Amber Archive Feb 2013: by subject

[AMBER] (no subject)
- Jason Swails (Tue Feb 05 2013 - 07:16:45 PST)
- BERGY (Tue Feb 05 2013 - 07:05:31 PST)
[AMBER] 0
- meandme_meandme2003.yahoo.com (Wed Feb 27 2013 - 19:54:29 PST)
[AMBER] 3D-RISM input file error
- Tyler Luchko (Tue Feb 05 2013 - 11:36:58 PST)
- Jason Swails (Tue Feb 05 2013 - 11:16:01 PST)
- WenJuan Huang (Tue Feb 05 2013 - 11:05:43 PST)
[AMBER] A doubt about averaging time in dynamic cross-correlation analysis
- aneesh cna (Sat Feb 02 2013 - 02:17:42 PST)
[AMBER] A general question about umbrella sampling
- Sajeewa Pemasinghe (Tue Feb 12 2013 - 14:48:10 PST)
- Aron Broom (Tue Feb 12 2013 - 13:16:01 PST)
- Sajeewa Pemasinghe (Tue Feb 12 2013 - 12:51:47 PST)
[AMBER] About EPTOT
- Jason Swails (Wed Feb 20 2013 - 16:47:08 PST)
- Mo Chen (Wed Feb 20 2013 - 15:50:01 PST)
[AMBER] about iwrap=1 and ntxo=2
- Jason Swails (Tue Feb 05 2013 - 12:27:48 PST)
- Thomas Evangelidis (Tue Feb 05 2013 - 11:20:43 PST)
- Thomas Evangelidis (Sat Feb 02 2013 - 12:08:40 PST)
[AMBER] active site rmsd (residue 5A around bound ligand) ???
- Daniel Roe (Tue Feb 05 2013 - 13:58:47 PST)
- HM (Tue Feb 05 2013 - 11:28:16 PST)
- HM (Tue Feb 05 2013 - 11:07:30 PST)
- Daniel Roe (Tue Feb 05 2013 - 09:20:19 PST)
- Daniel Roe (Tue Feb 05 2013 - 07:37:15 PST)
- HM (Tue Feb 05 2013 - 05:40:45 PST)
[AMBER] Adding buffer and salt
- Yun Shi (Thu Feb 07 2013 - 10:32:33 PST)
- Indrajit Deb (Thu Feb 07 2013 - 09:23:04 PST)
- Indrajit Deb (Thu Feb 07 2013 - 09:18:36 PST)
- Jason Swails (Thu Feb 07 2013 - 06:30:47 PST)
- Indrajit Deb (Thu Feb 07 2013 - 02:46:00 PST)
- Indrajit Deb (Thu Feb 07 2013 - 00:23:55 PST)
[AMBER] adding rings using sequence command
- Lachele Foley (Wed Feb 27 2013 - 12:29:19 PST)
- Jio M (Wed Feb 27 2013 - 01:52:49 PST)
- FyD (Wed Feb 27 2013 - 01:06:21 PST)
- Bill Ross (Tue Feb 26 2013 - 23:00:26 PST)
- Jio M (Tue Feb 26 2013 - 12:58:53 PST)
- Lachele Foley (Tue Feb 26 2013 - 12:49:47 PST)
- Jio M (Tue Feb 26 2013 - 12:37:29 PST)
- Jason Swails (Tue Feb 26 2013 - 12:25:43 PST)
- Jio M (Tue Feb 26 2013 - 12:19:49 PST)
- Lachele Foley (Tue Feb 26 2013 - 12:02:11 PST)
- Jio M (Tue Feb 26 2013 - 11:49:59 PST)
- Jason Swails (Tue Feb 26 2013 - 07:53:57 PST)
- Jio M (Tue Feb 26 2013 - 06:55:50 PST)
[AMBER] AMBER 10 install issue
- Joel Tyndall (Mon Feb 04 2013 - 12:28:21 PST)
- David A Case (Sun Feb 03 2013 - 14:36:17 PST)
- Joel Tyndall (Thu Jan 31 2013 - 17:27:50 PST)
[AMBER] amber 11 installation on server
- Mary Varughese (Mon Feb 25 2013 - 10:24:31 PST)
[AMBER] Amber 11 Installment problem
- Bill Ross (Sat Feb 23 2013 - 11:54:15 PST)
- Changqing Yan (Thu Feb 21 2013 - 19:12:45 PST)
- Jian Yin (Thu Feb 21 2013 - 18:34:48 PST)
- Jian Yin (Thu Feb 21 2013 - 17:44:34 PST)
- Bill Ross (Wed Feb 20 2013 - 19:36:17 PST)
- Changqing Yan (Wed Feb 20 2013 - 19:14:31 PST)
[AMBER] Amber 12 and CUDA 5.0 K20 vs GTX 680: GTX 680 is two time faster than K20
- Ross Walker (Fri Feb 08 2013 - 13:15:37 PST)
- Filippo Pullara (Fri Feb 08 2013 - 13:05:21 PST)
[AMBER] amber error about protein containing heme
- Bill Ross (Sat Feb 23 2013 - 12:04:49 PST)
- Prajwal Nandekar (Fri Feb 22 2013 - 08:33:30 PST)
- tianchuan1015 (Fri Feb 22 2013 - 06:31:08 PST)
- Prajwal Nandekar (Fri Feb 22 2013 - 01:42:17 PST)
- tianchuan1015 (Thu Feb 21 2013 - 23:58:31 PST)
[AMBER] Amber MD using NAMD
- Ilyas Yildirim (Thu Feb 28 2013 - 15:32:32 PST)
[AMBER] amber phosphorylated parameters
- Neha Gandhi (Mon Feb 25 2013 - 04:01:07 PST)
[AMBER] AMBER pmemd and pmemd.cuda, not restart files after minimization - fort.16 file instead
- David A Case (Wed Feb 06 2013 - 05:14:54 PST)
- Marko Wehle (Wed Feb 06 2013 - 03:47:40 PST)
- Daniel Roe (Tue Feb 05 2013 - 08:20:50 PST)
- Marko Wehle (Tue Feb 05 2013 - 03:07:47 PST)
- Ross Walker (Mon Feb 04 2013 - 08:55:01 PST)
- Daniel Roe (Mon Feb 04 2013 - 07:30:11 PST)
- Marko Wehle (Mon Feb 04 2013 - 04:31:21 PST)
[AMBER] AMBER-Tools cpptraj residue numbering incorrect
- Jason Swails (Tue Feb 05 2013 - 17:43:57 PST)
- Marko Wehle (Tue Feb 05 2013 - 13:27:53 PST)
- Daniel Roe (Mon Feb 04 2013 - 12:18:14 PST)
- Marko Wehle (Mon Feb 04 2013 - 11:03:22 PST)
- Daniel Roe (Mon Feb 04 2013 - 10:52:03 PST)
- Marko Wehle (Mon Feb 04 2013 - 07:52:55 PST)
[AMBER] amber11 installation test files
- Mary Varughese (Wed Feb 06 2013 - 20:05:19 PST)
- Mary Varughese (Mon Feb 04 2013 - 19:56:55 PST)
- David A Case (Mon Feb 04 2013 - 05:32:12 PST)
- Mary Varughese (Sun Feb 03 2013 - 21:11:30 PST)
[AMBER] aMD
- Romelia Salomon (Thu Feb 28 2013 - 08:22:09 PST)
- Moth, Chris (Thu Feb 28 2013 - 08:16:39 PST)
- Romelia Salomon (Thu Feb 28 2013 - 07:59:18 PST)
- Beale, John (Thu Feb 28 2013 - 05:27:17 PST)
[AMBER] Analysis in ptraj
- Hirdesh Kumar (Tue Feb 19 2013 - 03:06:06 PST)
- gargi borgohai (Tue Feb 19 2013 - 01:38:29 PST)
[AMBER] Anomalous Termination of PMEMD.CUDA jobs
- kurisaki (Fri Feb 15 2013 - 21:09:40 PST)
- Ross Walker (Fri Feb 15 2013 - 10:36:14 PST)
- kurisaki (Fri Feb 15 2013 - 01:27:38 PST)
- kurisaki (Wed Feb 13 2013 - 17:39:29 PST)
- Ross Walker (Wed Feb 13 2013 - 09:16:41 PST)
- kurisaki (Wed Feb 13 2013 - 02:17:05 PST)
- kurisaki (Wed Feb 13 2013 - 02:02:23 PST)
[AMBER] Application of mmpbsa
- DEBOSTUTI GHOSHDASTIDAR (Sun Feb 10 2013 - 21:46:31 PST)
[AMBER] atomic pair correlation function through PCA
- Daniel Roe (Mon Feb 18 2013 - 08:19:49 PST)
- Date, Mihir (Sun Feb 17 2013 - 20:35:26 PST)
[AMBER] average structure
- Jason Swails (Fri Feb 01 2013 - 05:15:28 PST)
- Urszula Uciechowska (Fri Feb 01 2013 - 02:31:55 PST)
[AMBER] bond angle fitting
- CHAMI F. (Wed Feb 27 2013 - 04:30:42 PST)
- Ross Walker (Tue Feb 26 2013 - 11:38:18 PST)
- Jason Swails (Tue Feb 26 2013 - 11:29:50 PST)
- CHAMI F. (Tue Feb 26 2013 - 11:17:09 PST)
[AMBER] Building a new structure!
