Amber Archive Mar 2016: by subject

[AMBER] 2016 ISQBP Meeting: early registration / abstract submission deadline approaching
- Vlad Cojocaru (Thu Mar 17 2016 - 01:50:08 PDT)
[AMBER] [Amber] Polarizable ff for vacuum
- Carlos Simmerling (Thu Mar 24 2016 - 10:05:22 PDT)
- David A Case (Thu Mar 24 2016 - 09:46:42 PDT)
- Edwin Aponte (Thu Mar 24 2016 - 09:41:52 PDT)
- Carlos Simmerling (Thu Mar 24 2016 - 09:16:19 PDT)
- Edwin Aponte (Thu Mar 24 2016 - 07:48:21 PDT)
[AMBER] [AmberTools15 & Amber14 Installation] Make Test Possible Failures Can Be Ignored or Not
- Hai Nguyen (Thu Mar 24 2016 - 15:02:13 PDT)
- Guqin Shi (Thu Mar 24 2016 - 13:48:56 PDT)
- Charles Lin (Thu Mar 24 2016 - 12:29:04 PDT)
- Guqin Shi (Thu Mar 24 2016 - 12:27:36 PDT)
- Guqin Shi (Thu Mar 24 2016 - 12:24:54 PDT)
- Ross Walker (Thu Mar 24 2016 - 12:22:56 PDT)
- Charles Lin (Thu Mar 24 2016 - 12:19:58 PDT)
- Guqin Shi (Thu Mar 24 2016 - 12:12:11 PDT)
[AMBER] [AmberTools15] “Cluster” with cpptraj: looking for SSR/SST ratio
- Guqin Shi (Mon Mar 28 2016 - 14:35:15 PDT)
[AMBER] A query about using random seed generator in simulations
- David A Case (Tue Mar 15 2016 - 06:58:52 PDT)
- anu chandra (Tue Mar 15 2016 - 05:14:45 PDT)
[AMBER] adding ion
- Carlos Simmerling (Tue Mar 01 2016 - 05:26:46 PST)
- Jason Swails (Tue Mar 01 2016 - 05:07:47 PST)
- zahra khatti (Mon Feb 29 2016 - 22:45:19 PST)
[AMBER] Align namelist for direct dipolar coupling restraints
- Francisco Corzana López (Thu Mar 31 2016 - 10:13:38 PDT)
- David A Case (Wed Mar 30 2016 - 10:18:05 PDT)
- Francisco Corzana López (Wed Mar 30 2016 - 08:59:39 PDT)
[AMBER] Amber 14 - "Error: Unsupported CUDA version 7.5 detected"
- Enrique Frio (Sun Mar 20 2016 - 20:53:10 PDT)
- Jason Swails (Fri Mar 18 2016 - 15:07:10 PDT)
- Enrique Frio (Fri Mar 18 2016 - 14:45:30 PDT)
- Jason Swails (Fri Mar 18 2016 - 10:15:55 PDT)
- Jason Swails (Fri Mar 18 2016 - 10:09:55 PDT)
- Enrique Frio (Fri Mar 18 2016 - 05:55:49 PDT)
- Enrique Frio (Fri Mar 18 2016 - 05:48:08 PDT)
- Enrique Frio (Thu Mar 17 2016 - 18:25:18 PDT)
- Jason Swails (Thu Mar 17 2016 - 16:05:47 PDT)
- Enrique Frio (Thu Mar 17 2016 - 15:55:15 PDT)
- Ross Walker (Thu Mar 17 2016 - 08:02:24 PDT)
- Enrique Frio (Thu Mar 17 2016 - 04:02:29 PDT)
[AMBER] Amber MD simulation - viewing artifacts in VMD?
- Enrique Frio (Tue Mar 29 2016 - 05:34:32 PDT)
- Carlos Simmerling (Tue Mar 29 2016 - 05:10:29 PDT)
- Enrique Frio (Tue Mar 29 2016 - 05:05:05 PDT)
[AMBER] Amber parameters for deprotonated threonine
- anu chandra (Thu Mar 24 2016 - 14:59:55 PDT)
- Carlos Simmerling (Thu Mar 24 2016 - 09:14:04 PDT)
- anu chandra (Thu Mar 24 2016 - 09:03:54 PDT)
[AMBER] amber14 installation
- David A Case (Tue Mar 29 2016 - 04:24:15 PDT)
- Carlos Romero (Mon Mar 28 2016 - 22:52:38 PDT)
[AMBER] AMBER:neutralisation of non integral charges
- Hannes Loeffler (Mon Mar 14 2016 - 06:37:42 PDT)
- Shilpa Gupta (Mon Mar 14 2016 - 06:22:42 PDT)
[AMBER] ambpdb could not read restart atoms/time.
- Daniel Roe (Thu Mar 10 2016 - 07:24:14 PST)
- David A Case (Thu Mar 10 2016 - 04:14:10 PST)
- Daniel Roe (Wed Mar 09 2016 - 20:32:02 PST)
- Kshatresh Dutta Dubey (Wed Mar 09 2016 - 20:30:21 PST)
- Bin Wang (Wed Mar 09 2016 - 19:41:31 PST)
- Bin Wang (Wed Mar 09 2016 - 19:40:09 PST)
- Bill Ross (Wed Mar 09 2016 - 19:25:02 PST)
- Bin Wang (Wed Mar 09 2016 - 19:07:31 PST)
[AMBER] aMD simulation of membrane protein ?
- Fabian gmail (Thu Mar 31 2016 - 08:00:27 PDT)
- Ofir Tal (Thu Mar 31 2016 - 07:10:27 PDT)
- Michael Shokhen (Thu Mar 31 2016 - 03:07:56 PDT)
- Michael Shokhen (Wed Mar 30 2016 - 03:18:51 PDT)
[AMBER] Analysis of Radius of gyration
- Daniel Roe (Fri Mar 04 2016 - 14:28:28 PST)
- Iqbal, Muhammad Sajid (Fri Mar 04 2016 - 14:19:26 PST)
[AMBER] AT_15 install/osx notes, xleap deselect not working
- Daniel Roe (Fri Mar 25 2016 - 09:35:05 PDT)
- Jason Swails (Fri Mar 25 2016 - 09:22:26 PDT)
- Bill Ross (Thu Mar 24 2016 - 18:27:08 PDT)
[AMBER] Attempting MC barostat change: Failed
- Niel Henriksen (Tue Mar 15 2016 - 09:49:32 PDT)
- Daniel Roe (Tue Mar 15 2016 - 07:42:37 PDT)
- Michael Shokhen (Tue Mar 15 2016 - 05:51:21 PDT)
[AMBER] bad atom type with MMPBSA decomposition?
