Amber Archive Sep 2016: by subject

[AMBER] "ATTN, need revision" in frcmod file / Could not find bond parameter & Could not find angle parameter
- Hannes Loeffler (Fri Sep 16 2016 - 12:16:22 PDT)
- ABEL Stephane 175950 (Fri Sep 16 2016 - 12:12:10 PDT)
- shahab shariati (Fri Sep 16 2016 - 11:25:50 PDT)
[AMBER] 2 ns heating in constant pH tutorial inquiry
- Jason Swails (Mon Sep 26 2016 - 08:45:48 PDT)
- Andrew Schaub (Sun Sep 25 2016 - 08:56:29 PDT)
[AMBER] [Amber] Periodic Box Issue
- Chase Zagorec-Marks (Tue Sep 06 2016 - 09:31:14 PDT)
- Adrian Roitberg (Tue Sep 06 2016 - 09:07:34 PDT)
- Chase Zagorec-Marks (Tue Sep 06 2016 - 09:04:41 PDT)
[AMBER] A refresher on how non-bonding terms are represented in a topology file.
- Jason Swails (Thu Sep 22 2016 - 07:24:49 PDT)
- Bill Ross (Wed Sep 21 2016 - 19:44:36 PDT)
- David A Case (Wed Sep 21 2016 - 19:29:18 PDT)
- Jason Swails (Wed Sep 21 2016 - 17:48:31 PDT)
- Christian Schafmeister (Wed Sep 21 2016 - 13:13:07 PDT)
- Daniel Roe (Wed Sep 21 2016 - 13:09:14 PDT)
- Christian Schafmeister (Wed Sep 21 2016 - 10:10:42 PDT)
[AMBER] about print_res in MMPBSA.py
- Jason Swails (Tue Sep 06 2016 - 13:37:58 PDT)
- Thomas Evangelidis (Tue Sep 06 2016 - 10:44:46 PDT)
- Jason Swails (Tue Sep 06 2016 - 09:37:57 PDT)
- Thomas Evangelidis (Tue Sep 06 2016 - 08:37:34 PDT)
[AMBER] accelerated MD
- Neha Gandhi (Thu Sep 01 2016 - 14:55:27 PDT)
[AMBER] ACS COMP award deadline for Spring 2017
- Carlos Simmerling (Wed Sep 28 2016 - 03:48:05 PDT)
[AMBER] adaptive qm/mm NVT, number of quantum atoms outside the legal range
- Dr. Andreas W. Goetz (Mon Sep 19 2016 - 20:46:27 PDT)
- Stregone (Mon Sep 19 2016 - 05:12:19 PDT)
[AMBER] Add Molecule symmetry to sander
- Carlos Simmerling (Sun Sep 11 2016 - 04:39:29 PDT)
- tanfei777.sina.cn (Sat Sep 10 2016 - 17:58:28 PDT)
[AMBER] AMBER installation help
- Huma Tahir (Sun Sep 18 2016 - 02:49:14 PDT)
- Hai Nguyen (Sat Sep 17 2016 - 15:37:02 PDT)
- Bill Ross (Sat Sep 17 2016 - 13:19:09 PDT)
- Huma Tahir (Sat Sep 17 2016 - 12:58:22 PDT)
[AMBER] Amber NaN error
- David A Case (Wed Sep 28 2016 - 06:04:45 PDT)
- DIAO Jianxiong (Tue Sep 27 2016 - 15:53:13 PDT)
[AMBER] Amber16: COM's in GPU version
- Ross Walker (Tue Sep 20 2016 - 08:05:43 PDT)
- Carlos Simmerling (Tue Sep 20 2016 - 07:53:13 PDT)
[AMBER] Any idea about this Amber compile bug?
- Scott Brozell (Thu Sep 01 2016 - 20:13:28 PDT)
- Jason Swails (Thu Sep 01 2016 - 17:53:07 PDT)
- David Cerutti (Thu Sep 01 2016 - 13:45:35 PDT)
[AMBER] aromatic ring plane distorted
- Bill Ross (Fri Sep 16 2016 - 10:26:40 PDT)
- Thomas Evangelidis (Fri Sep 16 2016 - 09:26:35 PDT)
- Carlos Simmerling (Fri Sep 16 2016 - 04:41:00 PDT)
- Thomas Evangelidis (Fri Sep 16 2016 - 04:03:03 PDT)
[AMBER] autocorr of hydrogen bonds
- David A Case (Thu Sep 01 2016 - 09:46:22 PDT)
- Roitberg,Adrian E (Thu Sep 01 2016 - 09:27:06 PDT)
- Osman, Roman (Thu Sep 01 2016 - 09:06:44 PDT)
[AMBER] autoimage bug?
- Daniel Roe (Wed Sep 28 2016 - 06:53:45 PDT)
- Filip Persson (Tue Sep 27 2016 - 23:48:13 PDT)
- Daniel Roe (Mon Sep 19 2016 - 07:20:50 PDT)
- Filip Persson (Thu Sep 08 2016 - 05:34:09 PDT)
- Filip Persson (Thu Sep 08 2016 - 05:32:36 PDT)
[AMBER] bad atom type: Mn
- Thomas Evangelidis (Mon Sep 12 2016 - 18:08:07 PDT)
[AMBER] Calculations of dG for protein-ions
- James Starlight (Sat Sep 10 2016 - 13:57:36 PDT)
[AMBER] Can amber handle carbon -- nitrogen double and single bond?
