AMBER Archive (2009) - Oct 2009 By Subject

482 messages sorted by: [ author ] [ date ] [ thread ]
About this archive

Starting: Thu Oct 01 2009 - 06:31:51 CDT
Ending: Sat Oct 31 2009 - 23:59:38 CDT

(files attached) RESP with -a and witout -a flag
- Jio M (Sat Oct 31 2009 - 00:17:55 CDT)
[AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber
- case (Wed Oct 14 2009 - 06:37:35 CDT)
- haifeng yuan (Tue Oct 13 2009 - 02:44:55 CDT)
[AMBER] "extra points" incompatibility with pmemd
- mousumi (Thu Oct 22 2009 - 00:20:48 CDT)
- Brent Krueger (Wed Oct 21 2009 - 07:28:58 CDT)
- case (Wed Oct 21 2009 - 07:22:28 CDT)
- Robert Duke (Wed Oct 21 2009 - 07:02:54 CDT)
- mousumi (Wed Oct 21 2009 - 02:57:51 CDT)
[AMBER] (no subject)
- Prakash Patodia (Sat Oct 17 2009 - 02:12:39 CDT)
[AMBER] [amber10] atom groups used in torsion constrain
- Han Zheng (Mon Oct 26 2009 - 13:09:07 CDT)
[AMBER] [Fwd: ligand exiting a protein cavity]
- Jason Swails (Fri Oct 30 2009 - 11:23:29 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 08:42:57 CDT)
- Jason Swails (Fri Oct 30 2009 - 08:07:17 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 00:43:22 CDT)
- Jason Swails (Thu Oct 29 2009 - 10:17:40 CDT)
- Kshatresh Dutta Dubey (Thu Oct 29 2009 - 09:44:28 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:36:13 CDT)
[AMBER] [Fwd: problem with minimization]
- Bill Ross (Fri Oct 23 2009 - 12:40:57 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 13:53:11 CDT)
- Bill Ross (Thu Oct 22 2009 - 11:49:45 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 07:46:32 CDT)
[AMBER] A bug in LEaP ?
- FyD (Sun Oct 11 2009 - 07:08:37 CDT)
[AMBER] A bug in LEaP II ?
- FyD (Sun Oct 25 2009 - 07:58:36 CDT)
[AMBER] Add the hydrogen to the carboxyl of the GLU residue?
- Carlos Simmerling (Wed Oct 14 2009 - 08:49:00 CDT)
- FyD (Wed Oct 14 2009 - 08:40:09 CDT)
- Andrew Purkiss-Trew (Wed Oct 14 2009 - 07:19:43 CDT)
- xuemeiwang1103 (Wed Oct 14 2009 - 07:05:48 CDT)
[AMBER] AMBER 11.
- case (Thu Oct 15 2009 - 11:52:51 CDT)
- Peter Winn (Thu Oct 15 2009 - 11:27:39 CDT)
[AMBER] AMBER FF and NAMD
- FyD (Fri Oct 16 2009 - 14:19:13 CDT)
- Nicolas Sapay (Fri Oct 16 2009 - 09:59:53 CDT)
- Hannes Loeffler (Fri Oct 16 2009 - 09:45:25 CDT)
- stefano_elli\_at_libero\.it (Fri Oct 16 2009 - 09:26:14 CDT)
[AMBER] amber parallel test fail
- Nahoum Anthony (Fri Oct 23 2009 - 10:12:40 CDT)
- Jason Swails (Fri Oct 23 2009 - 06:58:19 CDT)
- Nahoum Anthony (Fri Oct 23 2009 - 05:20:45 CDT)
[AMBER] amber8 pmemd trajectory coordinates problem
- Robert Duke (Tue Oct 20 2009 - 20:15:56 CDT)
- Robert Duke (Tue Oct 20 2009 - 20:03:37 CDT)
- Sergio Wong (Tue Oct 20 2009 - 19:49:11 CDT)
- Thomas Cheatham (Tue Oct 20 2009 - 19:39:22 CDT)
- wong105_at_llnl.gov (Tue Oct 20 2009 - 19:32:24 CDT)
[AMBER] Analyzing per-residue decomposition data
- manoj singh (Thu Oct 29 2009 - 15:18:45 CDT)
[AMBER] Any tutorial on the proper way to merge a ligand and protein?