- Kenneth Huang (Mon Mar 14 2016 - 06:58:25 PDT)
[AMBER] Bounds command with GIst
- peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 23:18:28 PST)
[AMBER] calculate free energy binding in presence of ions witn mmpbsa
- Carlos Romero (Sat Mar 26 2016 - 14:51:22 PDT)
- Josh Berryman (Thu Mar 17 2016 - 00:25:33 PDT)
- Carlos Romero (Tue Mar 01 2016 - 22:48:03 PST)
[AMBER] Calculating pair-wise interaction energy using MMPBSA for Gromacs files
- Daniel Roe (Tue Mar 22 2016 - 07:30:31 PDT)
- Suchetana Gupta (Mon Mar 21 2016 - 22:01:48 PDT)
[AMBER] Chamber tool, error using the prmtop and inpcrd files
- Jason Swails (Tue Mar 08 2016 - 05:09:08 PST)
- Anna Cebrian Prats (Tue Mar 08 2016 - 02:36:47 PST)
[AMBER] charge membrane
- Fabian gmail (Mon Mar 28 2016 - 02:18:59 PDT)
[AMBER] Clustering
- Daniel Roe (Fri Mar 25 2016 - 07:53:00 PDT)
- waleed zalloum (Fri Mar 25 2016 - 02:06:13 PDT)
[AMBER] Combining parameter of Phosphoserine with 99SBILDN+bsc0
- David A Case (Thu Mar 31 2016 - 04:52:11 PDT)
- A kS (Tue Mar 22 2016 - 23:09:11 PDT)
- Daniel Roe (Tue Mar 22 2016 - 07:25:15 PDT)
- A kS (Tue Mar 22 2016 - 05:22:53 PDT)
- Carlos Simmerling (Tue Mar 22 2016 - 04:29:03 PDT)
- A kS (Mon Mar 21 2016 - 23:25:09 PDT)
[AMBER] Command to display simulation completion time
- Hannes Loeffler (Thu Mar 31 2016 - 08:06:09 PDT)
- Ross Walker (Thu Mar 31 2016 - 07:56:38 PDT)
- Charlotte RIEUX (Thu Mar 31 2016 - 07:41:20 PDT)
- Sreemol G (Thu Mar 31 2016 - 07:27:25 PDT)
- Bill Ross (Thu Mar 31 2016 - 00:41:19 PDT)
- Bill Ross (Thu Mar 31 2016 - 00:35:34 PDT)
- Sreemol G (Wed Mar 30 2016 - 23:58:48 PDT)
[AMBER] Convergence problem with the SCC-DFTB example.
- Jinfeng Huang (Fri Mar 25 2016 - 07:55:26 PDT)
- Gustavo Seabra (Tue Mar 15 2016 - 12:09:05 PDT)
- Jinfeng Huang (Tue Mar 15 2016 - 01:29:17 PDT)
[AMBER] cpptraj mask definition
- David A Case (Tue Mar 29 2016 - 04:25:40 PDT)
- Weinzierl, Robert O J (Tue Mar 29 2016 - 03:51:26 PDT)
[AMBER] cpptraj molsurf: query on results
- Daniel Roe (Fri Mar 04 2016 - 14:16:31 PST)
- George Tzotzos (Thu Mar 03 2016 - 12:16:22 PST)
- Daniel Roe (Thu Mar 03 2016 - 07:30:45 PST)
- George Tzotzos (Wed Mar 02 2016 - 13:58:19 PST)
[AMBER] cpptraj rmsd error (Orthogonal box), unknown #frames, start=0 offset=1
- David A Case (Mon Mar 07 2016 - 08:55:04 PST)
- Daniel Roe (Mon Mar 07 2016 - 07:41:53 PST)
- Saman Yousuf ali (Sun Mar 06 2016 - 22:52:23 PST)
[AMBER] cpptraj surf
- George Tzotzos (Fri Mar 04 2016 - 13:35:45 PST)
[AMBER] Creating new atom
- Bill Ross (Wed Mar 09 2016 - 21:46:51 PST)
- Sreemol G (Wed Mar 09 2016 - 20:25:09 PST)
[AMBER] desc in leap
- Bill Ross (Thu Mar 24 2016 - 17:53:35 PDT)
- Daniel Roe (Thu Mar 24 2016 - 09:29:06 PDT)
- amirhossein taghavi (Thu Mar 24 2016 - 09:05:26 PDT)
[AMBER] Diffusion/msd cpptraj bug?
- Daniel Roe (Thu Mar 10 2016 - 08:18:03 PST)
- Timothy Christopher Schutt (Wed Mar 09 2016 - 13:13:54 PST)
- Daniel Roe (Wed Mar 09 2016 - 11:54:38 PST)
- Timothy Christopher Schutt (Wed Mar 09 2016 - 11:24:03 PST)
- Daniel Roe (Wed Mar 09 2016 - 10:07:32 PST)
- Daniel Roe (Wed Mar 09 2016 - 10:06:23 PST)
- Timothy Christopher Schutt (Wed Mar 09 2016 - 10:02:53 PST)
- Daniel Roe (Wed Mar 09 2016 - 07:41:14 PST)
- Bill Ross (Wed Mar 09 2016 - 00:13:42 PST)
- Timothy Christopher Schutt (Tue Mar 08 2016 - 22:43:56 PST)
- Daniel Roe (Tue Mar 08 2016 - 20:43:04 PST)
- Timothy Christopher Schutt (Tue Mar 08 2016 - 17:05:07 PST)
- David A Case (Tue Mar 08 2016 - 16:34:15 PST)
- Timothy Christopher Schutt (Tue Mar 08 2016 - 14:54:19 PST)
- Daniel Roe (Tue Mar 08 2016 - 14:38:22 PST)
- Timothy Christopher Schutt (Tue Mar 08 2016 - 14:30:00 PST)
- Daniel Roe (Tue Mar 08 2016 - 13:43:39 PST)
- Timothy Christopher Schutt (Tue Mar 08 2016 - 13:11:54 PST)
[AMBER] Dihedral angle values from .mdcrd file
- Vasantha Kumar (Wed Mar 02 2016 - 11:18:11 PST)
- Vasantha Kumar (Wed Mar 02 2016 - 11:18:10 PST)
- Daniel Roe (Wed Mar 02 2016 - 09:49:16 PST)
- Carlos Simmerling (Wed Mar 02 2016 - 04:10:18 PST)
- Vasantha Kumar (Wed Mar 02 2016 - 03:47:21 PST)
[AMBER] Doc of Amber to the html version
- David A Case (Wed Mar 02 2016 - 04:58:42 PST)
- FyD (Tue Mar 01 2016 - 01:25:09 PST)
[AMBER] Does the PBSA Calculation Include the Neutralizing Plasma？
- Ray Luo (Tue Mar 08 2016 - 20:43:23 PST)
- 姜阳 (Tue Mar 08 2016 - 19:27:01 PST)
[AMBER] energy calculation with cpptraj based on chamber topology file
- Jason Swails (Thu Mar 10 2016 - 09:35:17 PST)
- Song-Ho Chong (Thu Mar 10 2016 - 08:37:45 PST)
- Daniel Roe (Thu Mar 10 2016 - 08:07:48 PST)
- Song-Ho Chong (Thu Mar 10 2016 - 07:51:54 PST)
- Daniel Roe (Thu Mar 10 2016 - 07:34:00 PST)
- Song-Ho Chong (Thu Mar 10 2016 - 04:30:08 PST)
[AMBER] Error while creating neutralized topology and coordinates file
- David A Case (Wed Mar 02 2016 - 05:04:19 PST)
