AMBER] QM/MM Equilibration Errors
- David A Case (Thu Sep 10 2015 - 06:07:02 PDT)
- Brittany Boykin (Wed Sep 09 2015 - 14:41:55 PDT)
[AMBER] query
- ankita mehta (Fri Sep 18 2015 - 07:35:46 PDT)
- David A Case (Wed Sep 16 2015 - 12:14:22 PDT)
- Nic Steussy (Wed Sep 16 2015 - 08:47:56 PDT)
- ankita mehta (Wed Sep 16 2015 - 08:22:04 PDT)
- Jason Swails (Wed Sep 16 2015 - 08:17:14 PDT)
- ankita mehta (Wed Sep 16 2015 - 08:06:35 PDT)
- David A Case (Wed Sep 16 2015 - 07:02:35 PDT)
- Kenneth Huang (Wed Sep 16 2015 - 05:42:20 PDT)
- ankita mehta (Wed Sep 16 2015 - 03:27:32 PDT)
- David A Case (Tue Sep 15 2015 - 11:31:34 PDT)
- Kenneth Huang (Tue Sep 15 2015 - 06:38:05 PDT)
- ankita mehta (Tue Sep 15 2015 - 06:22:01 PDT)
[AMBER] Regarding AmberTool 14 installation
- Setyanto Md (Tue Sep 08 2015 - 01:42:55 PDT)
- MOHD HOMAIDUR RAHMAN (Tue Sep 08 2015 - 00:37:10 PDT)
- Setyanto Md (Mon Sep 07 2015 - 22:44:40 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Sep 07 2015 - 22:32:16 PDT)
- Setyanto Md (Mon Sep 07 2015 - 22:03:50 PDT)
[AMBER] Regarding Simulations of Ionic Liquids on GPU
- David A Case (Tue Sep 15 2015 - 05:48:45 PDT)
- MOHD HOMAIDUR RAHMAN (Mon Sep 14 2015 - 22:45:41 PDT)
[AMBER] REMD to sample the conformational space of a defined part of the system
- Sergey Samsonov (Fri Sep 11 2015 - 07:46:47 PDT)
- Carlos Simmerling (Fri Sep 11 2015 - 04:25:55 PDT)
- Sergey Samsonov (Fri Sep 11 2015 - 00:11:21 PDT)
- Jason Swails (Tue Sep 08 2015 - 13:15:02 PDT)
- Sergey Samsonov (Tue Sep 08 2015 - 07:05:47 PDT)
- Jason Swails (Tue Sep 08 2015 - 04:29:53 PDT)
- Sergey Samsonov (Tue Sep 08 2015 - 00:50:33 PDT)
[AMBER] RESP charge fitting
- FyD (Thu Sep 03 2015 - 22:57:47 PDT)
- David A Case (Thu Sep 03 2015 - 11:18:39 PDT)
- CHAMI F. (Thu Sep 03 2015 - 11:10:49 PDT)
[AMBER] setting a box
- mohammad r (Thu Sep 10 2015 - 10:45:10 PDT)
- David A Case (Thu Sep 10 2015 - 09:02:27 PDT)
- mohammad r (Thu Sep 10 2015 - 08:35:07 PDT)
[AMBER] several peptides in my input can be identified by cpptraj?
- Fabian gmail (Wed Sep 16 2015 - 08:20:58 PDT)
- Daniel Roe (Wed Sep 16 2015 - 08:02:07 PDT)
- Fabian gmail (Thu Sep 10 2015 - 03:05:50 PDT)
[AMBER] SHAKE&Vlimit
- David A Case (Mon Sep 21 2015 - 08:48:01 PDT)
- 罗艳玲 (Mon Sep 21 2015 - 04:48:51 PDT)
[AMBER] SHAKE&Vlimit
- Jason Swails (Mon Sep 21 2015 - 04:28:21 PDT)
- 罗艳玲 (Sun Sep 20 2015 - 18:56:30 PDT)
[AMBER] Simulation stops without errors
- Jason Swails (Thu Sep 17 2015 - 04:28:56 PDT)
- Bala subramanian (Thu Sep 17 2015 - 02:36:22 PDT)
- David A Case (Wed Sep 16 2015 - 05:56:09 PDT)
- Jason Swails (Wed Sep 16 2015 - 05:28:15 PDT)
- Bala subramanian (Wed Sep 16 2015 - 02:06:26 PDT)
- Jason Swails (Mon Sep 14 2015 - 06:08:56 PDT)
- Bala subramanian (Mon Sep 14 2015 - 00:46:49 PDT)
[AMBER] Splitting LES trajectory
- Daniel Roe (Wed Sep 16 2015 - 08:53:32 PDT)
- Sergey Samsonov (Wed Sep 16 2015 - 08:29:52 PDT)
[AMBER] sqm
- Sofia Vasilakaki (Tue Sep 15 2015 - 12:37:41 PDT)
- David A Case (Tue Sep 15 2015 - 11:39:57 PDT)
- Hannes Loeffler (Tue Sep 15 2015 - 07:34:01 PDT)
- Jason Swails (Tue Sep 15 2015 - 07:33:10 PDT)
- Sofia Vasilakaki (Tue Sep 15 2015 - 07:29:45 PDT)
- Hannes Loeffler (Tue Sep 15 2015 - 07:18:09 PDT)
- Sofia Vasilakaki (Tue Sep 15 2015 - 07:11:40 PDT)
[AMBER] T-REMD Reproducibility - Cluster v.s Desktop
- Thiago Lipinski Paes (Fri Sep 25 2015 - 12:04:16 PDT)
- Gustavo Seabra (Fri Sep 25 2015 - 11:18:20 PDT)
- Jason Swails (Fri Sep 25 2015 - 10:32:58 PDT)
- Carlos Simmerling (Fri Sep 25 2015 - 10:04:13 PDT)
- Thiago Lipinski Paes (Fri Sep 25 2015 - 09:58:49 PDT)
- Carlos Simmerling (Fri Sep 25 2015 - 09:17:12 PDT)
- Thiago Lipinski Paes (Fri Sep 25 2015 - 09:11:55 PDT)
[AMBER] Test
- George Tzotzos (Wed Sep 16 2015 - 05:18:31 PDT)
[AMBER] Testing the mail server
- George Tzotzos (Sun Sep 13 2015 - 14:51:27 PDT)
[AMBER] Trouble running Thermodynamic Integration in Amber14 with pmemd.