- FyD (Wed Feb 27 2013 - 01:35:01 PST)
- Ibrahim Said (Tue Feb 26 2013 - 10:45:20 PST)
- FyD (Thu Feb 21 2013 - 23:17:26 PST)
- Ibrahim Said (Thu Feb 21 2013 - 08:56:46 PST)
- FyD (Sun Feb 17 2013 - 04:38:42 PST)
- Ibrahim Said (Sun Feb 17 2013 - 01:08:48 PST)
- FyD (Fri Feb 15 2013 - 08:09:56 PST)
- Lachele Foley (Fri Feb 15 2013 - 07:11:41 PST)
- FyD (Fri Feb 15 2013 - 01:57:06 PST)
- Ibrahim Said (Thu Feb 14 2013 - 10:20:06 PST)
- FyD (Wed Feb 13 2013 - 23:00:33 PST)
- Ibrahim Said (Wed Feb 13 2013 - 00:37:50 PST)
[AMBER] Calculating Hydrogen bond energy
- Joseph Maxwell (Sun Feb 24 2013 - 06:39:20 PST)
- David A Case (Sat Feb 23 2013 - 06:05:26 PST)
- Ahmed Ayoub (Fri Feb 22 2013 - 23:55:01 PST)
[AMBER] Can we model the solvent implicitly outside a solvent shell (irregular shape)
- David A Case (Fri Feb 01 2013 - 05:03:19 PST)
- Debayan Chakraborty (Thu Jan 31 2013 - 19:29:49 PST)
[AMBER] Cannot open the input file: XYZ.pdb in rpdb(), exit
- David A Case (Thu Feb 14 2013 - 05:38:45 PST)
- Matthias Leeder (Thu Feb 14 2013 - 01:43:20 PST)
- David A Case (Wed Feb 13 2013 - 11:44:59 PST)
- Daniel Roe (Wed Feb 13 2013 - 11:04:30 PST)
- Matthias Leeder (Wed Feb 13 2013 - 10:42:02 PST)
[AMBER] change starting time of simulation
- Daniel Roe (Fri Feb 08 2013 - 07:43:08 PST)
- Daniel Roe (Fri Feb 08 2013 - 07:40:59 PST)
- Thomas Evangelidis (Fri Feb 08 2013 - 07:07:32 PST)
- David A Case (Fri Feb 08 2013 - 05:19:01 PST)
- Thomas Evangelidis (Fri Feb 08 2013 - 01:38:19 PST)
[AMBER] charge for NMA molecule
- Subrata Paul (Wed Feb 06 2013 - 04:58:57 PST)
[AMBER] charged molecule with antechamber
- Rebeca García Fandiño (Wed Feb 13 2013 - 11:19:56 PST)
- Ismail, Mohd F. (Wed Feb 13 2013 - 10:56:48 PST)
- Rebeca García Fandiño (Wed Feb 13 2013 - 10:45:47 PST)
[AMBER] Compilation problems for parallel build after applying patches
- Miguel Ortiz Lombardia (Tue Feb 12 2013 - 11:50:28 PST)
- Jason Swails (Tue Feb 12 2013 - 09:20:14 PST)
- Miguel Ortiz Lombardía (Tue Feb 12 2013 - 08:38:46 PST)
- Jason Swails (Tue Feb 12 2013 - 08:29:11 PST)
- Miguel Ortiz Lombardía (Tue Feb 12 2013 - 08:04:37 PST)
- Jason Swails (Tue Feb 12 2013 - 07:43:09 PST)
- Miguel Ortiz Lombardía (Tue Feb 12 2013 - 06:55:18 PST)
[AMBER] constant pH for transmemrane proteins
- Jason Swails (Thu Feb 21 2013 - 07:31:43 PST)
- Thomas Evangelidis (Thu Feb 21 2013 - 07:19:13 PST)
[AMBER] converting AMBER minimized file to PDB/MOL2
- Shashidhar Rao (Mon Feb 25 2013 - 12:43:37 PST)
- Jason Swails (Mon Feb 25 2013 - 12:27:54 PST)
- Kasam, Vinod (Mon Feb 25 2013 - 12:21:38 PST)
- Shashidhar Rao (Mon Feb 25 2013 - 12:17:26 PST)
[AMBER] Could you please remove me from AMBER mailing list
- Jason Swails (Tue Feb 05 2013 - 09:43:44 PST)
- Yulin Huang (Tue Feb 05 2013 - 09:32:48 PST)
[AMBER] crgmask and qmmm region compatibility
- David A Case (Thu Feb 21 2013 - 09:39:18 PST)
- Fabrício Bracht (Thu Feb 21 2013 - 06:44:02 PST)
[AMBER] Defining parameters for and undefined element. Solid Surface
- gabrielg.uvic.ca (Mon Feb 18 2013 - 14:10:14 PST)
[AMBER] density calculation in radial cpptraj
- Daniel Roe (Wed Feb 06 2013 - 08:43:50 PST)
- Asmita Gupta (Wed Feb 06 2013 - 00:21:23 PST)
- Daniel Roe (Tue Feb 05 2013 - 10:08:14 PST)
- Asmita Gupta (Tue Feb 05 2013 - 09:01:53 PST)
- David A Case (Mon Feb 04 2013 - 08:37:28 PST)
- Asmita Gupta (Mon Feb 04 2013 - 08:17:20 PST)
- Daniel Roe (Mon Feb 04 2013 - 07:36:28 PST)
- Asmita Gupta (Mon Feb 04 2013 - 02:08:24 PST)
[AMBER] Details about FF12SB
- Anselm Horn (Fri Feb 08 2013 - 10:54:21 PST)
[AMBER] dihedral distribution plot
- colvin (Tue Feb 26 2013 - 17:32:02 PST)
- Jason Swails (Mon Feb 25 2013 - 05:41:03 PST)
- colvin (Sun Feb 24 2013 - 21:33:06 PST)
[AMBER] distance restraints between the primary molecule and its periodic image
- Scott Le Grand (Sat Feb 09 2013 - 10:17:30 PST)
[AMBER] Dumping of center of mass coordinates of protein domain
- HM (Thu Feb 28 2013 - 03:54:15 PST)
- Daniel Roe (Tue Feb 19 2013 - 10:25:33 PST)
- Jason Swails (Tue Feb 19 2013 - 07:06:22 PST)
- HM (Tue Feb 19 2013 - 04:11:18 PST)