- Bill Ross (Wed Sep 28 2016 - 02:38:18 PDT)
- Ming Tang (Wed Sep 28 2016 - 01:43:52 PDT)
[AMBER] chamber in parmed (Amber16)
- Song-Ho Chong (Sun Sep 18 2016 - 17:52:22 PDT)
- Jason Swails (Sun Sep 18 2016 - 11:04:32 PDT)
- Song-Ho Chong (Sun Sep 18 2016 - 09:21:18 PDT)
[AMBER] change the atom charge in a restart simulations
- windy (Wed Aug 31 2016 - 18:53:55 PDT)
[AMBER] changeLJPair/pmemd.cuda
- David A Case (Fri Sep 16 2016 - 02:10:27 PDT)
- Batuhan Kav (Thu Sep 15 2016 - 13:32:23 PDT)
[AMBER] changepot
- Adrian Roitberg (Wed Sep 07 2016 - 11:53:17 PDT)
- Xiaoliu Zhang (Wed Sep 07 2016 - 11:49:10 PDT)
[AMBER] changing atom type
- Jacopo Sgrignani (Thu Sep 01 2016 - 01:43:19 PDT)
[AMBER] Checking AmberTools16 installation
- David A Case (Tue Sep 06 2016 - 05:52:56 PDT)
- Bence Hégely (Tue Sep 06 2016 - 05:24:34 PDT)
[AMBER] comparing pytraj vs. sander output
- Jason Swails (Tue Sep 13 2016 - 10:36:39 PDT)
- Niel Henriksen (Tue Sep 13 2016 - 09:56:36 PDT)
- Hai Nguyen (Tue Sep 13 2016 - 09:52:49 PDT)
- Niel Henriksen (Tue Sep 13 2016 - 09:48:25 PDT)
- Hai Nguyen (Tue Sep 13 2016 - 09:41:44 PDT)
- Hai Nguyen (Tue Sep 13 2016 - 09:39:52 PDT)
- Jason Swails (Tue Sep 13 2016 - 09:19:18 PDT)
- Hai Nguyen (Tue Sep 13 2016 - 09:06:56 PDT)
- Daniel Roe (Tue Sep 13 2016 - 08:29:42 PDT)
- Niel Henriksen (Tue Sep 13 2016 - 08:10:23 PDT)
- Daniel Roe (Tue Sep 13 2016 - 07:53:19 PDT)
- Nhai (Tue Sep 13 2016 - 07:40:38 PDT)
- Niel Henriksen (Tue Sep 13 2016 - 07:34:19 PDT)
- Jason Swails (Tue Sep 13 2016 - 03:48:01 PDT)
- Hai Nguyen (Mon Sep 12 2016 - 22:52:13 PDT)
- Niel Henriksen (Mon Sep 12 2016 - 22:07:57 PDT)
[AMBER] Continue a simulation run
- Hai Nguyen (Fri Sep 16 2016 - 10:51:20 PDT)
- Pooja Kesari (Fri Sep 16 2016 - 03:40:41 PDT)
- David A Case (Fri Sep 16 2016 - 02:05:49 PDT)
- Bilal Nizami (Thu Sep 15 2016 - 10:13:58 PDT)
- Pooja Kesari (Thu Sep 15 2016 - 08:18:47 PDT)
[AMBER] cpinutil.py describe flag
- Jason Swails (Mon Sep 12 2016 - 12:30:41 PDT)
- Elisa Pieri (Mon Sep 12 2016 - 08:44:48 PDT)
- Jason Swails (Mon Sep 12 2016 - 08:15:32 PDT)
- Elisa Pieri (Mon Sep 12 2016 - 07:47:03 PDT)
[AMBER] cpptraj
- Daniel Roe (Mon Sep 12 2016 - 10:43:31 PDT)
- Bill Ross (Mon Sep 12 2016 - 02:28:11 PDT)
- Beale, John (Mon Sep 12 2016 - 02:16:14 PDT)
[AMBER] cpptraj gist core dumped
- Steven Ramsey (Fri Sep 23 2016 - 08:34:48 PDT)
- Daniel Roe (Fri Sep 23 2016 - 05:22:11 PDT)
- Nhai (Fri Sep 23 2016 - 00:11:21 PDT)
- peter.schmidtke.discngine.servier.com (Thu Sep 22 2016 - 23:40:23 PDT)
[AMBER] create a cubic box of 4.5 nm
- David A Case (Mon Sep 26 2016 - 05:17:59 PDT)
- Jesmita Dhar (Mon Sep 26 2016 - 01:39:18 PDT)
[AMBER] delete residue in tleap
- Bill Ross (Sun Sep 18 2016 - 17:24:58 PDT)
- Thomas Evangelidis (Sun Sep 18 2016 - 16:55:35 PDT)
- Bill Ross (Sun Sep 18 2016 - 16:33:20 PDT)
- Thomas Evangelidis (Sun Sep 18 2016 - 15:46:19 PDT)
[AMBER] DFTB and slater koster files
- Markus Kaukonen (Wed Sep 21 2016 - 02:30:58 PDT)
[AMBER] dihedral PCA amber
- Neha Gandhi (Wed Sep 28 2016 - 03:19:46 PDT)
- Daniel Roe (Tue Sep 27 2016 - 05:42:11 PDT)
- Neha Gandhi (Mon Sep 26 2016 - 21:09:08 PDT)
- Daniel Roe (Fri Sep 23 2016 - 05:11:42 PDT)
- Bill Ross (Thu Sep 22 2016 - 19:14:46 PDT)
- Neha Gandhi (Thu Sep 22 2016 - 19:00:41 PDT)
- Daniel Roe (Thu Sep 22 2016 - 12:16:11 PDT)
- Neha Gandhi (Wed Sep 21 2016 - 20:08:10 PDT)
[AMBER] Disparities in H-bond lifetimes calculated through different approaches
- Daniel Roe (Thu Sep 29 2016 - 06:22:42 PDT)
- Praneeth Bommisetti (Wed Sep 28 2016 - 23:03:25 PDT)
[AMBER] distance based mask
- Kris Feher (Wed Sep 07 2016 - 12:52:08 PDT)
- Daniel Roe (Wed Sep 07 2016 - 12:26:07 PDT)
- Kris Feher (Wed Sep 07 2016 - 12:09:24 PDT)
[AMBER] DNA residue atom names.