- Sreemol G (Tue Mar 01 2016 - 22:54:08 PST)
- Mohammed Khaled Tumbi (Tue Mar 01 2016 - 03:41:42 PST)
- Bill Ross (Tue Mar 01 2016 - 03:38:47 PST)
- Sreemol G (Tue Mar 01 2016 - 03:33:44 PST)
[AMBER] Error while creating topology file after adding ions
- David A Case (Fri Mar 04 2016 - 05:49:50 PST)
- Marcelo Andrade Chagas (Fri Mar 04 2016 - 02:13:55 PST)
- Marcelo Andrade Chagas (Fri Mar 04 2016 - 01:55:46 PST)
- Sreemol G (Fri Mar 04 2016 - 01:14:49 PST)
- Bill Ross (Thu Mar 03 2016 - 22:39:57 PST)
- Sreemol G (Thu Mar 03 2016 - 21:40:26 PST)
- Nhai (Thu Mar 03 2016 - 21:30:20 PST)
- Sreemol G (Thu Mar 03 2016 - 21:24:45 PST)
- Hai Nguyen (Thu Mar 03 2016 - 21:08:00 PST)
- Sreemol G (Thu Mar 03 2016 - 21:04:18 PST)
- Bill Ross (Thu Mar 03 2016 - 20:55:03 PST)
- Sreemol G (Thu Mar 03 2016 - 20:40:03 PST)
[AMBER] Error with make test.parallel in AmberTools 15 installation
- anu chandra (Thu Mar 17 2016 - 06:03:51 PDT)
- Daniel Roe (Wed Mar 16 2016 - 09:32:38 PDT)
- anu chandra (Wed Mar 16 2016 - 09:28:10 PDT)
[AMBER] errors in plumed and amber14 patch
- Jason Swails (Thu Mar 17 2016 - 03:02:26 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Mar 17 2016 - 01:41:37 PDT)
- jixiaofeng (Thu Mar 17 2016 - 01:06:04 PDT)
[AMBER] errors in plumed and amber14 patch (Jason Swails)
- jixiaofeng (Sun Mar 20 2016 - 20:14:41 PDT)
- Jason Swails (Sun Mar 20 2016 - 10:14:40 PDT)
- jixiaofeng (Thu Mar 17 2016 - 19:12:38 PDT)
[AMBER] Failed installation of latest MCPB version
- Marcelo Andrade Chagas (Thu Mar 10 2016 - 10:52:54 PST)
- Marcelo Andrade Chagas (Thu Mar 10 2016 - 10:39:52 PST)
- Marcelo Andrade Chagas (Thu Mar 10 2016 - 10:38:38 PST)
- anu chandra (Thu Mar 10 2016 - 09:41:43 PST)
- Daniel Roe (Thu Mar 10 2016 - 08:16:21 PST)
- Marcelo Andrade Chagas (Thu Mar 10 2016 - 04:42:09 PST)
- anu chandra (Thu Mar 10 2016 - 04:37:18 PST)
[AMBER] for protein- RNA complex simulation
- Jiri Sponer (Sat Mar 05 2016 - 00:39:56 PST)
- Thomas Cheatham (Fri Mar 04 2016 - 20:09:30 PST)
- Sreemol G (Fri Mar 04 2016 - 19:49:46 PST)
[AMBER] Fwd: MMPBSA CalceError mmpbsa_py_energy failed with prmtop com.prmtop!
- Jason Swails (Wed Mar 23 2016 - 06:09:38 PDT)
- Annie Ancy (Wed Mar 23 2016 - 03:49:00 PDT)
[AMBER] Fwd: Optimize in Gaussian with RESP
- Jesmita Dhar (Fri Mar 11 2016 - 00:33:38 PST)
[AMBER] GAFF of Amber 'ff..' force field to prepare ligands?
- Karl Kirschner (Tue Mar 22 2016 - 04:43:33 PDT)
- alexander.zlobin (Tue Mar 22 2016 - 03:50:29 PDT)
[AMBER] GB Parameterization
- David A Case (Fri Mar 04 2016 - 09:35:53 PST)
- Taylor Harville (Fri Mar 04 2016 - 08:28:14 PST)
- David A Case (Fri Mar 04 2016 - 05:42:11 PST)
- Carlos Simmerling (Thu Mar 03 2016 - 19:51:48 PST)
- Taylor Harville (Thu Mar 03 2016 - 19:27:13 PST)
[AMBER] geforce 970 versus 780
- Gerald Monard (Mon Mar 28 2016 - 14:12:19 PDT)
- George Green (Wed Mar 09 2016 - 11:14:04 PST)
[AMBER] General question
- Ross Walker (Tue Mar 29 2016 - 09:54:52 PDT)
- George Tzotzos (Tue Mar 29 2016 - 09:35:22 PDT)
[AMBER] generate frcmod.user file for missing parameters
- FyD (Fri Mar 11 2016 - 04:48:00 PST)
- David A Case (Fri Mar 11 2016 - 04:33:41 PST)
- Jesmita Dhar (Fri Mar 11 2016 - 03:03:04 PST)
[AMBER] Gist calculation on clustered structures
- peter.schmidtke.discngine.servier.com (Mon Mar 07 2016 - 23:31:40 PST)
- Steven Ramsey (Tue Mar 01 2016 - 06:30:26 PST)
- peter.schmidtke.discngine.servier.com (Mon Feb 29 2016 - 23:23:01 PST)
[AMBER] GROMACS File Conversion Subtlety
- Daniel Roe (Sun Mar 20 2016 - 09:00:33 PDT)
- Daniel Roe (Sun Mar 20 2016 - 08:29:54 PDT)
- Mark Abraham (Sun Mar 20 2016 - 08:26:00 PDT)
- Jason Swails (Sun Mar 20 2016 - 08:03:03 PDT)
- Mark Abraham (Sat Mar 19 2016 - 12:32:57 PDT)
- Jason Swails (Sat Mar 19 2016 - 11:33:30 PDT)
- Mark Abraham (Sat Mar 19 2016 - 09:48:06 PDT)
- Daniel Roe (Sat Mar 19 2016 - 07:20:47 PDT)
- hannes.loeffler.stfc.ac.uk (Sat Mar 19 2016 - 00:42:00 PDT)
- Dr. Robert Molt (Fri Mar 18 2016 - 22:15:11 PDT)
- Thomas Cheatham (Fri Mar 18 2016 - 22:04:23 PDT)
- Mark Abraham (Fri Mar 18 2016 - 21:04:24 PDT)
- Daniel Roe (Fri Mar 18 2016 - 16:32:50 PDT)
- Dr. Robert Molt (Thu Mar 17 2016 - 17:18:28 PDT)
- Daniel Roe (Thu Mar 17 2016 - 17:13:43 PDT)
- Daniel Roe (Thu Mar 17 2016 - 17:09:21 PDT)
- Dr. Robert Molt (Thu Mar 17 2016 - 17:00:39 PDT)
- Daniel Roe (Thu Mar 17 2016 - 06:37:19 PDT)
- Robert Molt (Wed Mar 16 2016 - 23:03:10 PDT)
[AMBER] How did GAFF get force constants?
- Ruixing Wang (Wed Mar 16 2016 - 02:24:18 PDT)
- David Cerutti (Sat Mar 12 2016 - 16:01:50 PST)
- Thomas Cheatham (Fri Mar 11 2016 - 19:52:11 PST)
- David Cerutti (Tue Mar 08 2016 - 22:13:02 PST)
- Hai Nguyen (Tue Mar 08 2016 - 21:48:25 PST)
- Ruixing Wang (Tue Mar 08 2016 - 20:01:13 PST)
[AMBER] How does one derive parameters to modify GAFF?