[AMBER] Error analysing an RNA trajectory with anal
- Amparo Garcia Lopez (Thu Feb 28 2013 - 07:55:42 PST)
- Jason Swails (Thu Feb 28 2013 - 05:23:43 PST)
- Amparo Garcia Lopez (Thu Feb 28 2013 - 02:42:04 PST)
- Daniel Roe (Wed Feb 27 2013 - 12:08:59 PST)
- Amparo Garcia Lopez (Wed Feb 27 2013 - 10:44:50 PST)
[AMBER] error in nmode
- Jason Swails (Wed Feb 27 2013 - 07:07:13 PST)
- Jason Swails (Wed Feb 27 2013 - 07:05:02 PST)
- Rasha Alqus (Wed Feb 27 2013 - 07:03:03 PST)
- Jason Swails (Tue Feb 26 2013 - 09:01:42 PST)
- Rasha Alqus (Tue Feb 26 2013 - 08:46:16 PST)
[AMBER] Error in RNA simulation
- Jason Swails (Mon Feb 25 2013 - 05:00:51 PST)
- esmaeel azadian (Mon Feb 25 2013 - 04:25:14 PST)
[AMBER] Error initiating H-REMD
- Brian Radak (Fri Feb 01 2013 - 15:52:32 PST)
[AMBER] Error running large number of trajectories with multisander
- Daniel Roe (Mon Feb 11 2013 - 11:35:09 PST)
- Brian Radak (Mon Feb 11 2013 - 10:48:07 PST)
- Daniel Roe (Mon Feb 11 2013 - 10:30:42 PST)
- Brian Radak (Mon Feb 11 2013 - 07:42:21 PST)
[AMBER] error while running mmpbsa.py in amber12
- Ismail, Mohd F. (Fri Feb 01 2013 - 14:39:03 PST)
- Jason Swails (Fri Feb 01 2013 - 14:28:25 PST)
- Ismail, Mohd F. (Fri Feb 01 2013 - 14:22:19 PST)
[AMBER] Error with MMPBSA calculation
- Jason Swails (Tue Feb 19 2013 - 04:50:47 PST)
- aneesh cna (Mon Feb 18 2013 - 21:11:16 PST)
- Jason Swails (Mon Feb 18 2013 - 04:31:49 PST)
- aneesh cna (Mon Feb 18 2013 - 01:21:56 PST)
[AMBER] ERROR: the best APS is not zero, bonds involved by this atom are frozen
- David A Case (Tue Feb 05 2013 - 04:44:39 PST)
- Jonathan Saboury (Mon Feb 04 2013 - 21:32:46 PST)
- David A Case (Mon Feb 04 2013 - 08:45:30 PST)
- Jonathan Saboury (Sun Feb 03 2013 - 20:44:08 PST)
[AMBER] espgen cannot deal with Gaussian 09 log file
- Sören Wacker (Wed Feb 06 2013 - 05:22:59 PST)
- David A Case (Wed Feb 06 2013 - 04:53:55 PST)
- Sören Wacker (Wed Feb 06 2013 - 02:32:16 PST)
- HIMANSHU JOSHI (Mon Feb 04 2013 - 21:42:28 PST)
- Sören Wacker (Mon Feb 04 2013 - 04:04:41 PST)
- Tomasz Borowski (Mon Feb 04 2013 - 03:59:35 PST)
- HIMANSHU JOSHI (Mon Feb 04 2013 - 03:51:52 PST)
[AMBER] force field file
- David A Case (Tue Feb 26 2013 - 05:51:10 PST)
- 徐立平 (Mon Feb 25 2013 - 23:53:29 PST)
[AMBER] Fwd:
- Jason Swails (Tue Feb 05 2013 - 07:23:08 PST)
- BERGY (Tue Feb 05 2013 - 07:07:04 PST)
[AMBER] Fwd: charge for NMA molecule
- Subrata Paul (Wed Feb 06 2013 - 22:05:52 PST)
[AMBER] Fwd: Installing Amber in parallel whit Lion
- Jason Swails (Mon Feb 25 2013 - 03:01:25 PST)
- javier alejandro rendon carrillo (Sun Feb 24 2013 - 22:17:12 PST)
[AMBER] Fwd: PSF file, atom radii and chamber
- Jason Swails (Mon Feb 18 2013 - 05:25:16 PST)
- Massimiliano Porrini (Mon Feb 18 2013 - 01:04:46 PST)
[AMBER] Fwd: radial distribution function between atoms of the two masks
- Massimiliano Porrini (Mon Feb 25 2013 - 12:54:20 PST)
[AMBER] Fwd: Regarding the problem with ligand conformation
- aneesh cna (Fri Feb 01 2013 - 01:05:58 PST)
[AMBER] Fwd: Sampling of a point by a molecule while keeping the relative position of the molecule unchanged in TMD
- Sajeewa Pemasinghe (Fri Feb 01 2013 - 21:18:47 PST)
- Jason Swails (Fri Feb 01 2013 - 19:11:20 PST)
- Sajeewa Pemasinghe (Fri Feb 01 2013 - 14:59:54 PST)
[AMBER] generate MDCRD file for two points
- Jason Swails (Thu Feb 28 2013 - 07:17:21 PST)
- HM (Thu Feb 28 2013 - 06:29:04 PST)
- Jason Swails (Thu Feb 28 2013 - 05:33:28 PST)
- HM (Thu Feb 28 2013 - 04:00:32 PST)
[AMBER] glucose
- David A Case (Wed Feb 20 2013 - 08:41:37 PST)
- marta wisniewska. (Wed Feb 20 2013 - 07:58:25 PST)
[AMBER] GTX 680 vs GTX Titan
- Aron Broom (Thu Feb 28 2013 - 08:24:00 PST)
- filip fratev (Thu Feb 28 2013 - 08:09:51 PST)
- Gould, Ian R (Thu Feb 28 2013 - 05:52:06 PST)
- Gould, Ian R (Thu Feb 28 2013 - 05:40:59 PST)
- Jason Swails (Thu Feb 28 2013 - 05:29:30 PST)
- Gould, Ian R (Thu Feb 28 2013 - 02:49:38 PST)
- Gonzalo Jimenez (Thu Feb 28 2013 - 00:41:21 PST)
- Ross Walker (Thu Feb 28 2013 - 00:10:43 PST)
- Gonzalo Jimenez (Wed Feb 27 2013 - 23:22:33 PST)
[AMBER] GTX Titan was finally released