- Bill Ross (Fri Sep 16 2016 - 13:14:43 PDT)
- David A Case (Fri Sep 16 2016 - 02:19:51 PDT)
- Christian Schafmeister (Thu Sep 15 2016 - 17:57:41 PDT)
[AMBER] error in sander minimization
- Prayagraj Fandilolu (Fri Sep 02 2016 - 07:30:45 PDT)
- David A Case (Thu Sep 01 2016 - 09:41:54 PDT)
- Prayagraj Fandilolu (Thu Sep 01 2016 - 04:45:13 PDT)
[AMBER] Error in the second step using MCPB.py
- Pengfei Li (Fri Sep 30 2016 - 19:49:17 PDT)
- Tiffani Rovira (Thu Sep 29 2016 - 02:26:41 PDT)
[AMBER] Error: cannot run "/share/apps/amber/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
- Samuel Bowerman (Tue Sep 13 2016 - 11:00:05 PDT)
- shahab shariati (Tue Sep 13 2016 - 04:31:45 PDT)
- shahab shariati (Tue Sep 13 2016 - 04:28:03 PDT)
- shahab shariati (Tue Sep 13 2016 - 04:25:41 PDT)
[AMBER] FATAL: Atom .R<CLEU 124>.A<H13 34> does not have a type. Failed to generate parameters Parameter file was not saved.
- Yeng-Tseng Wang (Wed Sep 14 2016 - 15:03:29 PDT)
- David A Case (Wed Sep 14 2016 - 06:40:52 PDT)
- Bill Ross (Tue Sep 13 2016 - 23:32:36 PDT)
- shahab shariati (Tue Sep 13 2016 - 22:29:57 PDT)
[AMBER] fixing concentration in implicit solvent simulation
- David A Case (Thu Sep 22 2016 - 06:10:20 PDT)
- Jason Swails (Wed Sep 21 2016 - 17:58:00 PDT)
- Chitrak Gupta (Wed Sep 21 2016 - 13:11:51 PDT)
- Carlos Simmerling (Tue Sep 20 2016 - 08:42:49 PDT)
- Chitrak Gupta (Tue Sep 20 2016 - 08:12:48 PDT)
[AMBER] FMN parameters
- ruqaiya khalil (Thu Sep 29 2016 - 02:51:05 PDT)
- Bill Ross (Thu Sep 29 2016 - 00:48:34 PDT)
- Bill Ross (Wed Sep 28 2016 - 23:47:46 PDT)
- ruqaiya khalil (Wed Sep 28 2016 - 22:46:13 PDT)
[AMBER] Follow up
- David A Case (Fri Sep 16 2016 - 02:13:40 PDT)
- Mochena, Mogus D. (Thu Sep 15 2016 - 14:15:48 PDT)
[AMBER] Force field ff14SB
- Anna Cebrian Prats (Wed Sep 14 2016 - 09:11:16 PDT)
- Carlos Simmerling (Wed Sep 14 2016 - 09:05:33 PDT)
- Jason Swails (Wed Sep 14 2016 - 09:00:34 PDT)
- Anna Cebrian Prats (Wed Sep 14 2016 - 04:06:44 PDT)
[AMBER] frame wise MMPBSA energy difference
- Hirdesh Kumar (Wed Sep 21 2016 - 07:12:39 PDT)
- Jason Swails (Wed Sep 21 2016 - 06:46:53 PDT)
- Hirdesh Kumar (Wed Sep 21 2016 - 02:15:07 PDT)
[AMBER] Fullerene RESP charges derivation
- FyD (Tue Sep 20 2016 - 02:01:13 PDT)
- David A Case (Wed Sep 14 2016 - 06:36:42 PDT)
- Fabio Bologna (Tue Sep 13 2016 - 06:04:41 PDT)
[AMBER] Fwd: File redirection commands with targeted MD
- Michael Shokhen (Fri Sep 09 2016 - 01:36:01 PDT)
- Bill Ross (Thu Sep 08 2016 - 10:03:56 PDT)
- Sonia Ziada (Thu Sep 08 2016 - 07:45:22 PDT)
- Florent Barbault (Thu Sep 08 2016 - 07:24:02 PDT)
- Sonia Ziada (Thu Sep 08 2016 - 06:37:39 PDT)
- Carlos Simmerling (Thu Sep 08 2016 - 06:26:31 PDT)
- Sonia Ziada (Thu Sep 08 2016 - 06:11:32 PDT)
- Sonia Ziada (Fri Sep 02 2016 - 00:03:35 PDT)
[AMBER] Fwd: lig.frcmod file is not formed
- Vishal Nemaysh (Mon Sep 05 2016 - 00:08:32 PDT)
[AMBER] Fwd: MD stop at different time period without giving any error
- David A Case (Thu Sep 01 2016 - 04:35:05 PDT)
- Garima Singh (Thu Sep 01 2016 - 01:39:30 PDT)
[AMBER] Fwd: query with amber
- Bill Ross (Wed Sep 14 2016 - 23:26:03 PDT)
- Pooja Kesari (Wed Sep 14 2016 - 21:47:20 PDT)
- David A Case (Wed Sep 14 2016 - 06:54:41 PDT)
- Bill Ross (Wed Sep 14 2016 - 01:27:07 PDT)
- Pooja Kesari (Wed Sep 14 2016 - 00:12:40 PDT)
- Bill Ross (Tue Sep 13 2016 - 23:39:41 PDT)
- Pooja Kesari (Tue Sep 13 2016 - 23:00:50 PDT)
[AMBER] generating topology file for non-standard amino acid
- David A Case (Sat Sep 10 2016 - 09:40:36 PDT)
- Chitrak Gupta (Fri Sep 09 2016 - 15:17:06 PDT)
[AMBER] Glaycam04 version for q4md-CD FF
- FyD (Tue Sep 20 2016 - 05:43:19 PDT)
- Lachele Foley (Tue Sep 20 2016 - 02:08:41 PDT)
- FyD (Tue Sep 20 2016 - 01:57:00 PDT)
- Helen Lvy (Thu Sep 15 2016 - 07:20:41 PDT)
[AMBER] GROMACS File Conversion Subtlety
- Mark Abraham (Mon Sep 05 2016 - 08:19:19 PDT)
[AMBER] hbond and autoimage
- Daniel Roe (Fri Sep 16 2016 - 06:17:11 PDT)
- Francesco Gentile (Thu Sep 15 2016 - 23:24:29 PDT)
[AMBER] historical changes to LYN charges in amber03
- Mark Abraham (Tue Sep 06 2016 - 07:08:24 PDT)
- David A Case (Mon Sep 05 2016 - 17:45:05 PDT)
- Carlos Simmerling (Mon Sep 05 2016 - 09:41:43 PDT)
- Mark Abraham (Mon Sep 05 2016 - 09:05:44 PDT)
- Carlos Simmerling (Mon Sep 05 2016 - 08:56:47 PDT)
- Mark Abraham (Mon Sep 05 2016 - 08:40:38 PDT)
[AMBER] How aggressively should bond, angle, torsion parameters be coalesced?