- Scott Brozell (Fri Oct 16 2009 - 14:40:56 CDT)
[AMBER] B-factor
- Cristina Sisu (Sat Oct 17 2009 - 05:58:34 CDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 17:16:35 CDT)
- Cristina Sisu (Thu Oct 15 2009 - 12:04:25 CDT)
[AMBER] binding energy
- steinbrt_at_rci.rutgers.edu (Fri Oct 16 2009 - 06:27:24 CDT)
- Simon Becker (Fri Oct 16 2009 - 04:28:39 CDT)
[AMBER] building quadruplex with NAB
- case (Tue Oct 27 2009 - 21:23:29 CDT)
- Peter Varnai (Tue Oct 27 2009 - 15:00:09 CDT)
[AMBER] can I run EVB in other ensemble than NVE?
- case (Tue Oct 20 2009 - 12:08:58 CDT)
- Jose Borreguero (Tue Oct 20 2009 - 11:57:04 CDT)
[AMBER] Can I use other ntb options in constant pH simulation
- Jason Swails (Wed Oct 21 2009 - 06:42:42 CDT)
- nicholus bhattacharjee (Wed Oct 21 2009 - 04:26:43 CDT)
[AMBER] Centering and reimaging with ptraj- stop rotating.
- Bill Ross (Tue Oct 20 2009 - 00:14:10 CDT)
- Thomas Cheatham (Mon Oct 19 2009 - 22:47:07 CDT)
- ben rodriguez (Mon Oct 19 2009 - 22:00:26 CDT)
[AMBER] charges for heme-cys in p450
- FyD (Fri Oct 23 2009 - 05:57:43 CDT)
- Jayalakshmi Sridhar (Thu Oct 22 2009 - 11:03:08 CDT)
[AMBER] Circular RNA topology file
- Filip Lankas (Mon Oct 26 2009 - 05:13:46 CDT)
- case (Wed Oct 21 2009 - 14:06:17 CDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 21 2009 - 13:26:04 CDT)
[AMBER] Combine and rename group of residues in xleap
- case (Fri Oct 09 2009 - 08:32:57 CDT)
- Lili Peng (Wed Oct 07 2009 - 16:49:23 CDT)
[AMBER] Compiling Amber with gfortran-4.5.0 on a mac
- Mengjuei Hsieh (Tue Oct 06 2009 - 21:05:54 CDT)
- Ben Roberts (Fri Oct 02 2009 - 09:20:47 CDT)
- case (Fri Oct 02 2009 - 08:19:11 CDT)
[AMBER] Computing an Hessian matrix using NAB
- Brut Marie (Tue Oct 13 2009 - 14:00:53 CDT)
- Brut Marie (Tue Oct 13 2009 - 13:56:19 CDT)
- case (Tue Oct 13 2009 - 07:13:42 CDT)
- Brut Marie (Mon Oct 12 2009 - 17:12:44 CDT)
[AMBER] contradictive hydrogen bonds using ptraj
- Binbin Liu (Mon Oct 26 2009 - 11:42:20 CDT)
[AMBER] Conversion of Gaussian output file into mol2
- Junmei Wang (Thu Oct 29 2009 - 10:45:27 CDT)
- megha bajaj (Wed Oct 28 2009 - 03:00:35 CDT)
[AMBER] Conversion of Gaussian output file to mol2
- megha bajaj (Wed Oct 28 2009 - 02:49:51 CDT)
[AMBER] cross correlation analysis with ptraj
- Junmei Wang (Thu Oct 15 2009 - 11:49:29 CDT)
[AMBER] decomposing energies
- Beroza, Paul (Thu Oct 01 2009 - 11:15:07 CDT)
[AMBER] decomposition and calculation of entropy
- Qinghua Liao (Sat Oct 10 2009 - 01:13:49 CDT)
[AMBER] DG improper torsion problem, two missing parameters
- Bill Ross (Fri Oct 09 2009 - 12:25:30 CDT)
- case (Fri Oct 09 2009 - 06:46:34 CDT)
- Youn Kyeung Lee (Fri Oct 09 2009 - 02:02:03 CDT)
[AMBER] Different optimized structures with HF and B3LYP
- Karl Kirschner (Fri Oct 02 2009 - 03:07:08 CDT)
- Sanghwa Han (Fri Oct 02 2009 - 02:50:10 CDT)
[AMBER] Different results for different computers
- Robert Duke (Sat Oct 31 2009 - 17:56:28 CDT)
- Jason Swails (Sat Oct 31 2009 - 14:57:34 CDT)
- manoj singh (Sat Oct 31 2009 - 14:47:36 CDT)
- cyk5056 (Sat Oct 31 2009 - 14:39:59 CDT)
[AMBER] Dihedral energy profile in a single molecule
- Jason Swails (Fri Oct 16 2009 - 10:02:35 CDT)
- Frank X. Vázquez (Fri Oct 16 2009 - 09:55:53 CDT)
[AMBER] Dipole moment visualization.