- filip fratev (Wed Feb 27 2013 - 11:21:17 PST)
- Marek Maly (Wed Feb 27 2013 - 10:23:20 PST)
- Scott Le Grand (Tue Feb 26 2013 - 08:14:01 PST)
- Ross Walker (Mon Feb 25 2013 - 17:46:23 PST)
- filip fratev (Mon Feb 25 2013 - 14:39:04 PST)
- Aron Broom (Sat Feb 23 2013 - 12:12:49 PST)
- filip fratev (Sat Feb 23 2013 - 11:33:34 PST)
- Ross Walker (Fri Feb 22 2013 - 20:45:06 PST)
- Aron Broom (Fri Feb 22 2013 - 20:03:16 PST)
- filip fratev (Fri Feb 22 2013 - 17:28:18 PST)
- Ross Walker (Wed Feb 20 2013 - 13:03:28 PST)
- Marek Maly (Wed Feb 20 2013 - 05:22:55 PST)
- Aron Broom (Tue Feb 19 2013 - 15:01:20 PST)
- Ross Walker (Tue Feb 19 2013 - 14:18:01 PST)
- David A Case (Tue Feb 19 2013 - 13:39:12 PST)
- Scott Le Grand (Tue Feb 19 2013 - 13:27:38 PST)
- filip fratev (Tue Feb 19 2013 - 11:59:39 PST)
- Ross Walker (Tue Feb 19 2013 - 11:24:54 PST)
- Scott Le Grand (Tue Feb 19 2013 - 11:08:36 PST)
- Ross Walker (Tue Feb 19 2013 - 10:43:28 PST)
- Ilyas Yildirim (Tue Feb 19 2013 - 10:37:41 PST)
- Marek Maly (Tue Feb 19 2013 - 10:14:01 PST)
- Ross Walker (Tue Feb 19 2013 - 09:58:54 PST)
- Ross Walker (Tue Feb 19 2013 - 09:46:42 PST)
- Marek Maly (Tue Feb 19 2013 - 08:55:24 PST)
- filip fratev (Tue Feb 19 2013 - 08:40:12 PST)
[AMBER] hbond analysis acceptor atoms
- DEBOSTUTI GHOSHDASTIDAR (Wed Feb 06 2013 - 21:51:26 PST)
- Daniel Roe (Wed Feb 06 2013 - 09:32:39 PST)
- DEBOSTUTI GHOSHDASTIDAR (Wed Feb 06 2013 - 09:08:50 PST)
[AMBER] Hbond analysis in ptraj
- Daniel Roe (Wed Feb 06 2013 - 09:30:31 PST)
- DEBOSTUTI GHOSHDASTIDAR (Tue Feb 05 2013 - 22:00:54 PST)
- Daniel Roe (Tue Feb 05 2013 - 07:27:02 PST)
- DEBOSTUTI GHOSHDASTIDAR (Tue Feb 05 2013 - 05:07:17 PST)
[AMBER] heme parameters
- Giulia (Mon Feb 25 2013 - 05:58:15 PST)
[AMBER] How to calculate the vibrational frequancy
- David A Case (Tue Feb 19 2013 - 09:50:54 PST)
- Rasha Alqus (Tue Feb 19 2013 - 08:47:11 PST)
[AMBER] How to save secondary structure gnuplot as image
- HM (Fri Feb 01 2013 - 07:06:58 PST)
[AMBER] Hydrogens AMBER 1H6 and 2H6 vs. Glycam H61 and H62 for Glucose
- Kepa K. Burusco (Mon Feb 11 2013 - 12:49:19 PST)
- Lachele Foley (Lists) (Mon Feb 11 2013 - 12:01:42 PST)
- Lachele Foley (Lists) (Mon Feb 11 2013 - 06:47:45 PST)
- Kepa K. Burusco (Mon Feb 11 2013 - 05:48:07 PST)
[AMBER] iAPBS
- Robert Konecny (Tue Feb 05 2013 - 10:42:48 PST)
- George Tzotzos (Tue Feb 05 2013 - 05:57:31 PST)
[AMBER] idecomp output frequency
- Jason Swails (Wed Feb 13 2013 - 18:30:16 PST)
- Adam Mepham (Wed Feb 13 2013 - 17:56:20 PST)
[AMBER] igb=7 & 8 CalcError: "pathway" failed with prmtop "protein".prmtop
- psu4.uic.edu (Wed Feb 20 2013 - 11:03:57 PST)
- Jason Swails (Tue Feb 12 2013 - 05:01:51 PST)
- psu4.uic.edu (Mon Feb 11 2013 - 22:23:42 PST)
- Jason Swails (Thu Feb 07 2013 - 19:24:55 PST)
- psu4.uic.edu (Thu Feb 07 2013 - 17:23:39 PST)
- Hai Nguyen (Mon Feb 04 2013 - 14:55:29 PST)
- Jason Swails (Mon Feb 04 2013 - 14:16:26 PST)
- psu4.uic.edu (Mon Feb 04 2013 - 13:47:52 PST)
- Daniel Roe (Mon Feb 04 2013 - 07:46:52 PST)
- psu4.uic.edu (Sun Feb 03 2013 - 13:55:38 PST)
- Carlos Simmerling (Sat Feb 02 2013 - 19:08:22 PST)
- psu4.uic.edu (Sat Feb 02 2013 - 15:48:00 PST)
[AMBER] Inquiry from beginner
- David A Case (Mon Feb 11 2013 - 05:16:13 PST)
- rajith bhaskar (Sun Feb 10 2013 - 20:55:15 PST)
[AMBER] Install amber in Mac Lion
- Jason Swails (Tue Feb 26 2013 - 17:51:58 PST)
- javier alejandro rendon carrillo (Tue Feb 26 2013 - 16:57:16 PST)
[AMBER] Issues with idecomp
- Jason Swails (Mon Feb 11 2013 - 14:32:46 PST)
- Adam Mepham (Mon Feb 11 2013 - 14:17:30 PST)
- Daniel Roe (Sun Feb 10 2013 - 10:11:21 PST)
- Adam Mepham (Sat Feb 09 2013 - 20:55:19 PST)
[AMBER] issues with PDB file and tleap
- Massimiliano Porrini (Thu Feb 07 2013 - 06:56:44 PST)
- Jerome.GOLEBIOWSKI.unice.fr (Thu Feb 07 2013 - 05:00:40 PST)
- Massimiliano Porrini (Thu Feb 07 2013 - 03:45:58 PST)
[AMBER] Kepler GTX680 MD Workstation
- Charles Do (Tue Feb 19 2013 - 19:38:15 PST)
- Ross Walker (Tue Feb 19 2013 - 19:29:07 PST)
- Charles Do (Tue Feb 19 2013 - 19:12:31 PST)
[AMBER] leap insert missing atoms in aminoacids according to ...