- David Cerutti (Mon Mar 28 2016 - 19:52:02 PDT)
- David A Case (Mon Mar 28 2016 - 18:13:13 PDT)
- David Cerutti (Mon Mar 28 2016 - 14:34:11 PDT)
[AMBER] How is ΔGnonpolar computed in MMPBSA.py in AMBER 14? (inp=2 in &pb namelist)
- Stefan Ivanov (Sun Mar 13 2016 - 22:11:33 PDT)
- Ray Luo (Sun Mar 13 2016 - 20:52:30 PDT)
- Stefan Ivanov (Sun Mar 13 2016 - 19:11:01 PDT)
- Ray Luo (Sat Mar 12 2016 - 20:21:58 PST)
- Stefan Ivanov (Fri Mar 11 2016 - 23:28:32 PST)
[AMBER] How to deal with fractional electron unit charges on small molecules??
- Hannes Loeffler (Mon Mar 07 2016 - 02:52:23 PST)
- SHAILESH KUMAR (Mon Mar 07 2016 - 02:30:44 PST)
[AMBER] How to interpret MMGBSA ligand binding free energy decomposition results
- Daniel Roe (Wed Mar 09 2016 - 07:55:37 PST)
- Jason Swails (Wed Mar 09 2016 - 04:41:00 PST)
- Carlos Simmerling (Wed Mar 09 2016 - 03:13:24 PST)
- Zhang Marc (Wed Mar 09 2016 - 00:26:15 PST)
- Jason Swails (Tue Mar 08 2016 - 18:44:13 PST)
- Zhang Marc (Tue Mar 08 2016 - 09:08:08 PST)
[AMBER] How to using distance based strip action and generate the corresponding prmtop
- Daniel Roe (Wed Mar 09 2016 - 07:51:30 PST)
- windy (Wed Mar 09 2016 - 07:02:39 PST)
[AMBER] Hydrophobic solution environment ???
- Mijiddorj Batsaikhan (Thu Mar 31 2016 - 06:53:08 PDT)
- David A Case (Wed Mar 30 2016 - 10:24:00 PDT)
- Mijiddorj Batsaikhan (Wed Mar 30 2016 - 09:33:17 PDT)
[AMBER] I have a problem when installing GPU version of Pmemd(Amber14).
- Ross Walker (Tue Mar 01 2016 - 08:13:04 PST)
- yhzahsc (Tue Mar 01 2016 - 00:44:07 PST)
[AMBER] Igb and salt concentration for GBSA
- Jason Swails (Fri Mar 11 2016 - 17:50:39 PST)
- Carlos Simmerling (Fri Mar 11 2016 - 17:37:41 PST)
- Nhai (Fri Mar 11 2016 - 17:24:41 PST)
- Jason Swails (Fri Mar 11 2016 - 16:51:59 PST)
- Arati Paudyal (Fri Mar 11 2016 - 15:09:02 PST)
[AMBER] IMPORTANT FOR 12-6-4 USERS
- Pengfei Li (Sat Mar 05 2016 - 18:30:10 PST)
[AMBER] Inquiry regarding amber installation
- David A Case (Tue Mar 01 2016 - 11:25:04 PST)
- Sreemol G (Mon Feb 29 2016 - 22:05:14 PST)
[AMBER] Installation error amber14
- David A Case (Thu Mar 10 2016 - 04:17:28 PST)
- Dr. M. K. Yadav (Thu Mar 10 2016 - 00:28:20 PST)
[AMBER] interview with David Case
- Nhai (Tue Mar 22 2016 - 22:19:28 PDT)
- Nikolai Skrynnikov (Tue Mar 22 2016 - 22:02:17 PDT)
[AMBER] Is there a shift of QM energy in a QM/MM simulation?
- Pengfei Li (Fri Mar 18 2016 - 05:26:47 PDT)
[AMBER] ISQBP 2016 meeting - registration opened!
- Thomas Cheatham (Sun Mar 13 2016 - 22:15:46 PDT)
[AMBER] Lifetime analysis of backbone hydrogen bonds
- Daniel Roe (Mon Mar 14 2016 - 13:46:32 PDT)
- Krantzman, Kristin D (Mon Mar 14 2016 - 13:37:02 PDT)
- Krantzman, Kristin D (Mon Mar 14 2016 - 13:34:30 PDT)
- Daniel Roe (Mon Mar 14 2016 - 12:45:09 PDT)
- Krantzman, Kristin D (Mon Mar 14 2016 - 12:28:55 PDT)
[AMBER] LINMEN
- David A Case (Tue Mar 01 2016 - 17:53:40 PST)
- Arati Paudyal (Tue Mar 01 2016 - 14:48:58 PST)
[AMBER] long bond lengths after parmed.py setMolecules command in metal-containing system
- David A Case (Mon Mar 07 2016 - 08:51:55 PST)
- Arjun Narayanan (Mon Mar 07 2016 - 08:03:34 PST)
- Daniel Roe (Mon Mar 07 2016 - 07:44:41 PST)
- Arjun Narayanan (Mon Mar 07 2016 - 05:19:59 PST)
- Arjun Narayanan (Mon Mar 07 2016 - 04:58:28 PST)
- Jason Swails (Fri Mar 04 2016 - 19:00:40 PST)
- Arjun Narayanan (Fri Mar 04 2016 - 08:26:36 PST)
[AMBER] Lower energy frame from summary.EPTOT
- Jason Swails (Fri Mar 11 2016 - 17:53:29 PST)
- Vasantha Kumar (Fri Mar 11 2016 - 08:49:20 PST)
- David A Case (Fri Mar 11 2016 - 04:32:03 PST)
- Vasantha Kumar (Fri Mar 11 2016 - 01:06:47 PST)
[AMBER] membrane protein complex preparation
- Bill Ross (Wed Mar 30 2016 - 04:23:19 PDT)
- Fabian Glaser (Wed Mar 30 2016 - 02:59:11 PDT)
- Bill Ross (Wed Mar 30 2016 - 00:46:09 PDT)
- Dickson, Callum J (Tue Mar 29 2016 - 10:12:00 PDT)
- Fabian gmail (Tue Mar 29 2016 - 08:28:06 PDT)
- Fabian gmail (Tue Mar 29 2016 - 03:26:14 PDT)
- Dickson, Callum J (Mon Mar 28 2016 - 09:42:03 PDT)
- Fabian gmail (Mon Mar 28 2016 - 08:14:56 PDT)
- Dickson, Callum J (Mon Mar 28 2016 - 08:01:42 PDT)
- Fabian gmail (Mon Mar 28 2016 - 07:42:19 PDT)
- Dickson, Callum J (Mon Mar 28 2016 - 06:52:38 PDT)
- Fabian gmail (Mon Mar 28 2016 - 04:15:16 PDT)
[AMBER] membrane protein problem
- David Cerutti (Sat Mar 26 2016 - 15:51:14 PDT)
- Chris Moth (Sat Mar 26 2016 - 15:14:51 PDT)
- Bill Ross (Sat Mar 26 2016 - 13:45:37 PDT)
- Jason Swails (Sat Mar 26 2016 - 13:08:16 PDT)
- Michael Shokhen (Sat Mar 26 2016 - 12:45:42 PDT)
- Jason Swails (Sat Mar 26 2016 - 12:18:05 PDT)
- Michael Shokhen (Sat Mar 26 2016 - 11:35:55 PDT)
[AMBER] mmgbsa_error
- David A Case (Fri Mar 04 2016 - 05:55:16 PST)
- Jason Swails (Fri Mar 04 2016 - 05:11:02 PST)
- chemjxn (Fri Mar 04 2016 - 01:00:03 PST)