- Christian Schafmeister (Sat Sep 24 2016 - 13:03:34 PDT)
- W. Andeas Svrcek-Seiler (Sat Sep 24 2016 - 12:26:07 PDT)
- Christian Schafmeister (Sat Sep 24 2016 - 06:58:11 PDT)
[AMBER] How by residue decomposition in MMPBSA.py is performed?
- Jason Swails (Tue Sep 13 2016 - 05:28:40 PDT)
- Irina Ivanova (Mon Sep 12 2016 - 21:53:48 PDT)
[AMBER] How to "not" strip an ion (say Mg) in MMPBSA
- Jason Swails (Wed Sep 14 2016 - 08:58:20 PDT)
- Bruno Falcone (Wed Sep 14 2016 - 08:13:52 PDT)
- Hirdesh Kumar (Wed Sep 14 2016 - 03:06:57 PDT)
[AMBER] How to 2D-RDF in cpptraj.
- Saman Yousuf ali (Thu Sep 22 2016 - 01:05:25 PDT)
[AMBER] How to assign frame range for cpptraj analysis?
- sunyeping (Wed Sep 07 2016 - 02:44:36 PDT)
- Anna Cebrian Prats (Wed Sep 07 2016 - 02:21:06 PDT)
- sunyeping (Wed Sep 07 2016 - 02:04:30 PDT)
[AMBER] how to center a polipeptide inside a solvent box
- David A Case (Fri Sep 02 2016 - 05:37:57 PDT)
- Elisa Pieri (Fri Sep 02 2016 - 03:01:02 PDT)
- Jason Swails (Thu Sep 01 2016 - 17:47:04 PDT)
- Elisa Pieri (Thu Sep 01 2016 - 05:27:59 PDT)
[AMBER] How to fixed residues in amber?
- David A Case (Tue Sep 06 2016 - 04:20:40 PDT)
- windy (Mon Sep 05 2016 - 19:32:36 PDT)
[AMBER] How to get GppNHp parameters.
- Dd H (Fri Sep 16 2016 - 19:44:46 PDT)
[AMBER] How to read prmtop file flag pointer section
- Jason Swails (Fri Sep 30 2016 - 12:35:02 PDT)
- Xiaoyu Wang (Fri Sep 30 2016 - 11:43:05 PDT)
[AMBER] Hydrophobic interactions in MM-GBSA
- Carlos Simmerling (Sun Sep 04 2016 - 16:37:44 PDT)
- Nhai (Sun Sep 04 2016 - 14:56:29 PDT)
- Atila Petrosian (Sun Sep 04 2016 - 14:14:37 PDT)
- Carlos Simmerling (Sun Sep 04 2016 - 14:02:44 PDT)
- Atila Petrosian (Sun Sep 04 2016 - 13:37:01 PDT)
[AMBER] Implicit solvent with GPU AMBER and Pulling direction in SMD
- Ana Bergues (Thu Sep 22 2016 - 00:38:16 PDT)
[AMBER] Installing amber tools on ubuntu
- chandan patel (Sat Sep 17 2016 - 15:30:22 PDT)
- Bill Ross (Sat Sep 17 2016 - 13:20:31 PDT)
- neelam wafa (Sat Sep 17 2016 - 13:07:37 PDT)
[AMBER] invoking MPI_ABORT causes Open MPI to kill all MPI processes.
- David A Case (Wed Sep 28 2016 - 11:53:52 PDT)
- Nhai (Wed Sep 28 2016 - 08:12:47 PDT)
- Pooja Kesari (Wed Sep 28 2016 - 07:47:42 PDT)
- David A Case (Wed Sep 28 2016 - 06:09:46 PDT)
- Pooja Kesari (Wed Sep 28 2016 - 04:38:28 PDT)
[AMBER] Issue regarding parametrization
- David A Case (Tue Sep 27 2016 - 05:11:46 PDT)
- Mahrukh Imtiaz (Tue Sep 27 2016 - 04:22:41 PDT)
[AMBER] LEaP and PARMSETs
- David A Case (Fri Sep 30 2016 - 04:57:06 PDT)
[AMBER] lig.frcmod file is not formed
- Vishal Nemaysh (Sat Sep 03 2016 - 07:37:58 PDT)
[AMBER] lipid bilayer
- Sofia Vasilakaki (Sat Sep 10 2016 - 16:17:05 PDT)
[AMBER] mdin for LIO interface
- Hector A. Baldoni (Wed Sep 28 2016 - 04:03:53 PDT)
[AMBER] minimzation & MD in vacuo
- Thomas Evangelidis (Thu Sep 22 2016 - 16:01:03 PDT)
- Thomas Evangelidis (Thu Sep 22 2016 - 09:54:48 PDT)
[AMBER] MM-PBSA calculation in different temprature
- shahab shariati (Fri Sep 23 2016 - 07:03:32 PDT)
- Adrian Roitberg (Fri Sep 23 2016 - 05:45:58 PDT)
- shahab shariati (Fri Sep 23 2016 - 05:07:04 PDT)
[AMBER] MM-PBSA, Protein-nucleic acids free energy calculations
- Jiri Sponer (Wed Sep 14 2016 - 11:27:16 PDT)
- hari krishna (Wed Sep 14 2016 - 10:54:13 PDT)
- Vlad Cojocaru (Wed Sep 14 2016 - 07:57:36 PDT)