- Jason Swails (Thu Feb 21 2013 - 08:55:50 PST)
- Marta Perez (Thu Feb 21 2013 - 07:59:20 PST)
[AMBER] ligand moving out of protein incorrect imaging of trajectory using image and center commands with amber 10
- ET (Fri Feb 22 2013 - 14:38:29 PST)
- Daniel Roe (Fri Feb 22 2013 - 14:17:14 PST)
- ET (Fri Feb 22 2013 - 13:45:20 PST)
- Daniel Roe (Fri Feb 22 2013 - 12:19:08 PST)
- ET (Fri Feb 22 2013 - 10:10:20 PST)
[AMBER] Linear peptide using non standard amino acids
- Jason Swails (Thu Feb 21 2013 - 14:01:38 PST)
- moitrayee.mbu.iisc.ernet.in (Thu Feb 21 2013 - 13:12:03 PST)
[AMBER] Missing comma in input file
- Jason Swails (Tue Feb 19 2013 - 08:29:01 PST)
- Sasha Perkins (Tue Feb 19 2013 - 08:18:03 PST)
[AMBER] missing parameter of B in .frcmod
- David A Case (Fri Feb 08 2013 - 05:15:33 PST)
- 纪晓峰 (Thu Feb 07 2013 - 19:19:54 PST)
[AMBER] MM PBSA and entropy decomposition
- Aron Broom (Sun Feb 17 2013 - 04:09:47 PST)
- Holger Gohlke (Sun Feb 17 2013 - 04:01:48 PST)
- Aron Broom (Sat Feb 16 2013 - 13:05:12 PST)
- Jason Swails (Sat Feb 16 2013 - 12:24:14 PST)
- Aron Broom (Sat Feb 16 2013 - 10:06:30 PST)
[AMBER] mmgbsa minimisation failing with error in trajene()
- ET (Mon Feb 25 2013 - 14:45:13 PST)
- ET (Mon Feb 25 2013 - 04:42:14 PST)
[AMBER] MMGBSA/MMPBSA Decomposition Analysis
- Jason Swails (Thu Feb 28 2013 - 10:21:10 PST)
- Vivek Shankar Bharadwaj (Thu Feb 28 2013 - 10:00:00 PST)
- Jason Swails (Wed Feb 27 2013 - 18:02:36 PST)
- Jason Swails (Wed Feb 27 2013 - 17:53:50 PST)
- Aron Broom (Wed Feb 27 2013 - 16:44:51 PST)
- Vivek Shankar Bharadwaj (Wed Feb 27 2013 - 16:28:38 PST)
[AMBER] MMPBSA free energy
- Soumya Lipsa Rath (Tue Feb 26 2013 - 06:04:07 PST)
- Jason Swails (Tue Feb 26 2013 - 04:50:35 PST)
- Soumya Lipsa Rath (Tue Feb 26 2013 - 03:50:13 PST)
[AMBER] MMPBSA problem
- David A Case (Tue Feb 26 2013 - 05:48:04 PST)
- Jason Swails (Tue Feb 26 2013 - 05:40:17 PST)
- Tommy Yap (Mon Feb 25 2013 - 18:15:05 PST)
[AMBER] MMPBSA.py: about sasopt value with inp=1
- Miguel Ortiz Lombardía (Wed Feb 13 2013 - 06:15:22 PST)
- Miguel Ortiz Lombardía (Wed Feb 13 2013 - 05:55:45 PST)
[AMBER] mmpbsa_py_nabnmode for single macromolecule
- Dwight McGee (Wed Feb 20 2013 - 08:17:54 PST)
- Rasha Alqus (Wed Feb 20 2013 - 07:27:16 PST)
[AMBER] Modified amino acid parameter generation
- moitrayee.mbu.iisc.ernet.in (Thu Feb 28 2013 - 09:59:28 PST)
[AMBER] NaN error in restart file
- Anselm Horn (Fri Feb 08 2013 - 04:05:24 PST)
- Shobana, G . (Fri Feb 08 2013 - 02:26:46 PST)
[AMBER] NMA(n-methylacetamide)
- FyD (Tue Feb 12 2013 - 01:16:45 PST)
- Subrata Paul (Mon Feb 11 2013 - 07:35:17 PST)
- Jason Swails (Mon Feb 11 2013 - 03:01:19 PST)
- Subrata Paul (Mon Feb 11 2013 - 02:31:33 PST)
- FyD (Sun Feb 10 2013 - 08:40:31 PST)
- David A Case (Fri Feb 08 2013 - 05:21:59 PST)
- Subrata Paul (Fri Feb 08 2013 - 02:12:31 PST)
[AMBER] NPT with pmemd.amoeba.MPI Density alway decreasing
- Jason Swails (Wed Feb 27 2013 - 11:23:56 PST)
- Cheng Wang (Wed Feb 27 2013 - 11:16:51 PST)
- Jason Swails (Wed Feb 27 2013 - 03:58:38 PST)
- Cheng Wang (Tue Feb 26 2013 - 15:30:56 PST)
[AMBER] OPLS to AMBER vdw parameters conversion
- Prabal Maiti (Tue Feb 05 2013 - 13:34:55 PST)
- Prabal Maiti (Tue Feb 05 2013 - 12:07:01 PST)
[AMBER] parmed.py error IndexError: list index out of range
- Jason Swails (Thu Feb 07 2013 - 12:40:51 PST)
- Jason Swails (Thu Feb 07 2013 - 08:13:30 PST)
- Jio M (Thu Feb 07 2013 - 07:52:49 PST)
[AMBER] PBSA vs MMPBSA.py
- Daniel Roe (Mon Feb 25 2013 - 07:18:25 PST)
- Jason Swails (Mon Feb 25 2013 - 04:44:14 PST)
- eneas.usal.es (Sun Feb 24 2013 - 23:57:12 PST)
[AMBER] PCA analysis query
- Daniel Roe (Mon Feb 18 2013 - 08:29:03 PST)
- Vaibhav Dixit (Sun Feb 17 2013 - 23:34:23 PST)
[AMBER] PCI-E 2.0 vs 3.0 (AMD vs INTEL?)
- Jonathan Gough (Thu Feb 28 2013 - 18:53:41 PST)
[AMBER] periodic image of octahedron box in VMD
- Ilyas Yildirim (Tue Feb 26 2013 - 19:04:56 PST)
- Jason Swails (Tue Feb 26 2013 - 18:37:06 PST)
- 吴云剑 (Tue Feb 26 2013 - 18:10:08 PST)
[AMBER] phosporylated residue connectivity problem
- BALA SUBRAMANI G L (Tue Feb 05 2013 - 01:15:14 PST)
[AMBER] pka calculation energy by residue
- Adam Mepham (Sat Feb 16 2013 - 15:46:28 PST)
[AMBER] PMEMD amd mmpbsa.py mpi
- Chris Chris (Sat Feb 09 2013 - 22:42:54 PST)
- Chris Chris (Fri Feb 08 2013 - 17:09:26 PST)
- Jason Swails (Fri Feb 08 2013 - 16:41:43 PST)
- Chris Chris (Fri Feb 08 2013 - 16:08:44 PST)
[AMBER] possibility to increase max . num. of bonded atoms ?