- Jason Swails (Thu Mar 03 2016 - 03:52:59 PST)
- chemjxn (Thu Mar 03 2016 - 00:10:35 PST)
- chemjxn (Thu Mar 03 2016 - 00:09:42 PST)
[AMBER] mmpbsa discrepancies
- George Tzotzos (Wed Mar 23 2016 - 05:44:02 PDT)
- Jason Swails (Tue Mar 22 2016 - 18:45:18 PDT)
- George Tzotzos (Mon Mar 21 2016 - 10:05:36 PDT)
[AMBER] MMPBSA doubt
- Mary Varughese (Tue Mar 22 2016 - 16:26:24 PDT)
- Ray Luo (Tue Mar 22 2016 - 11:08:51 PDT)
- Mary Varughese (Tue Mar 22 2016 - 02:43:11 PDT)
- Ray Luo (Mon Mar 21 2016 - 23:11:15 PDT)
- Mary Varughese (Mon Mar 21 2016 - 19:06:45 PDT)
- Ray Luo (Mon Mar 21 2016 - 17:39:19 PDT)
- Mary Varughese (Fri Mar 18 2016 - 21:48:15 PDT)
- Ray Luo (Fri Mar 18 2016 - 18:13:36 PDT)
- Mary Varughese (Wed Mar 16 2016 - 02:20:21 PDT)
[AMBER] MMPBSA error
- Ray Luo (Sat Mar 12 2016 - 20:00:12 PST)
- Arati Paudyal (Sat Mar 12 2016 - 11:07:18 PST)
- Hira Jabeen (Tue Mar 01 2016 - 21:56:42 PST)
[AMBER] mmpbsa.py question
- Carlos Romero (Tue Mar 01 2016 - 11:03:44 PST)
[AMBER] MMPBSApy - APBS bug
- Marek Maly (Sat Mar 26 2016 - 10:09:30 PDT)
[AMBER] more extra points needed
- Ivanov, Maxim (Tue Mar 01 2016 - 18:31:49 PST)
- David Cerutti (Mon Feb 29 2016 - 21:09:38 PST)
[AMBER] MPI_ABORT in pH-REMD
- Daniel Roe (Mon Mar 21 2016 - 08:23:52 PDT)
- Elisa Pieri (Mon Mar 21 2016 - 08:13:05 PDT)
- Jason Swails (Mon Mar 21 2016 - 07:59:21 PDT)
- Elisa Pieri (Mon Mar 21 2016 - 02:46:21 PDT)
- Bin ZOU (Mon Mar 21 2016 - 02:36:25 PDT)
- Elisa Pieri (Mon Mar 21 2016 - 02:08:42 PDT)
- Jason Swails (Fri Mar 18 2016 - 11:46:33 PDT)
- Elisa Pieri (Fri Mar 18 2016 - 06:05:02 PDT)
[AMBER] mpirun .... hwloc
- David A Case (Fri Mar 25 2016 - 04:20:15 PDT)
- Marcelo Andrade Chagas (Thu Mar 24 2016 - 11:29:03 PDT)
[AMBER] Need Amber entropy calculated values
- Ayesha Kanwal (Sat Mar 12 2016 - 14:29:11 PST)
- psu4.uic.edu (Sat Mar 12 2016 - 14:12:01 PST)
- Jason Swails (Tue Mar 01 2016 - 04:56:14 PST)
- Ayesha Kanwal (Tue Mar 01 2016 - 00:51:38 PST)
[AMBER] need help for using Re_fit
- Jesmita Dhar (Wed Mar 30 2016 - 04:45:37 PDT)
[AMBER] Need python code for the calculation of binding energy
- Jason Swails (Wed Mar 30 2016 - 05:36:10 PDT)
- Ayesha Kanwal (Wed Mar 30 2016 - 03:21:55 PDT)
[AMBER] nitro tyrosine
- FyD (Fri Mar 18 2016 - 05:03:12 PDT)
- Wu Xu (Thu Mar 17 2016 - 19:06:00 PDT)
[AMBER] nonnative contacts
- Krantzman, Kristin D (Fri Mar 25 2016 - 08:53:55 PDT)
- Daniel Roe (Fri Mar 25 2016 - 08:08:04 PDT)
- Krantzman, Kristin D (Thu Mar 24 2016 - 10:27:09 PDT)
[AMBER] Normal Mode Job Allocation Failure
- Cockroft, Nicholas T. (Wed Mar 23 2016 - 11:12:50 PDT)
- Daniel Roe (Wed Mar 23 2016 - 08:54:59 PDT)
- Cockroft, Nicholas T. (Mon Mar 21 2016 - 08:18:03 PDT)
[AMBER] nucleic acid residue representation in leap
- David A Case (Sat Mar 05 2016 - 06:45:04 PST)
- Vlad Cojocaru (Sat Mar 05 2016 - 01:28:30 PST)
- Sreemol G (Fri Mar 04 2016 - 23:26:03 PST)
- Jason Swails (Fri Mar 04 2016 - 23:14:01 PST)
- Hai Nguyen (Fri Mar 04 2016 - 23:13:08 PST)
- Sreemol G (Fri Mar 04 2016 - 23:04:00 PST)
[AMBER] On alphabetizing impropers
- Bill Ross (Fri Mar 25 2016 - 12:03:42 PDT)
- Bill Ross (Fri Mar 25 2016 - 12:01:02 PDT)
- David Cerutti (Fri Mar 25 2016 - 09:08:09 PDT)
- Jason Swails (Fri Mar 25 2016 - 09:04:46 PDT)
- David Cerutti (Fri Mar 25 2016 - 08:07:42 PDT)
- Jason Swails (Fri Mar 25 2016 - 05:47:20 PDT)
- Jason Swails (Fri Mar 25 2016 - 05:43:01 PDT)
- David A Case (Fri Mar 25 2016 - 04:14:33 PDT)
- David Cerutti (Thu Mar 24 2016 - 21:21:12 PDT)
- Bill Ross (Thu Mar 24 2016 - 18:35:51 PDT)
- David Cerutti (Thu Mar 24 2016 - 15:40:09 PDT)
- Bill Ross (Thu Mar 24 2016 - 12:24:30 PDT)
- Brent Krueger (Thu Mar 24 2016 - 09:22:47 PDT)
- David A Case (Thu Mar 24 2016 - 09:00:04 PDT)
- David Cerutti (Thu Mar 24 2016 - 07:47:20 PDT)
- Brent Krueger (Thu Mar 24 2016 - 06:53:18 PDT)
- David A Case (Thu Mar 24 2016 - 04:23:29 PDT)
- Christian Schafmeister (Wed Mar 23 2016 - 23:10:18 PDT)
- David Cerutti (Wed Mar 23 2016 - 23:02:56 PDT)
- Bill Ross (Wed Mar 23 2016 - 23:01:10 PDT)
- David Cerutti (Wed Mar 23 2016 - 22:42:52 PDT)
[AMBER] On Amber to Gromacs Parameter Conversion
- Robert Molt (Fri Mar 11 2016 - 18:47:35 PST)
- Jason Swails (Fri Mar 11 2016 - 17:51:49 PST)
- Robert Molt (Fri Mar 11 2016 - 17:33:03 PST)
- Jason Swails (Fri Mar 11 2016 - 16:50:09 PST)
- Robert Molt (Fri Mar 11 2016 - 12:28:42 PST)
- Hai Nguyen (Fri Mar 11 2016 - 11:11:52 PST)
- Hai Nguyen (Fri Mar 11 2016 - 08:00:29 PST)
- Robert Molt (Fri Mar 11 2016 - 05:32:30 PST)
- Sarah Witzke (Fri Mar 11 2016 - 03:57:24 PST)
- Hai Nguyen (Thu Mar 10 2016 - 22:21:25 PST)
- Robert Molt (Thu Mar 10 2016 - 20:48:23 PST)
- Hai Nguyen (Thu Mar 10 2016 - 19:32:47 PST)
- Robert Molt (Thu Mar 10 2016 - 17:45:00 PST)
- Daniel Roe (Thu Mar 10 2016 - 13:53:15 PST)