- David A Case (Wed Sep 14 2016 - 06:49:43 PDT)
- Carlos Simmerling (Wed Sep 14 2016 - 03:02:12 PDT)
- hari krishna (Tue Sep 13 2016 - 22:30:10 PDT)
[AMBER] MMPBSA analysis for a heme protein
- David A Case (Wed Sep 07 2016 - 04:50:03 PDT)
- Smriti Sharma (Tue Sep 06 2016 - 22:07:34 PDT)
[AMBER] MMPBSA with different external Dielectric Constant
- Jason Swails (Mon Sep 12 2016 - 20:41:56 PDT)
- Elvis Martis (Mon Sep 12 2016 - 20:12:03 PDT)
- Adrian Roitberg (Mon Sep 12 2016 - 08:29:04 PDT)
- Jason Swails (Mon Sep 12 2016 - 05:28:21 PDT)
- Elvis Martis (Mon Sep 12 2016 - 03:15:25 PDT)
[AMBER] MMPBSA.py error Your ligand residues must be sequential in your complex
- Dwight McGee (Wed Sep 28 2016 - 07:19:12 PDT)
- maryam azimzadehirani (Wed Sep 28 2016 - 06:06:42 PDT)
[AMBER] netcdf trajectory
- Markowska (Fri Sep 30 2016 - 06:08:08 PDT)
- Daniel Roe (Fri Sep 30 2016 - 05:28:58 PDT)
- Markowska (Fri Sep 30 2016 - 01:29:50 PDT)
- Hai Nguyen (Mon Sep 26 2016 - 10:31:39 PDT)
- Kshatresh Dutta Dubey (Mon Sep 26 2016 - 06:25:19 PDT)
- Jason Swails (Sun Sep 25 2016 - 09:58:10 PDT)
- Bill Ross (Sun Sep 25 2016 - 09:45:24 PDT)
- Bill Ross (Sun Sep 25 2016 - 09:31:08 PDT)
- TERREUX RAPHAEL (Sun Sep 25 2016 - 01:28:09 PDT)
- Andrew Bostick (Sun Sep 25 2016 - 01:20:29 PDT)
- Bill Ross (Sun Sep 25 2016 - 00:44:48 PDT)
- Bill Ross (Sun Sep 25 2016 - 00:30:14 PDT)
- Andrew Bostick (Sun Sep 25 2016 - 00:09:01 PDT)
- Hirdesh Kumar (Sat Sep 24 2016 - 23:06:38 PDT)
- Bill Ross (Sat Sep 24 2016 - 13:53:48 PDT)
- Andrew Bostick (Sat Sep 24 2016 - 13:39:38 PDT)
- David A Case (Fri Sep 23 2016 - 05:23:52 PDT)
- Daniel Roe (Fri Sep 23 2016 - 05:17:38 PDT)
- Andrew Bostick (Fri Sep 23 2016 - 01:28:50 PDT)
[AMBER] noshakemask and qmshake
- Fabrício Bracht (Thu Sep 01 2016 - 11:34:47 PDT)
[AMBER] NVIDIA GTX-970 Class Action Suit $30 settlement link
- Ross Walker (Mon Sep 12 2016 - 12:03:23 PDT)
[AMBER] on periodic conditions and unspecified launch failure
- Jason Swails (Fri Sep 30 2016 - 05:06:03 PDT)
- Elisa Pieri (Fri Sep 30 2016 - 04:42:21 PDT)
- David A Case (Thu Sep 29 2016 - 11:53:59 PDT)
- Jason Swails (Thu Sep 29 2016 - 09:40:28 PDT)
- Elisa Pieri (Wed Sep 28 2016 - 13:46:26 PDT)
[AMBER] On the simulation of phosphate ions in water solution
- Niel Henriksen (Thu Sep 08 2016 - 19:08:17 PDT)
- Casalini Tommaso (Thu Sep 08 2016 - 01:49:56 PDT)
[AMBER] Parameters for GppNHp ligand.
- Dd H (Wed Sep 14 2016 - 07:31:29 PDT)
[AMBER] Parmchk - missing improper parameter for nitro group
- David A Case (Thu Sep 22 2016 - 06:34:00 PDT)
- Miha Purg (Wed Sep 21 2016 - 00:25:45 PDT)
[AMBER] Parmchk - missing nitro improper
- Miha Purg (Mon Sep 19 2016 - 11:50:37 PDT)
[AMBER] Parmed.py, deleteBond and setBond
- Aronica, Pietro (Sun Sep 04 2016 - 21:18:05 PDT)
[AMBER] PCA plotting
- Jason Swails (Mon Sep 12 2016 - 05:36:11 PDT)
- waleed zalloum (Sun Sep 11 2016 - 04:00:32 PDT)
[AMBER] PGI Fortran/C/C++ workstation
- Hector A. Baldoni (Mon Sep 26 2016 - 05:51:34 PDT)
- Hector A. Baldoni (Mon Sep 26 2016 - 05:29:32 PDT)
[AMBER] Plot activesite water vs time.
- mmaestre (Wed Sep 21 2016 - 22:15:46 PDT)
- Saman Yousuf ali (Wed Sep 21 2016 - 22:00:29 PDT)
- mmaestre (Wed Sep 21 2016 - 21:49:10 PDT)
- Saman Yousuf ali (Wed Sep 21 2016 - 21:24:38 PDT)
[AMBER] PME calculation for Vacuum?