- Marek Maly (Wed Feb 27 2013 - 12:27:07 PST)
- David A Case (Wed Feb 27 2013 - 12:25:27 PST)
- Marek Maly (Wed Feb 27 2013 - 11:40:32 PST)
- Bill Ross (Wed Feb 27 2013 - 11:18:19 PST)
- Jason Swails (Wed Feb 27 2013 - 11:12:43 PST)
- Marek Maly (Wed Feb 27 2013 - 10:03:52 PST)
- Bill Ross (Mon Feb 25 2013 - 17:44:46 PST)
- Jason Swails (Mon Feb 25 2013 - 17:19:17 PST)
- Marek Maly (Mon Feb 25 2013 - 16:31:22 PST)
- David A Case (Sun Feb 24 2013 - 07:22:22 PST)
- Marek Maly (Sat Feb 23 2013 - 19:43:18 PST)
[AMBER] problem in nmode
- Rasha Alqus (Wed Feb 20 2013 - 09:11:37 PST)
- Jason Swails (Wed Feb 20 2013 - 06:50:25 PST)
- Rasha Alqus (Wed Feb 20 2013 - 06:39:39 PST)
[AMBER] problem in running MMPBSA
- Saugata Hazra (Mon Feb 25 2013 - 15:20:51 PST)
- Jason Swails (Mon Feb 25 2013 - 11:29:16 PST)
- Saugata Hazra (Mon Feb 25 2013 - 10:33:33 PST)
- Jason Swails (Sun Feb 24 2013 - 06:43:13 PST)
- Alessandro Contini (Sun Feb 24 2013 - 00:29:28 PST)
- Saugata Hazra (Sat Feb 23 2013 - 16:51:20 PST)
- Alessandro Contini (Wed Feb 20 2013 - 00:50:17 PST)
- Saugata Hazra (Wed Feb 20 2013 - 00:08:04 PST)
- Jason Swails (Tue Feb 19 2013 - 06:43:34 PST)
- Saugata Hazra (Tue Feb 19 2013 - 06:31:43 PST)
- Jason Swails (Tue Feb 19 2013 - 06:00:37 PST)
- Saugata Hazra (Tue Feb 19 2013 - 05:02:45 PST)
[AMBER] Problem in running TREMD in AMBER10
- Sajeewa Pemasinghe (Sat Feb 09 2013 - 09:44:21 PST)
- Jason Swails (Sat Feb 09 2013 - 09:27:16 PST)
- Sajeewa Pemasinghe (Sat Feb 09 2013 - 09:06:18 PST)
- Jason Swails (Sat Feb 09 2013 - 08:45:53 PST)
- Sajeewa Pemasinghe (Fri Feb 08 2013 - 21:30:42 PST)
- Sajeewa Pemasinghe (Fri Feb 08 2013 - 13:37:19 PST)
- Ross Walker (Fri Feb 08 2013 - 13:17:28 PST)
- Ross Walker (Fri Feb 08 2013 - 13:12:12 PST)
- Sajeewa Pemasinghe (Fri Feb 08 2013 - 13:11:06 PST)
- Sajeewa Pemasinghe (Fri Feb 08 2013 - 13:04:01 PST)
- Jason Swails (Fri Feb 08 2013 - 12:53:49 PST)
- Ross Walker (Fri Feb 08 2013 - 12:46:09 PST)
- Sajeewa Pemasinghe (Fri Feb 08 2013 - 12:37:45 PST)
[AMBER] problem reading CHARMM lipid parameters into chamber
- Sally Pias (Thu Feb 21 2013 - 08:32:30 PST)
- Jason Swails (Thu Feb 21 2013 - 04:25:47 PST)
- BERGY (Wed Feb 20 2013 - 20:49:22 PST)
- Jason Swails (Wed Feb 20 2013 - 05:06:43 PST)
- Sally Pias (Tue Feb 19 2013 - 13:07:56 PST)
[AMBER] Problem related to different version of amber
- Jian Yin (Wed Feb 20 2013 - 11:39:33 PST)
- Changqing Yan (Tue Feb 19 2013 - 23:42:18 PST)
[AMBER] Problem related to the bfactor calculation
- Daniel Roe (Tue Feb 26 2013 - 13:30:22 PST)
- Sindrila Dutta banik (Mon Feb 25 2013 - 23:24:20 PST)
- Aron Broom (Mon Feb 25 2013 - 23:08:29 PST)
- Sindrila Dutta banik (Mon Feb 25 2013 - 21:03:39 PST)
[AMBER] Problem related to the umbrella sampling
- Sindrila Dutta banik (Fri Feb 08 2013 - 21:34:13 PST)
- Sindrila Dutta banik (Fri Feb 08 2013 - 11:44:02 PST)
- Brian Radak (Fri Feb 08 2013 - 10:07:02 PST)
- Sindrila Dutta banik (Fri Feb 08 2013 - 09:30:03 PST)
[AMBER] Problem related with umbrella sampling
- Brian Radak (Fri Feb 08 2013 - 06:13:54 PST)
- Sindrila Dutta banik (Fri Feb 08 2013 - 03:20:13 PST)
[AMBER] Problem to run sander with more than 60 atom types
- Elise Duboué-Dijon (Thu Feb 28 2013 - 09:11:57 PST)
- Jason Swails (Thu Feb 28 2013 - 09:02:01 PST)
- Elise Duboué-Dijon (Thu Feb 28 2013 - 08:51:03 PST)
- Jason Swails (Thu Feb 28 2013 - 07:14:17 PST)
- Elise Duboué-Dijon (Thu Feb 28 2013 - 06:24:10 PST)
[AMBER] problem using autoimage from cpptraj
- Jason Swails (Sun Feb 10 2013 - 14:33:56 PST)
- Jonathan Saboury (Sun Feb 10 2013 - 13:19:45 PST)
- Daniel Roe (Sat Feb 09 2013 - 18:01:37 PST)
- Jonathan Saboury (Sat Feb 09 2013 - 17:13:26 PST)
- Daniel Roe (Fri Feb 08 2013 - 20:57:17 PST)
- Jonathan Saboury (Fri Feb 08 2013 - 20:35:23 PST)
[AMBER] Problem using solvatebox for large, linear peptide
- Joe Passman (Tue Feb 05 2013 - 12:47:00 PST)
- Jason Swails (Fri Feb 01 2013 - 19:22:54 PST)
- David A Case (Fri Feb 01 2013 - 18:36:20 PST)
- Ismail, Mohd F. (Fri Feb 01 2013 - 15:34:54 PST)
- Joe Passman (Fri Feb 01 2013 - 15:32:49 PST)
- David A Case (Fri Feb 01 2013 - 13:14:27 PST)
- Jason Swails (Fri Feb 01 2013 - 05:00:01 PST)
- Joe Passman (Thu Jan 31 2013 - 18:16:09 PST)
[AMBER] problem with 3-ring system in antechamber
- Leandro Bortot (Fri Feb 08 2013 - 12:55:28 PST)
- David A Case (Fri Feb 08 2013 - 12:20:40 PST)
- Leandro Bortot (Fri Feb 08 2013 - 11:14:48 PST)
- David A Case (Fri Feb 08 2013 - 10:53:32 PST)
- Leandro Bortot (Fri Feb 08 2013 - 10:18:27 PST)
- David A Case (Fri Feb 08 2013 - 08:41:19 PST)
- Leandro Bortot (Fri Feb 08 2013 - 07:59:49 PST)
[AMBER] problem with strip water some distance away from peptide
- Daniel Roe (Fri Feb 08 2013 - 15:08:59 PST)
- Do Yong Kim (Fri Feb 08 2013 - 15:06:39 PST)
- Daniel Roe (Thu Feb 07 2013 - 17:24:02 PST)
- Do Yong Kim (Thu Feb 07 2013 - 16:03:16 PST)
[AMBER] problem with umbrella sampling
- Sindrila Dutta banik (Fri Feb 08 2013 - 09:33:13 PST)
[AMBER] Problem with xleap/tleap
- Daniel Roe (Wed Feb 20 2013 - 10:22:18 PST)