- K.R. (Thu Oct 01 2009 - 16:37:29 CDT)
[AMBER] Distance Replica Exchange
- Steve Seibold (Fri Oct 09 2009 - 09:21:13 CDT)
- Carlos Simmerling (Fri Oct 09 2009 - 08:40:17 CDT)
- Steve Seibold (Fri Oct 09 2009 - 08:18:44 CDT)
[AMBER] DMF solvent box
- FyD (Thu Oct 08 2009 - 23:08:59 CDT)
- Abhishek Banerjee (Thu Oct 08 2009 - 22:41:02 CDT)
- FyD (Wed Oct 07 2009 - 15:34:35 CDT)
- Abhishek Banerjee (Tue Oct 06 2009 - 23:10:22 CDT)
[AMBER] eigenvalues add up to more than trace of matrix
- Hannes Loeffler (Fri Oct 16 2009 - 08:50:50 CDT)
- Jason Swails (Fri Oct 16 2009 - 08:29:13 CDT)
- Yaw Sing TAN (Thu Oct 15 2009 - 22:14:59 CDT)
[AMBER] Energy-from-MM/PBSA-VS-experiment
- Rilei Yu (Sun Oct 11 2009 - 17:51:26 CDT)
- Jason Swails (Sun Oct 11 2009 - 09:54:08 CDT)
- Rilei Yu (Sun Oct 11 2009 - 07:53:00 CDT)
[AMBER] Environment Variables in Cygwin Don't Remain
- Bill Ross (Thu Oct 01 2009 - 13:57:43 CDT)
- Jack Shultz (Thu Oct 01 2009 - 12:12:19 CDT)
- Wallace Kunin (Thu Oct 01 2009 - 11:54:29 CDT)
[AMBER] error in AMBer distance constraint
- Carlos Simmerling (Tue Oct 27 2009 - 06:28:22 CDT)
- xuemeiwang1103 (Mon Oct 26 2009 - 02:35:08 CDT)
- Bill Ross (Sun Oct 25 2009 - 22:03:19 CDT)
- Carlos Simmerling (Sun Oct 25 2009 - 21:38:23 CDT)
- xuemeiwang1103 (Sun Oct 25 2009 - 21:24:09 CDT)
[AMBER] error in distance restraint
- Carlos Simmerling (Thu Oct 29 2009 - 05:20:13 CDT)
- xuemeiwang1103 (Wed Oct 28 2009 - 22:43:55 CDT)
- Carlos Simmerling (Wed Oct 28 2009 - 15:48:13 CDT)
- Adrian Roitberg (Wed Oct 28 2009 - 09:01:07 CDT)
- xuemeiwang1103 (Wed Oct 28 2009 - 08:56:48 CDT)
[AMBER] error message from iAPBS
- Oliver Kuhn (Mon Oct 19 2009 - 06:47:32 CDT)
[AMBER] Error: unable to find mopac charges in mopac.out
- case (Tue Oct 20 2009 - 06:45:59 CDT)
- Rilei Yu (Tue Oct 20 2009 - 02:12:19 CDT)
- Ross Walker (Tue Oct 20 2009 - 00:50:17 CDT)
- Rilei Yu (Tue Oct 20 2009 - 00:34:34 CDT)
[AMBER] ff03 parameter for GDP and GTP
- FyD (Sun Oct 11 2009 - 06:42:25 CDT)
- Carlos Simmerling (Sat Oct 10 2009 - 06:36:35 CDT)
- FyD (Sat Oct 10 2009 - 00:52:27 CDT)
- FyD (Fri Oct 09 2009 - 15:38:08 CDT)
- mmg8_at_ualberta.ca (Fri Oct 09 2009 - 09:30:46 CDT)
- Carlos Simmerling (Fri Oct 09 2009 - 08:09:32 CDT)
- case (Fri Oct 09 2009 - 08:03:02 CDT)
- Carlos Simmerling (Fri Oct 09 2009 - 07:45:04 CDT)
- FyD (Fri Oct 09 2009 - 05:37:40 CDT)
- mmg8_at_ualberta.ca (Thu Oct 08 2009 - 20:05:18 CDT)
[AMBER] File format for reading in charges in antechamber
- Dean Cuebas (Sun Oct 04 2009 - 15:20:42 CDT)
[AMBER] Fwd: Group specification
- Bill Ross (Thu Oct 08 2009 - 15:22:54 CDT)
- Bill Ross (Thu Oct 08 2009 - 15:15:44 CDT)
- Carlos Simmerling (Thu Oct 08 2009 - 13:35:43 CDT)
- Pavan G (Thu Oct 08 2009 - 13:30:09 CDT)
[AMBER] GAFF parameter
- Ross Walker (Tue Oct 20 2009 - 13:50:18 CDT)
- Jason Swails (Tue Oct 20 2009 - 09:57:09 CDT)
- stefano_elli\_at_libero\.it (Tue Oct 20 2009 - 08:26:26 CDT)
[AMBER] Gaussian log file error
- megha bajaj (Sat Oct 31 2009 - 08:10:22 CDT)
[AMBER] HBOND analysis
- Marcin Krol (Tue Oct 20 2009 - 10:42:35 CDT)
[AMBER] How create PRMTOP and INCPRD for surface?