- Hai Nguyen (Thu Mar 10 2016 - 13:13:08 PST)
- Robert Molt (Thu Mar 10 2016 - 12:55:13 PST)
- Robert Molt (Thu Mar 10 2016 - 12:55:19 PST)
[AMBER] Optimize in Gaussian with RESP
- FyD (Fri Mar 11 2016 - 04:42:24 PST)
- Jesmita Dhar (Fri Mar 11 2016 - 04:40:27 PST)
- FyD (Fri Mar 11 2016 - 04:27:19 PST)
- David A Case (Fri Mar 11 2016 - 04:19:43 PST)
- Jesmita Dhar (Thu Mar 10 2016 - 22:47:21 PST)
- David A Case (Wed Mar 09 2016 - 04:43:49 PST)
- Marcelo Andrade Chagas (Wed Mar 09 2016 - 04:40:12 PST)
- Jesmita Dhar (Wed Mar 09 2016 - 00:37:50 PST)
- Jesmita Dhar (Wed Mar 09 2016 - 00:36:50 PST)
[AMBER] Paradynamics simulations with Amber
- Pengfei Li (Sat Mar 12 2016 - 05:10:13 PST)
- lipengfei_mail (Fri Mar 11 2016 - 22:36:51 PST)
- David A Case (Fri Mar 11 2016 - 04:26:22 PST)
- lipengfei_mail (Thu Mar 10 2016 - 23:02:13 PST)
[AMBER] parmed -setBond command
- Daniel Roe (Mon Mar 14 2016 - 11:36:04 PDT)
- Balaji Selvam (Mon Mar 14 2016 - 11:19:39 PDT)
[AMBER] PBSA fails with error message PB Bomb in epsmap(): epsz out of range
- Ray Luo (Fri Mar 18 2016 - 18:16:12 PDT)
- Bruno Falcone (Wed Mar 16 2016 - 07:27:22 PDT)
- Ray Luo (Tue Mar 15 2016 - 15:16:48 PDT)
- Bruno Falcone (Tue Mar 15 2016 - 14:55:20 PDT)
[AMBER] Periodicity box
- Fabian Glaser (Wed Mar 30 2016 - 09:21:02 PDT)
[AMBER] problem in nmode calculation by NAB
- David A Case (Mon Mar 28 2016 - 14:34:01 PDT)
- Sanjib Paul (Mon Mar 28 2016 - 07:19:37 PDT)
[AMBER] problem in plotting total energy graphs by perl script
- Sehrish Naz Aijaz (Wed Mar 30 2016 - 21:38:44 PDT)
- Daniel Roe (Wed Mar 30 2016 - 04:46:24 PDT)
- Sehrish Naz Aijaz (Wed Mar 30 2016 - 00:49:34 PDT)
- Jason Swails (Tue Mar 29 2016 - 02:57:25 PDT)
- Sehrish Naz Aijaz (Mon Mar 28 2016 - 21:03:01 PDT)
- Daniel Roe (Mon Mar 28 2016 - 06:37:52 PDT)
- Sehrish Naz Aijaz (Mon Mar 28 2016 - 02:54:44 PDT)
- Daniel Roe (Fri Mar 25 2016 - 07:48:40 PDT)
- Sehrish Naz Aijaz (Fri Mar 25 2016 - 04:18:01 PDT)
- Bill Ross (Thu Mar 24 2016 - 22:41:07 PDT)
- Bill Ross (Thu Mar 24 2016 - 22:39:25 PDT)
- Sehrish Naz Aijaz (Thu Mar 24 2016 - 21:59:13 PDT)
- David A Case (Tue Mar 22 2016 - 09:57:05 PDT)
- Daniel Roe (Tue Mar 22 2016 - 09:01:00 PDT)
- Sehrish Naz Aijaz (Tue Mar 22 2016 - 08:50:41 PDT)
- Daniel Roe (Mon Mar 21 2016 - 07:38:16 PDT)
- Bill Ross (Sun Mar 20 2016 - 22:10:36 PDT)
- Sehrish Naz Aijaz (Sun Mar 20 2016 - 21:58:01 PDT)
- Sehrish Naz Aijaz (Sun Mar 20 2016 - 21:56:46 PDT)
- Jason Swails (Sun Mar 20 2016 - 10:12:40 PDT)
- Bill Ross (Sat Mar 19 2016 - 13:11:40 PDT)
- Sehrish Naz Aijaz (Sat Mar 19 2016 - 03:29:52 PDT)
- Sehrish Naz Aijaz (Sat Mar 19 2016 - 03:16:30 PDT)
- Hai Nguyen (Sat Mar 19 2016 - 02:48:35 PDT)
- Sehrish Naz Aijaz (Sat Mar 19 2016 - 02:26:32 PDT)
- Hai Nguyen (Sat Mar 19 2016 - 01:55:51 PDT)
- Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:25:27 PDT)
[AMBER] problem running MD for diphosphoric acid anion
- Nhai (Wed Mar 16 2016 - 00:58:32 PDT)
- necmettin pirinccioglu (Wed Mar 16 2016 - 00:36:52 PDT)
- David A Case (Thu Mar 03 2016 - 06:24:22 PST)
- chandan patel (Thu Mar 03 2016 - 03:07:13 PST)
- Bill Ross (Thu Mar 03 2016 - 01:22:43 PST)
- necmettin pirinccioglu (Thu Mar 03 2016 - 00:49:28 PST)
[AMBER] Problem with 'hydrogen' having multiple bonds using SHAKEH
- David A Case (Sat Mar 12 2016 - 09:19:09 PST)
- alexander.zlobin (Sat Mar 12 2016 - 06:47:28 PST)
[AMBER] problem with ionized residues
- Carlos Simmerling (Thu Mar 10 2016 - 03:47:31 PST)
- Michael Shokhen (Thu Mar 10 2016 - 03:33:25 PST)
- Carlos Simmerling (Thu Mar 10 2016 - 03:16:15 PST)
- Michael Shokhen (Thu Mar 10 2016 - 02:30:20 PST)
[AMBER] Problems running MD simulations with pseudocontact shifts as restraints
- Francisco Corzana López (Wed Mar 23 2016 - 13:43:54 PDT)
- Gustavo Seabra (Wed Mar 23 2016 - 13:15:55 PDT)
- Francisco Corzana López (Wed Mar 23 2016 - 09:34:41 PDT)
- Gustavo Seabra (Wed Mar 23 2016 - 06:34:00 PDT)
- Francisco Corzana López (Wed Mar 23 2016 - 01:44:12 PDT)
[AMBER] Problems when trying to improve angle parameters whith paramfit
- Robin Betz (Mon Mar 14 2016 - 15:38:56 PDT)
- David Cerutti (Mon Mar 14 2016 - 15:07:10 PDT)
- Jérémie KNOOPS [531802] (Mon Mar 14 2016 - 14:34:57 PDT)
- David Cerutti (Mon Mar 14 2016 - 09:42:53 PDT)
- Sigurd Friis Truelsen (Mon Mar 14 2016 - 08:28:52 PDT)
[AMBER] Production phase for MMPBSA
- Hannes Loeffler (Wed Mar 09 2016 - 09:08:21 PST)
- Hannes Loeffler (Wed Mar 09 2016 - 08:30:21 PST)
- Arati Paudyal (Wed Mar 09 2016 - 05:53:56 PST)
- Andy Watkins (Wed Mar 09 2016 - 02:10:24 PST)
- Hannes Loeffler (Wed Mar 09 2016 - 01:49:41 PST)
- Andy Watkins (Wed Mar 09 2016 - 01:06:31 PST)
- Jason Swails (Tue Mar 08 2016 - 18:39:39 PST)
- Arati Paudyal (Tue Mar 08 2016 - 11:06:10 PST)
[AMBER] Proper nfft* parameters for a very long solvent box?