- Jason Swails (Wed Feb 20 2013 - 10:20:02 PST)
- Ibrahim Moustafa (Wed Feb 20 2013 - 10:14:07 PST)
[AMBER] PROBLEMS IN SETTING UP PHOSPHORYLATED SIMULATION MODELS
- David A Case (Wed Feb 20 2013 - 04:39:46 PST)
- Jason Swails (Wed Feb 20 2013 - 04:31:03 PST)
- Theodosia Teo (Tue Feb 19 2013 - 22:11:07 PST)
- case (Tue Feb 19 2013 - 16:51:24 PST)
- Theodosia Teo (Tue Feb 19 2013 - 13:35:48 PST)
- David A Case (Tue Feb 19 2013 - 04:45:09 PST)
- Theodosia Teo (Mon Feb 18 2013 - 19:46:53 PST)
[AMBER] problems starting amber
- Ayesha Fatima (Wed Feb 13 2013 - 19:51:31 PST)
- Daniel Sindhikara (Wed Feb 13 2013 - 19:22:34 PST)
- Ayesha Fatima (Wed Feb 13 2013 - 19:00:02 PST)
[AMBER] Problems with MMPBSA.py for running pbsa calculations
- Ray Luo, Ph.D. (Tue Feb 12 2013 - 16:06:35 PST)
- Ray Luo, Ph.D. (Mon Feb 11 2013 - 15:24:02 PST)
- manikanthan bhavaraju (Mon Feb 11 2013 - 14:58:17 PST)
- Jason Swails (Mon Feb 11 2013 - 14:06:56 PST)
- Ray Luo, Ph.D. (Mon Feb 11 2013 - 13:08:01 PST)
- manikanthan bhavaraju (Mon Feb 11 2013 - 12:48:28 PST)
- Jason Swails (Mon Feb 11 2013 - 03:18:20 PST)
- WenJuan Huang (Sun Feb 10 2013 - 21:04:05 PST)
- Ray Luo, Ph.D. (Sat Feb 09 2013 - 13:17:00 PST)
- manikanthan bhavaraju (Sat Feb 09 2013 - 12:36:19 PST)
[AMBER] problems with NAB
- uday spike (Tue Feb 19 2013 - 00:25:55 PST)
- Jason Swails (Sat Feb 16 2013 - 05:47:30 PST)
- uday spike (Sat Feb 16 2013 - 01:34:51 PST)
- Daniel Sindhikara (Thu Feb 07 2013 - 00:03:15 PST)
- uday spike (Wed Feb 06 2013 - 23:49:37 PST)
[AMBER] Problems with ti using DFTB for zinc bound hydroxyl
- Fabrício Bracht (Mon Feb 04 2013 - 12:00:32 PST)
- Brian Radak (Mon Feb 04 2013 - 11:51:45 PST)
- Fabrício Bracht (Mon Feb 04 2013 - 11:21:10 PST)
- Brian Radak (Mon Feb 04 2013 - 10:52:26 PST)
- Fabrício Bracht (Mon Feb 04 2013 - 10:31:16 PST)
- Brian Radak (Sun Feb 03 2013 - 09:19:00 PST)
- Fabrício Bracht (Sat Feb 02 2013 - 17:33:53 PST)
- Brian Radak (Sat Feb 02 2013 - 13:03:35 PST)
- Fabrício Bracht (Sat Feb 02 2013 - 11:35:04 PST)
[AMBER] protein-protein binding free energy
- Vaibhav Dixit (Sat Feb 02 2013 - 21:03:09 PST)
- David A Case (Fri Feb 01 2013 - 18:40:43 PST)
- Date, Mihir (Fri Feb 01 2013 - 15:14:33 PST)
[AMBER] pseudoatom
- FyD (Mon Feb 25 2013 - 12:48:08 PST)
- Jason Swails (Mon Feb 25 2013 - 04:55:57 PST)
- Anne Kichler (Mon Feb 25 2013 - 03:32:41 PST)
[AMBER] PSF file, atom radii and chamber
- Massimiliano Porrini (Mon Feb 11 2013 - 10:05:48 PST)
[AMBER] ptraj RMSD- spikes in RMSD and co-ordinates at 0.000
- Cassandra Churchill (Thu Feb 07 2013 - 09:46:09 PST)
- Daniel Roe (Wed Feb 06 2013 - 10:34:20 PST)
- Cassandra Churchill (Wed Feb 06 2013 - 09:58:18 PST)
[AMBER] qmshake=1 did not prevent bonds from being broken
- Fabrício Bracht (Wed Feb 20 2013 - 13:30:03 PST)
- Brian Radak (Wed Feb 20 2013 - 11:08:07 PST)
- Fabrício Bracht (Wed Feb 20 2013 - 10:56:33 PST)
- Brian Radak (Wed Feb 20 2013 - 06:08:08 PST)
- Fabrício Bracht (Tue Feb 19 2013 - 14:32:49 PST)
[AMBER] Query about checking of convergence in REMD
- Carlos Simmerling (Wed Feb 06 2013 - 04:32:35 PST)
- gargi borgohai (Wed Feb 06 2013 - 04:21:24 PST)
[AMBER] Query regarding cpptraj multiple input in a single file
- Daniel Roe (Fri Feb 01 2013 - 07:29:48 PST)
- HM (Fri Feb 01 2013 - 07:11:59 PST)
[AMBER] Query regarding PNA-DNA duplex parameterization in AMBER
- Souvik Sur (Fri Feb 08 2013 - 23:26:19 PST)
[AMBER] question on input for MMPBSA.py
- Shashidhar Rao (Tue Feb 26 2013 - 08:03:53 PST)
- Jason Swails (Tue Feb 26 2013 - 07:27:35 PST)
- Shashidhar Rao (Tue Feb 26 2013 - 06:56:15 PST)
- Jason Swails (Mon Feb 25 2013 - 17:20:37 PST)
- Shashidhar Rao (Mon Feb 25 2013 - 13:08:32 PST)
[AMBER] Question regarding wham and umbrella sampling
- Aron Broom (Mon Feb 25 2013 - 14:52:37 PST)
- Brian Radak (Mon Feb 25 2013 - 13:07:00 PST)
- Fabrício Bracht (Mon Feb 25 2013 - 13:29:13 PST)
- Aron Broom (Mon Feb 25 2013 - 13:06:59 PST)
- Fabrício Bracht (Mon Feb 25 2013 - 12:09:23 PST)
[AMBER] radial distribution function between atoms of the two masks
- Massimiliano Porrini (Thu Feb 21 2013 - 06:12:24 PST)
[AMBER] randomizeions with cpptraj
- David A Case (Wed Feb 20 2013 - 04:44:45 PST)
- Asmita Gupta (Wed Feb 20 2013 - 02:56:43 PST)
[AMBER] regarding frcmod preparation
- Aparna P (Fri Feb 22 2013 - 06:16:13 PST)
- Prajwal Nandekar (Fri Feb 22 2013 - 03:11:57 PST)
- Aparna P (Fri Feb 22 2013 - 03:07:46 PST)
[AMBER] remd exchange acceptance
- Adrian Roitberg (Thu Feb 28 2013 - 04:37:40 PST)
- Daniel Sindhikara (Thu Feb 28 2013 - 02:02:36 PST)
- Kim Hyunsik (Wed Feb 27 2013 - 22:08:24 PST)
[AMBER] restart file with *********** problem
- Daniel Roe (Fri Feb 08 2013 - 07:36:36 PST)
- Dr. M. Venkata Satish Kumar (Fri Feb 08 2013 - 00:18:19 PST)
[AMBER] rmsd of Ethanol
- Daniel Roe (Tue Feb 05 2013 - 14:03:56 PST)
- Chinthaka Ratnaweera (Tue Feb 05 2013 - 10:52:38 PST)
- Daniel Roe (Tue Feb 05 2013 - 10:13:58 PST)
- Chinthaka Ratnaweera (Tue Feb 05 2013 - 08:37:37 PST)