- Mochena, Mogus D. (Sat Sep 10 2016 - 09:30:55 PDT)
- David A Case (Sat Sep 10 2016 - 09:19:07 PDT)
- Bill Ross (Fri Sep 09 2016 - 14:35:24 PDT)
- Bill Ross (Fri Sep 09 2016 - 14:19:10 PDT)
- Mochena, Mogus D. (Fri Sep 09 2016 - 14:10:53 PDT)
- Charles Lin (Fri Sep 09 2016 - 11:51:12 PDT)
- Bill Ross (Fri Sep 09 2016 - 11:49:06 PDT)
- Mochena, Mogus D. (Fri Sep 09 2016 - 11:36:27 PDT)
[AMBER] pmemd Segmentation fault on Tutorial A27
- liu junjun (Mon Sep 12 2016 - 15:08:19 PDT)
- liu junjun (Mon Sep 12 2016 - 09:01:33 PDT)
[AMBER] pmemd.cuda: multiple bonds illegal for SHAKEH
- Jason Swails (Mon Sep 26 2016 - 08:36:55 PDT)
- Hannes Loeffler (Mon Sep 26 2016 - 07:57:31 PDT)
[AMBER] positive electrostatic energy MM-PBSA
- David A Case (Wed Sep 21 2016 - 04:38:36 PDT)
- Trang Nguyen (Tue Sep 20 2016 - 22:03:34 PDT)
[AMBER] Potential Energy in 3D-RISM
- Tyler Luchko (Lists) (Wed Sep 14 2016 - 15:07:03 PDT)
- Maksim Mišin (Wed Sep 14 2016 - 12:16:29 PDT)
[AMBER] Pressure of the system during equilibration
- Daniel Roe (Thu Sep 29 2016 - 06:28:17 PDT)
- Debodyuti Dutta (Thu Sep 29 2016 - 06:01:20 PDT)
[AMBER] problem about Using ParmEd or xParmEd
- Jason Swails (Mon Sep 26 2016 - 08:32:52 PDT)
- 杨金鹏 (Mon Sep 26 2016 - 04:06:02 PDT)
[AMBER] Problem regarding sccdftb not converging
- Thakur, Abhishek (Fri Sep 30 2016 - 09:07:04 PDT)
- amitosh gautam (Thu Sep 29 2016 - 22:36:34 PDT)
[AMBER] Problem with atommap function in cpptraj (v16)
- Daniel Roe (Tue Sep 20 2016 - 08:11:15 PDT)
- Samuel Bowerman (Tue Sep 20 2016 - 08:01:29 PDT)
- Daniel Roe (Tue Sep 20 2016 - 07:06:49 PDT)
[AMBER] Problem with CRD files
- Daniel Roe (Tue Sep 20 2016 - 08:24:35 PDT)
- Daniel Roe (Mon Sep 19 2016 - 07:12:24 PDT)
- dhanasekar.mbu.iisc.ernet.in (Fri Sep 16 2016 - 02:55:38 PDT)
- Hai Nguyen (Thu Sep 15 2016 - 07:22:15 PDT)
- dhanasekar.mbu.iisc.ernet.in (Wed Sep 14 2016 - 23:24:10 PDT)
- Nhai (Thu Sep 08 2016 - 10:35:36 PDT)
- Nhai (Thu Sep 08 2016 - 10:25:25 PDT)
- dhanasekar.mbu.iisc.ernet.in (Thu Sep 08 2016 - 08:05:38 PDT)
[AMBER] Problem with MCPB.py workflow after calculation of force constants.
- Pengfei Li (Thu Sep 08 2016 - 07:58:24 PDT)
- Marcelo Andrade Chagas (Wed Sep 07 2016 - 08:16:23 PDT)
- Abhi Acharya (Wed Sep 07 2016 - 02:15:49 PDT)
[AMBER] Problems about creating ligand leap input files
- Bill Ross (Sun Sep 11 2016 - 21:14:47 PDT)
- 康宁 (Sun Sep 11 2016 - 20:37:20 PDT)
[AMBER] QMMM simulation with user-specified basis set in amber
- zycz138.126.com (Thu Sep 01 2016 - 20:31:59 PDT)
[AMBER] query regarding radial distribution function plot.
- Daniel Roe (Tue Sep 06 2016 - 18:26:53 PDT)
- Saman Yousuf ali (Tue Sep 06 2016 - 14:08:46 PDT)
[AMBER] query regaridng unrestarint minimization step
- Saman Yousuf ali (Fri Sep 02 2016 - 00:29:56 PDT)
[AMBER] Question about QM/MM
- Anna Cebrian Prats (Wed Sep 07 2016 - 07:48:00 PDT)
- Adrian Roitberg (Tue Sep 06 2016 - 08:36:18 PDT)
- Anna Cebrian Prats (Tue Sep 06 2016 - 08:26:29 PDT)
- Adrian Roitberg (Tue Sep 06 2016 - 07:44:25 PDT)
- Anna Cebrian Prats (Tue Sep 06 2016 - 05:57:54 PDT)
- David A Case (Tue Sep 06 2016 - 04:17:09 PDT)
- Anna Cebrian Prats (Mon Sep 05 2016 - 09:14:31 PDT)
- Marc van der Kamp (Fri Sep 02 2016 - 12:09:18 PDT)
- Adrian Roitberg (Fri Sep 02 2016 - 10:59:31 PDT)
- Fabrício Bracht (Fri Sep 02 2016 - 10:57:31 PDT)
- Adrian Roitberg (Fri Sep 02 2016 - 10:54:07 PDT)
- Fabrício Bracht (Fri Sep 02 2016 - 10:46:06 PDT)
- Adrian Roitberg (Fri Sep 02 2016 - 10:37:53 PDT)
- Fabrício Bracht (Fri Sep 02 2016 - 10:34:20 PDT)
- Adrian Roitberg (Fri Sep 02 2016 - 10:09:35 PDT)
- Fabrício Bracht (Fri Sep 02 2016 - 10:03:30 PDT)