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 13:28:04 PDT)
- David Cerutti (Wed Mar 30 2016 - 13:25:21 PDT)
- Ross Walker (Wed Mar 30 2016 - 13:14:36 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 13:08:03 PDT)
- David Cerutti (Wed Mar 30 2016 - 12:46:42 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Mar 30 2016 - 11:14:59 PDT)
[AMBER] protein-RNA complex simulation
- Vlad Cojocaru (Fri Mar 11 2016 - 22:59:10 PST)
- Thomas Cheatham (Fri Mar 11 2016 - 22:21:27 PST)
- Thomas Cheatham (Fri Mar 11 2016 - 22:19:05 PST)
- Sreemol G (Fri Mar 11 2016 - 22:07:45 PST)
- David A Case (Fri Mar 11 2016 - 05:49:08 PST)
- Carlos Simmerling (Fri Mar 11 2016 - 05:47:07 PST)
- Vlad Cojocaru (Fri Mar 11 2016 - 05:33:07 PST)
- Sreemol G (Fri Mar 11 2016 - 05:26:32 PST)
- Vlad Cojocaru (Fri Mar 11 2016 - 05:04:33 PST)
- Sreemol G (Fri Mar 11 2016 - 04:47:18 PST)
- David A Case (Fri Mar 11 2016 - 04:35:03 PST)
- Sreemol G (Fri Mar 11 2016 - 03:57:51 PST)
[AMBER] pseudo trajectories for 4 centers of mass?
- Daniel Roe (Wed Mar 16 2016 - 10:01:54 PDT)
- Hirdesh Kumar (Wed Mar 16 2016 - 09:58:29 PDT)
- Daniel Roe (Tue Mar 15 2016 - 07:31:19 PDT)
- Hirdesh Kumar (Tue Mar 15 2016 - 05:54:46 PDT)
- Daniel Roe (Sun Mar 13 2016 - 13:40:39 PDT)
- Hai Nguyen (Sun Mar 13 2016 - 11:53:39 PDT)
- Vlad Cojocaru (Sun Mar 13 2016 - 11:11:09 PDT)
- Hirdesh Kumar (Sun Mar 13 2016 - 10:57:46 PDT)
- Daniel Roe (Tue Mar 08 2016 - 07:02:38 PST)
- Hirdesh Kumar (Tue Mar 08 2016 - 06:34:48 PST)
[AMBER] pseudo trajectories with 4 center of mass?
- Daniel Roe (Thu Mar 03 2016 - 11:53:53 PST)
- Hirdesh Kumar (Thu Mar 03 2016 - 11:49:23 PST)
[AMBER] Query regarding NMR refinement
- David A Case (Fri Mar 04 2016 - 06:00:50 PST)
- Madhura De (Fri Mar 04 2016 - 02:47:15 PST)
[AMBER] questions about mol2 and pdb file.
- Hannes Loeffler (Thu Mar 24 2016 - 07:12:57 PDT)
- David A Case (Thu Mar 24 2016 - 04:16:23 PDT)
- FyD (Thu Mar 24 2016 - 02:04:29 PDT)
- hannes.loeffler.stfc.ac.uk (Thu Mar 24 2016 - 00:26:48 PDT)
- Hong Sun (Wed Mar 23 2016 - 20:57:22 PDT)
[AMBER] R: R: Fwd: cpinutil.py problem
- Jason Swails (Fri Mar 11 2016 - 09:00:29 PST)
- Elisa Pieri (Fri Mar 11 2016 - 04:03:10 PST)
[AMBER] reading Amber trajectory files with chamber topology file
- Song-Ho Chong (Mon Feb 29 2016 - 08:24:04 PST)
- Song-Ho Chong (Mon Feb 29 2016 - 08:01:36 PST)
- Song-Ho Chong (Mon Feb 29 2016 - 07:31:12 PST)
[AMBER] red server error: ddikick.x: Fatal error detected
- FyD (Fri Mar 18 2016 - 03:18:07 PDT)
- Hannes Loeffler (Wed Mar 16 2016 - 03:56:56 PDT)
- Jesmita Dhar (Wed Mar 16 2016 - 03:44:10 PDT)
[AMBER] References
- Robert Molt (Fri Mar 11 2016 - 08:07:31 PST)
- Christina Bergonzo (Fri Mar 11 2016 - 08:05:28 PST)
- Hadeer ELHabashy (Fri Mar 11 2016 - 08:04:02 PST)
- Christina Bergonzo (Fri Mar 11 2016 - 07:57:26 PST)
- Hadeer ELHabashy (Fri Mar 11 2016 - 07:55:29 PST)
[AMBER] regarding mm-pbsa calculation
- Ray Luo (Fri Mar 04 2016 - 21:32:14 PST)
- neha chaudhary (Fri Mar 04 2016 - 20:58:10 PST)
[AMBER] Relation between binding affinity and free enegy
- Sangita Kachhap (Thu Mar 31 2016 - 21:49:55 PDT)
- Carlos Simmerling (Mon Mar 28 2016 - 12:36:09 PDT)
- Sangita Kachhap (Mon Mar 28 2016 - 11:55:34 PDT)
[AMBER] restart file error
- Jason Swails (Fri Mar 18 2016 - 14:19:30 PDT)
- Bill Ross (Fri Mar 18 2016 - 12:47:01 PDT)
- Sidhu, Khushwant (Dr.) (Fri Mar 18 2016 - 03:59:37 PDT)
[AMBER] RMSD of 0 for coordinated ion
- Francesco Gentile (Fri Mar 25 2016 - 12:23:17 PDT)
- Daniel Roe (Thu Mar 24 2016 - 18:28:25 PDT)
- Francesco Gentile (Thu Mar 24 2016 - 16:19:19 PDT)
- Daniel Roe (Thu Mar 24 2016 - 09:20:00 PDT)
- Bill Ross (Wed Mar 23 2016 - 21:40:00 PDT)
- Hai Nguyen (Wed Mar 23 2016 - 21:30:28 PDT)
- Francesco Gentile (Wed Mar 23 2016 - 21:25:36 PDT)
[AMBER] RMSD too high after simulation
- Carlos Simmerling (Sat Mar 12 2016 - 03:09:02 PST)
- Arati Paudyal (Fri Mar 11 2016 - 18:07:23 PST)
- conor parks (Fri Mar 11 2016 - 17:50:32 PST)
- Carlos Simmerling (Fri Mar 11 2016 - 17:49:13 PST)
- Arati Paudyal (Fri Mar 11 2016 - 17:41:36 PST)
[AMBER] rmsd y axis value deviation.