[AMBER] Sander error - Segmentation fault (core dumped)
- David A Case (Fri Feb 15 2013 - 11:51:49 PST)
- Symon Gathiaka (Fri Feb 15 2013 - 11:28:51 PST)
[AMBER] scaling problem in RADIAL of CPPTRAJ
- Marek Maly (Fri Feb 01 2013 - 12:54:50 PST)
- Marek Maly (Fri Feb 01 2013 - 12:40:07 PST)
- Thomas Cheatham (Fri Feb 01 2013 - 10:30:48 PST)
- Marek Maly (Fri Feb 01 2013 - 10:00:24 PST)
- Daniel Roe (Fri Feb 01 2013 - 09:41:03 PST)
- Marek Maly (Fri Feb 01 2013 - 08:51:35 PST)
- Daniel Roe (Fri Feb 01 2013 - 08:02:56 PST)
- Marek Maly (Thu Jan 31 2013 - 21:27:54 PST)
- Marek Maly (Thu Jan 31 2013 - 15:47:13 PST)
[AMBER] setting certain atoms as static
- David A Case (Wed Feb 06 2013 - 04:51:18 PST)
- Jonathan Saboury (Tue Feb 05 2013 - 23:14:11 PST)
[AMBER] Setting up a Periodic Box Size
- Jason Swails (Sat Feb 02 2013 - 12:36:04 PST)
- Jonathan Saboury (Sat Feb 02 2013 - 11:36:15 PST)
[AMBER] short bonds in average pdb
- Vaibhav Dixit (Wed Feb 20 2013 - 01:17:57 PST)
- Vaibhav Dixit (Wed Feb 20 2013 - 01:04:37 PST)
[AMBER] silhouette.pl
- Tamer Ibrahim (Mon Feb 04 2013 - 07:35:45 PST)
[AMBER] simulation MD - basic questions
- Jian Yin (Fri Feb 08 2013 - 13:29:11 PST)
- Anne Kichler (Thu Feb 07 2013 - 02:54:17 PST)
[AMBER] simulation of a nucleic acid linked on a gold surface
- FyD (Wed Feb 13 2013 - 23:06:47 PST)
- Ilyas Yildirim (Wed Feb 13 2013 - 17:17:58 PST)
- Barbault Florent (Wed Feb 13 2013 - 11:54:18 PST)
[AMBER] Small bug in MMPBSA.py tutorial
- Jason Swails (Sun Feb 17 2013 - 06:58:18 PST)
- Vaibhav Dixit (Sat Feb 16 2013 - 21:21:37 PST)
- Jason Swails (Sat Feb 16 2013 - 12:24:51 PST)
- George A. Khoury (Sat Feb 16 2013 - 09:47:03 PST)
[AMBER] spectrum simulation
- francesco oteri (Sun Feb 24 2013 - 12:56:18 PST)
[AMBER] Steered Molecular Dynamics
- case (Sun Feb 10 2013 - 09:41:12 PST)
- Mannan (Sat Feb 09 2013 - 17:28:56 PST)
- Mannan (Sat Feb 09 2013 - 17:29:11 PST)
- Mannan (Fri Feb 08 2013 - 06:05:32 PST)
[AMBER] test
- David A Case (Fri Feb 15 2013 - 08:13:33 PST)
[AMBER] the position of counterion
- Daniel Roe (Sun Feb 17 2013 - 11:42:28 PST)
- Sun (Sun Feb 17 2013 - 10:54:00 PST)
[AMBER] TI without ifsc = 1 crashes
- steinbrt.rci.rutgers.edu (Wed Feb 27 2013 - 00:36:31 PST)
- Fabrício Bracht (Tue Feb 26 2013 - 16:02:59 PST)
- Jason Swails (Tue Feb 26 2013 - 15:31:55 PST)
- Fabrício Bracht (Tue Feb 26 2013 - 15:02:32 PST)
[AMBER] topology file issue with entropy calculation
- Rejwan (Thu Feb 07 2013 - 11:48:22 PST)
- Jason Swails (Wed Feb 06 2013 - 18:24:23 PST)
- Rejwan (Wed Feb 06 2013 - 17:14:29 PST)
- David A Case (Tue Feb 05 2013 - 04:46:28 PST)
- Rejwan (Mon Feb 04 2013 - 22:58:01 PST)
[AMBER] unspecified launch failure launching kernel kRecalculateVelocities
- Ross Walker (Fri Feb 22 2013 - 15:04:41 PST)
- Symon Gathiaka (Fri Feb 22 2013 - 10:58:04 PST)
[AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
- Sangita Kachhap (Mon Feb 04 2013 - 08:21:03 PST)
- Jiri Sponer (Mon Feb 04 2013 - 07:37:12 PST)
- Sangita Kachhap (Mon Feb 04 2013 - 07:21:58 PST)
- Jiri Sponer (Mon Feb 04 2013 - 05:01:24 PST)
- Sangita Kachhap (Mon Feb 04 2013 - 04:39:14 PST)
[AMBER] Using cpptraj to trim a range of water residues while maintaining a periodic box
- Joe Passman (Mon Feb 11 2013 - 20:51:44 PST)
- Daniel Roe (Sun Feb 10 2013 - 18:58:03 PST)
- Jason Swails (Sun Feb 10 2013 - 18:32:30 PST)
- Joe Passman (Sun Feb 10 2013 - 17:15:21 PST)
[AMBER] Using OPLS force field parameters in Amber MD run
- DEBOSTUTI GHOSHDASTIDAR (Thu Feb 21 2013 - 05:39:48 PST)
- Jason Swails (Thu Feb 21 2013 - 05:22:24 PST)
- DEBOSTUTI GHOSHDASTIDAR (Wed Feb 20 2013 - 23:13:56 PST)
[AMBER] VIBRATIONAL FREQUANCY USING NMODE
- Daniel Roe (Wed Feb 13 2013 - 13:24:18 PST)
- Rasha Alqus (Wed Feb 13 2013 - 05:32:43 PST)
[AMBER] Warnings when saving prmtop and inpcrd files.
- Jason Swails (Mon Feb 11 2013 - 03:06:05 PST)
- Sanjib Paul (Sun Feb 10 2013 - 23:39:51 PST)
[AMBER] What algorithm does ptraj use for solvation of eigen-value problem.
- kurisaki (Sat Feb 16 2013 - 22:35:30 PST)
- case (Sat Feb 16 2013 - 07:03:54 PST)
- kurisaki (Sat Feb 16 2013 - 00:14:35 PST)
- Daniel Roe (Fri Feb 15 2013 - 23:55:10 PST)
- kurisaki (Fri Feb 15 2013 - 21:40:50 PST)
- Daniel Roe (Fri Feb 15 2013 - 07:43:18 PST)
- kurisaki (Fri Feb 15 2013 - 01:08:46 PST)
[AMBER] Wrong Annotation of PREPIN generated by RESIDUEGEN
- David A Case (Mon Feb 11 2013 - 05:12:28 PST)
- kurisaki (Sun Feb 10 2013 - 19:47:06 PST)
- case (Sun Feb 10 2013 - 09:43:54 PST)
- kurisaki (Sun Feb 10 2013 - 01:20:26 PST)
[AMBER] xleap could not find the type Cl-
- Sanjib Paul (Sat Feb 09 2013 - 09:54:03 PST)
- David A Case (Sat Feb 09 2013 - 06:49:20 PST)
- Sanjib Paul (Sat Feb 09 2013 - 04:26:32 PST)
[AMBER] xleap problem using savemol2
- Jason Swails (Tue Feb 19 2013 - 07:07:41 PST)
- Charles Do (Tue Feb 19 2013 - 06:54:32 PST)
- Jason Swails (Mon Feb 18 2013 - 10:51:50 PST)
- Charles Do (Mon Feb 18 2013 - 10:44:38 PST)
glucose
- m.wisniewska.aol.pl (Wed Feb 20 2013 - 09:11:09 PST)

Amber Archive Feb 2013 by subject