- Gustavo Seabra (Fri Sep 02 2016 - 09:17:30 PDT)
- Adrian Roitberg (Fri Sep 02 2016 - 08:27:46 PDT)
- Anna Cebrian Prats (Fri Sep 02 2016 - 02:01:06 PDT)
[AMBER] question on the reference data of GIST
- Tom Kurtzman (Thu Sep 08 2016 - 08:04:18 PDT)
- David A Case (Thu Sep 08 2016 - 05:02:01 PDT)
- Shunsuke Mizutani (Thu Sep 08 2016 - 01:54:31 PDT)
[AMBER] R: Fullerene RESP charges derivation
- Fabio Bologna (Wed Sep 14 2016 - 07:18:52 PDT)
[AMBER] Radial Distribution Function
- David A Case (Thu Sep 08 2016 - 05:04:40 PDT)
- Fatema Al-Haddad [fy14fmah] (Thu Sep 08 2016 - 02:27:02 PDT)
[AMBER] radial distribution function from 1drism calculation
- Tyler Luchko (Lists) (Thu Sep 01 2016 - 13:26:05 PDT)
- Jingyi Yan (Thu Sep 01 2016 - 12:21:32 PDT)
[AMBER] Regarding the use of sed command to replace water
- David A Case (Thu Sep 01 2016 - 04:30:01 PDT)
- MOHD HOMAIDUR RAHMAN (Wed Aug 31 2016 - 21:29:51 PDT)
[AMBER] RESP charge fitting error in MCPB.py
- zycz138.126.com (Mon Sep 26 2016 - 17:54:06 PDT)
[AMBER] resp charges in LIPID14
- Dickson, Callum J (Tue Sep 06 2016 - 06:43:36 PDT)
- jojartb.jgypk.u-szeged.hu (Tue Sep 06 2016 - 04:55:21 PDT)
[AMBER] Restrain in Umbrella Sampling
- ATUL KUMAR (Sun Sep 25 2016 - 07:12:10 PDT)
[AMBER] RMS-fit during PCA
- Hai Nguyen (Fri Sep 02 2016 - 08:42:03 PDT)
- Anasuya Dighe (Fri Sep 02 2016 - 02:38:31 PDT)
[AMBER] Save the average structure from two pdb files
- Hai Nguyen (Fri Sep 30 2016 - 15:47:01 PDT)
- Iqbal, Muhammad Sajid (Fri Sep 30 2016 - 15:22:11 PDT)
[AMBER] scaling of mpi version of pmemd.mpi (AMBER14) and that of the MMPBSA.py.MPI
- Jason Swails (Thu Sep 29 2016 - 11:26:07 PDT)
- Kris Feher (Wed Sep 28 2016 - 12:40:37 PDT)
[AMBER] SCC-DFTB
- Dr. Andreas W. Goetz (Mon Sep 19 2016 - 20:53:29 PDT)
- Thakur, Abhishek (Mon Sep 19 2016 - 07:44:03 PDT)
- Adrian Roitberg (Mon Sep 12 2016 - 09:09:22 PDT)
- Thakur, Abhishek (Mon Sep 12 2016 - 09:04:01 PDT)
[AMBER] Segmentation fault in tleap when using "sequence" command
- Lane Votapka (Thu Sep 22 2016 - 09:12:22 PDT)
- Daniel Roe (Thu Sep 22 2016 - 08:51:36 PDT)
- Lane Votapka (Thu Sep 22 2016 - 08:21:00 PDT)
- Carlos Simmerling (Thu Sep 22 2016 - 08:17:20 PDT)
- Lane Votapka (Thu Sep 22 2016 - 08:14:07 PDT)
- Lane Votapka (Thu Sep 22 2016 - 08:01:08 PDT)
- Bill Ross (Wed Sep 21 2016 - 17:34:26 PDT)
- Daniel Roe (Wed Sep 21 2016 - 17:12:34 PDT)
- Daniel Roe (Wed Sep 21 2016 - 17:11:17 PDT)
- Lane Votapka (Wed Sep 21 2016 - 13:31:58 PDT)
[AMBER] Select a snapshot
- Daniel Roe (Mon Sep 05 2016 - 18:41:40 PDT)
- Anna Cebrian Prats (Mon Sep 05 2016 - 02:42:24 PDT)
[AMBER] setup time with pmemd.cuda
- Daniel Mermelstein (Sat Sep 24 2016 - 10:54:43 PDT)
- Hannes Loeffler (Sat Sep 24 2016 - 02:05:46 PDT)
- Scott Brozell (Thu Sep 22 2016 - 06:17:00 PDT)
- Hannes Loeffler (Thu Sep 22 2016 - 03:10:34 PDT)
- Ross Walker (Wed Sep 21 2016 - 15:23:39 PDT)
- Hannes Loeffler (Wed Sep 21 2016 - 13:17:38 PDT)
- Ross Walker (Wed Sep 21 2016 - 13:08:11 PDT)
- Hannes Loeffler (Wed Sep 21 2016 - 13:01:38 PDT)
- Ross Walker (Wed Sep 21 2016 - 12:16:40 PDT)
- Hannes Loeffler (Wed Sep 21 2016 - 11:06:34 PDT)
[AMBER] Signal: Segmentation fault (11)
- David A Case (Wed Sep 28 2016 - 11:53:28 PDT)
- shahab shariati (Wed Sep 28 2016 - 05:35:08 PDT)
- David A Case (Mon Sep 26 2016 - 18:04:26 PDT)
- shahab shariati (Mon Sep 26 2016 - 12:01:40 PDT)
- David A Case (Sun Sep 25 2016 - 13:38:58 PDT)
- shahab shariati (Sun Sep 25 2016 - 02:10:03 PDT)
[AMBER] Simulation of protein complex with four protein chains
- Jag Silwal (Sat Sep 17 2016 - 12:30:01 PDT)
[AMBER] Speed issue with Accelerated molecular dynamics.