- Daniel Roe (Wed Mar 16 2016 - 12:12:32 PDT)
- Saman Yousuf ali (Wed Mar 16 2016 - 12:04:40 PDT)
- Hannes Loeffler (Wed Mar 16 2016 - 04:59:52 PDT)
- Saman Yousuf ali (Wed Mar 16 2016 - 03:29:58 PDT)
- Hannes Loeffler (Wed Mar 16 2016 - 03:08:39 PDT)
- Saman Yousuf ali (Wed Mar 16 2016 - 02:55:35 PDT)
[AMBER] salt concentration KCl
- Fabian gmail (Tue Mar 29 2016 - 07:23:23 PDT)
- Dickson, Callum J (Tue Mar 29 2016 - 06:25:07 PDT)
- Fabian gmail (Tue Mar 29 2016 - 03:33:35 PDT)
[AMBER] set up for a binding event MD
- Arnoult, Eric [JRDUS] (Fri Mar 25 2016 - 13:47:06 PDT)
- Carlos Simmerling (Fri Mar 25 2016 - 07:30:05 PDT)
- Arnoult, Eric [JRDUS] (Fri Mar 25 2016 - 07:24:57 PDT)
- Marcos Serrou do Amaral (Tue Mar 22 2016 - 19:41:04 PDT)
- Jason Swails (Tue Mar 22 2016 - 18:48:08 PDT)
- Arnoult, Eric [JRDUS] (Fri Mar 18 2016 - 11:02:17 PDT)
[AMBER] shell script
- Marc van der Kamp (Wed Mar 16 2016 - 02:18:34 PDT)
- Daniel Roe (Tue Mar 15 2016 - 19:35:53 PDT)
- yhzahsc (Tue Mar 15 2016 - 19:27:35 PDT)
[AMBER] Sign of outputs of MMPBSA.py
- Jason Swails (Thu Mar 03 2016 - 17:34:31 PST)
- Aronica, Pietro (Thu Mar 03 2016 - 08:02:58 PST)
[AMBER] SP3 Nitrogen planarity issue with ff14SB
- Carlos Simmerling (Thu Mar 31 2016 - 02:51:51 PDT)
- Prayagraj Fandilolu (Wed Mar 30 2016 - 20:13:23 PDT)
- Carlos Simmerling (Tue Mar 22 2016 - 04:30:13 PDT)
- Prayagraj Fandilolu (Mon Mar 21 2016 - 22:28:16 PDT)
- David A Case (Wed Mar 02 2016 - 04:54:58 PST)
- Prayagraj Fandilolu (Wed Mar 02 2016 - 01:48:07 PST)
- Carlos Simmerling (Tue Mar 01 2016 - 16:49:22 PST)
- Prayagraj Fandilolu (Mon Feb 29 2016 - 21:37:14 PST)
[AMBER] strange output with nativecontacts command
- Krantzman, Kristin D (Thu Mar 24 2016 - 10:32:25 PDT)
- Daniel Roe (Tue Mar 22 2016 - 12:38:30 PDT)
- Krantzman, Kristin D (Tue Mar 22 2016 - 11:58:55 PDT)
- Daniel Roe (Mon Mar 21 2016 - 18:52:21 PDT)
- Krantzman, Kristin D (Mon Mar 21 2016 - 17:57:19 PDT)
- Daniel Roe (Mon Mar 21 2016 - 17:53:30 PDT)
- Krantzman, Kristin D (Mon Mar 21 2016 - 17:22:06 PDT)
[AMBER] Strange problem of running MD simulation with sander ?
- David A Case (Wed Mar 30 2016 - 08:40:47 PDT)
- Jinfeng Huang (Wed Mar 30 2016 - 08:07:28 PDT)
[AMBER] tests dont work after installation
- Marcelo Andrade Chagas (Wed Mar 16 2016 - 11:19:10 PDT)
- Daniel Roe (Wed Mar 16 2016 - 10:56:25 PDT)
- Wesley Alves (Wed Mar 16 2016 - 10:48:02 PDT)
[AMBER] tests dont work for serial, parallel or cuda amber instalation
- Daniel Roe (Wed Mar 09 2016 - 10:44:21 PST)
- Wesley Alves (Wed Mar 09 2016 - 08:57:24 PST)
[AMBER] tests dont work for serial, parallel or cuda amber instalation.
- Daniel Roe (Mon Mar 07 2016 - 13:23:07 PST)
- Wesley Alves (Mon Mar 07 2016 - 12:20:05 PST)
[AMBER] The basis for selecting step sizes
- hannes.loeffler.stfc.ac.uk (Fri Mar 18 2016 - 00:19:56 PDT)
- Bin ZOU (Thu Mar 17 2016 - 22:51:41 PDT)
[AMBER] TIP3P
- Wu Xu (Sat Mar 12 2016 - 16:51:39 PST)
- David Cerutti (Sat Mar 12 2016 - 15:57:31 PST)
- Wu Xu (Sat Mar 12 2016 - 14:11:44 PST)
[AMBER] topology file for a graphene oxide with repetitive pattern
- FyD (Fri Mar 18 2016 - 03:22:00 PDT)
- Hannes Loeffler (Wed Mar 16 2016 - 03:27:13 PDT)
- Jesmita Dhar (Wed Mar 16 2016 - 03:07:29 PDT)
[AMBER] torsion angle rmsd by cpptraj ?
- David A Case (Tue Mar 29 2016 - 09:35:23 PDT)
- Michael Shokhen (Tue Mar 29 2016 - 05:00:49 PDT)
[AMBER] Training and Innovation Course in Drug Design
- Thomas Exner (Thu Mar 17 2016 - 08:02:56 PDT)
[AMBER] trajin reads box info from a trajectory with no box info.
- Jose Borreguero (Mon Mar 28 2016 - 14:14:17 PDT)
- Daniel Roe (Mon Mar 28 2016 - 14:07:10 PDT)
- Jose Borreguero (Mon Mar 28 2016 - 13:21:41 PDT)
[AMBER] Tutorial 18 - CpHMD with pmemd
- R.G. Mantell (Tue Mar 22 2016 - 10:31:34 PDT)
- Jason Swails (Tue Mar 22 2016 - 09:36:01 PDT)
- Jason Swails (Tue Mar 22 2016 - 09:03:25 PDT)
- Marcos Serrou do Amaral (Tue Mar 22 2016 - 08:37:15 PDT)
- R.G. Mantell (Tue Mar 22 2016 - 05:09:45 PDT)
[AMBER] velocity auto correlation function
- Daniel Roe (Thu Mar 10 2016 - 07:43:03 PST)
- Vertika Gautam (Wed Mar 09 2016 - 21:25:02 PST)
problem in plotting total energy graph by using perl script
- Hai Nguyen (Sat Mar 19 2016 - 01:23:34 PDT)
- Sehrish Naz Aijaz (Sat Mar 19 2016 - 01:20:41 PDT)
shell script
- yhzahsc (Wed Mar 16 2016 - 17:54:06 PDT)

Amber Archive Mar 2016 by subject