- Jason Swails (Mon Sep 07 2015 - 10:49:05 PDT)
- Timothy Christopher Schutt (Mon Sep 07 2015 - 09:48:49 PDT)
- hannes.loeffler.stfc.ac.uk (Fri Sep 04 2015 - 10:17:27 PDT)
- Timothy Christopher Schutt (Fri Sep 04 2015 - 10:10:18 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Sep 03 2015 - 23:38:07 PDT)
- David A Case (Thu Sep 03 2015 - 18:14:27 PDT)
- Timothy Christopher Schutt (Thu Sep 03 2015 - 15:04:26 PDT)
[AMBER] Updates for PBSA energy calculations
- Jason Swails (Wed Sep 30 2015 - 15:00:18 PDT)
- Christina Berti (Wed Sep 30 2015 - 13:14:04 PDT)
- David A Case (Wed Sep 30 2015 - 11:41:23 PDT)
- Christina Berti (Wed Sep 30 2015 - 08:50:49 PDT)
- Ray Luo, Ph.D. (Tue Sep 29 2015 - 09:57:05 PDT)
- Jason Swails (Mon Sep 28 2015 - 22:07:47 PDT)
- Christina Berti (Mon Sep 28 2015 - 16:17:04 PDT)
[AMBER] Usage of off-diagonal coupling parameters for EVB model
- bijyalaxmi athokpam (Tue Sep 22 2015 - 00:38:17 PDT)
[AMBER] vlimit exceeded and high temperature
- Ruth Helena Tichauer (Fri Sep 18 2015 - 05:48:55 PDT)
- Jason Swails (Fri Sep 18 2015 - 04:29:13 PDT)
- Ruth Helena Tichauer (Fri Sep 18 2015 - 01:52:23 PDT)
- Jason Swails (Wed Sep 16 2015 - 08:07:41 PDT)
- Ruth Helena Tichauer (Wed Sep 16 2015 - 06:16:29 PDT)
- David A Case (Tue Sep 15 2015 - 11:52:01 PDT)
- Ruth Helena Tichauer (Tue Sep 15 2015 - 09:06:34 PDT)
[AMBER] warning when using cpptraj on BB atoms missing
- Fabian Glaser (Mon Sep 21 2015 - 09:09:24 PDT)
- Daniel Roe (Mon Sep 21 2015 - 07:54:32 PDT)
- Fabian gmail (Mon Sep 21 2015 - 07:16:43 PDT)
[AMBER] watershell cpptraj question
- Daniel Roe (Tue Sep 08 2015 - 08:54:01 PDT)
- Travis Hughes (Tue Sep 08 2015 - 08:08:37 PDT)
[AMBER] What is wrong with the minimization?
- David A Case (Mon Sep 14 2015 - 14:40:47 PDT)
- Jason Swails (Mon Sep 14 2015 - 09:22:57 PDT)
- Huggins, Esther, C (Mon Sep 14 2015 - 09:12:07 PDT)
- Jason Swails (Mon Sep 14 2015 - 09:02:20 PDT)
- Huggins, Esther, C (Mon Sep 14 2015 - 07:14:42 PDT)
- David A Case (Sun Sep 13 2015 - 21:08:41 PDT)
- Huggins, Esther, C (Sun Sep 13 2015 - 17:30:50 PDT)
[AMBER] wrap problem with QM/MM
- Covington, Cody Lance (Mon Sep 28 2015 - 07:18:49 PDT)
- Marc van der Kamp (Mon Sep 28 2015 - 01:01:22 PDT)
- Covington, Cody Lance (Sun Sep 27 2015 - 13:49:38 PDT)
[AMBER] xmgrace in microsoft
- Ye Mei (Thu Sep 17 2015 - 22:55:54 PDT)
- Martina Devi (Thu Sep 17 2015 - 22:43:50 PDT)
- Luciano Costa (Fri Sep 11 2015 - 19:14:13 PDT)
- Martina Devi (Thu Sep 10 2015 - 06:43:13 PDT)
- David A Case (Thu Sep 10 2015 - 06:37:17 PDT)
- Jason Swails (Thu Sep 10 2015 - 06:31:26 PDT)
- Martina Devi (Thu Sep 10 2015 - 06:03:09 PDT)
degraded GPU performance
- Alessandro Contini (Tue Sep 22 2015 - 07:50:08 PDT)
important
- Do Yong Kim (Wed Sep 09 2015 - 00:06:23 PDT)
No output
- Damiano Spadoni (Sat Sep 12 2015 - 13:52:00 PDT)

Amber Archive Sep 2015 by subject