- Abhilash J (Sun Sep 11 2016 - 01:54:44 PDT)
- Marc van der Kamp (Sun Sep 11 2016 - 01:33:48 PDT)
- Abhilash J (Sun Sep 11 2016 - 00:35:47 PDT)
[AMBER] strip waters using distance criteria
- Hai Nguyen (Sat Sep 24 2016 - 23:13:04 PDT)
- Thomas Evangelidis (Sat Sep 24 2016 - 17:14:13 PDT)
- Daniel Roe (Fri Sep 23 2016 - 12:45:09 PDT)
- Thomas Evangelidis (Fri Sep 23 2016 - 06:23:07 PDT)
[AMBER] Switching from PM3-PDDG to SCC-DFT method
- Adrian Roitberg (Wed Sep 07 2016 - 15:29:56 PDT)
- Thakur, Abhishek (Wed Sep 07 2016 - 14:02:20 PDT)
[AMBER] Tcl problem
- Elisa Pieri (Wed Sep 28 2016 - 00:58:19 PDT)
- Jason Swails (Tue Sep 27 2016 - 08:41:47 PDT)
- Jason Swails (Tue Sep 27 2016 - 08:40:12 PDT)
- Hai Nguyen (Tue Sep 27 2016 - 08:37:47 PDT)
- Elisa Pieri (Tue Sep 27 2016 - 07:40:19 PDT)
- Jason Swails (Tue Sep 27 2016 - 07:26:59 PDT)
- Elisa Pieri (Tue Sep 27 2016 - 06:59:02 PDT)
[AMBER] Temperature connected to the dipole convergence in the output
- David A Case (Tue Sep 06 2016 - 06:57:15 PDT)
- BLEY Michael (Mon Sep 05 2016 - 07:39:57 PDT)
[AMBER] tleap cannot solvate unit in amber16
- windy (Tue Sep 27 2016 - 22:33:39 PDT)
- Christina Bergonzo (Tue Sep 27 2016 - 06:25:26 PDT)
- windy (Tue Sep 27 2016 - 05:53:00 PDT)
[AMBER] Trajectory analysis
- Hai Nguyen (Fri Sep 02 2016 - 09:45:57 PDT)
- Anna Cebrian Prats (Fri Sep 02 2016 - 08:05:39 PDT)
[AMBER] Unable to find mopac charges in mopac.out
- David A Case (Fri Sep 02 2016 - 05:31:07 PDT)
- Sneha Rai (Fri Sep 02 2016 - 00:00:45 PDT)
- Ashutosh Shandilya (Thu Sep 01 2016 - 23:46:15 PDT)
- David A Case (Thu Sep 01 2016 - 11:49:57 PDT)
- Marcelo Andrade Chagas (Thu Sep 01 2016 - 11:37:16 PDT)
- Sneha Rai (Thu Sep 01 2016 - 11:31:16 PDT)
- Hannes Loeffler (Thu Sep 01 2016 - 11:01:23 PDT)
- Sneha Rai (Thu Sep 01 2016 - 10:55:58 PDT)
- Marcelo Andrade Chagas (Thu Sep 01 2016 - 05:42:09 PDT)
- Sneha Rai (Thu Sep 01 2016 - 05:29:18 PDT)
[AMBER] Unstable SHAKE
- ABHIJEET CHOWDHURY (Thu Sep 22 2016 - 08:53:49 PDT)
- Carlos Simmerling (Thu Sep 22 2016 - 08:52:35 PDT)
- Daniel Roe (Thu Sep 22 2016 - 08:52:17 PDT)
- ABHIJEET CHOWDHURY (Thu Sep 22 2016 - 08:49:51 PDT)
[AMBER] Upgrade AMBER 14 to 16
- David A Case (Thu Sep 08 2016 - 04:58:06 PDT)
- Anton Perera (Thu Sep 08 2016 - 01:44:52 PDT)
[AMBER] using boundary information from previous run
- David A Case (Fri Sep 30 2016 - 07:17:45 PDT)
- Hirdesh Kumar (Fri Sep 30 2016 - 05:54:46 PDT)
- Daniel Roe (Fri Sep 30 2016 - 05:25:10 PDT)
- Hirdesh Kumar (Fri Sep 30 2016 - 05:19:48 PDT)
- David A Case (Fri Sep 30 2016 - 04:22:09 PDT)
- Hirdesh Kumar (Fri Sep 30 2016 - 01:53:31 PDT)
- David A Case (Thu Sep 29 2016 - 12:05:29 PDT)
- Daniel Roe (Thu Sep 29 2016 - 06:38:42 PDT)
- Hirdesh Kumar (Thu Sep 29 2016 - 04:45:46 PDT)
[AMBER] WARNING: The unperturbed charge of the unit: -0.99 is not zero.
- David A Case (Fri Sep 16 2016 - 02:08:28 PDT)
- shahab shariati (Thu Sep 15 2016 - 11:41:22 PDT)
[AMBER] what is DFTB and SCC-DFTB
- Thakur, Abhishek (Tue Sep 20 2016 - 12:29:18 PDT)
- Marc van der Kamp (Tue Sep 20 2016 - 11:41:08 PDT)
- Thakur, Abhishek (Tue Sep 20 2016 - 07:55:50 PDT)
[AMBER] Which is the best thermostat for cMD?
- Dd H (Tue Sep 06 2016 - 19:11:46 PDT)
- David A Case (Tue Sep 06 2016 - 06:41:37 PDT)
- Dd H (Fri Sep 02 2016 - 01:15:21 PDT)
[AMBER] why does my computer cannot access to Internet after Installing ambertool 16
- Bill Ross (Mon Sep 05 2016 - 18:20:12 PDT)
- Jason Swails (Mon Sep 05 2016 - 18:03:36 PDT)
- Bill Ross (Mon Sep 05 2016 - 10:11:01 PDT)
- sunyeping (Mon Sep 05 2016 - 07:24:23 PDT)
- Bill Ross (Sun Sep 04 2016 - 21:44:16 PDT)
- sunyeping (Sun Sep 04 2016 - 21:39:21 PDT)
- Bill Ross (Sun Sep 04 2016 - 17:53:08 PDT)
- sunyeping (Sun Sep 04 2016 - 16:30:20 PDT)
- David A Case (Sun Sep 04 2016 - 15:01:02 PDT)
- Bill Ross (Sun Sep 04 2016 - 02:22:56 PDT)
- sunyeping (Sun Sep 04 2016 - 01:35:20 PDT)
[AMBER] 回复： Enforced Symmetry?
- tanfei777.sina.cn (Sun Sep 11 2016 - 18:02:50 PDT)
[AMBER] 答复: Amber NaN error
- David A Case (Thu Sep 29 2016 - 11:57:18 PDT)
- DIAO Jianxiong (Wed Sep 28 2016 - 14:24:12 PDT)
Add Molecule symmetry to sander
- Jason Swails (Tue Sep 13 2016 - 05:30:11 PDT)
- tanfei777.sina.cn (Sun Sep 11 2016 - 06:53:00 PDT)
car_to_files.py in AMBER16 is not available.
- Jinfeng Huang (Thu Sep 22 2016 - 02:23:43 PDT)

Amber Archive Sep 2016 by subject