- rrd (Sat Oct 17 2009 - 21:40:02 CDT)
[AMBER] How to add a hydrogen to the residue?
- case (Wed Oct 14 2009 - 06:51:08 CDT)
- xuemeiwang1103 (Tue Oct 13 2009 - 22:57:53 CDT)
[AMBER] How to create FF for diamond.
- rrd (Tue Oct 20 2009 - 01:16:07 CDT)
[AMBER] how to get hold of older versions of MKL ?
- Ross Walker (Mon Oct 19 2009 - 11:58:54 CDT)
- Jason Swails (Mon Oct 19 2009 - 05:54:45 CDT)
- Nahoum Anthony (Mon Oct 19 2009 - 03:59:57 CDT)
[AMBER] How to introduce the second protein molecule into simulation box?
- Jason Swails (Fri Oct 16 2009 - 08:15:57 CDT)
- Siddharth Rastogi (Fri Oct 16 2009 - 02:00:03 CDT)
[AMBER] How to prepare the acetate ion file in leap?
- Balazs Jojart (Tue Oct 13 2009 - 02:36:03 CDT)
- xuemeiwang1103 (Tue Oct 13 2009 - 02:05:57 CDT)
[AMBER] iAPBS - how to set the right grid dimensions
- Robert Konecny (Wed Oct 14 2009 - 08:21:07 CDT)
- Oliver Kuhn (Wed Oct 14 2009 - 08:16:28 CDT)
- Robert Konecny (Tue Oct 13 2009 - 12:12:04 CDT)
- Oliver Kuhn (Tue Oct 13 2009 - 10:17:06 CDT)
- Robert Konecny (Tue Oct 13 2009 - 09:42:12 CDT)
- Oliver Kuhn (Tue Oct 13 2009 - 03:36:27 CDT)
[AMBER] inhibitor prepin not recognized in xleap
- Bill Ross (Fri Oct 23 2009 - 13:32:03 CDT)
- Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:05:46 CDT)
- Jayalakshmi Sridhar (Fri Oct 23 2009 - 10:56:40 CDT)
[AMBER] installation of Amber on OSX
- Jason Swails (Wed Oct 14 2009 - 17:41:31 CDT)
- case (Wed Oct 14 2009 - 17:10:04 CDT)
- David Watson (Wed Oct 14 2009 - 17:03:51 CDT)
- Ramgopal Mettu (Wed Oct 14 2009 - 16:46:59 CDT)
[AMBER] Is it the way to do simulation in vacuum
- Ross Walker (Fri Oct 30 2009 - 14:15:01 CDT)
- Carlos Simmerling (Fri Oct 30 2009 - 11:10:22 CDT)
- Jason Swails (Fri Oct 30 2009 - 11:06:14 CDT)
- Carlos Simmerling (Fri Oct 30 2009 - 08:26:20 CDT)
- case (Fri Oct 30 2009 - 07:49:46 CDT)
- nicholus bhattacharjee (Fri Oct 30 2009 - 06:11:03 CDT)
- Carlos Simmerling (Fri Oct 30 2009 - 05:21:49 CDT)
- nicholus bhattacharjee (Fri Oct 30 2009 - 05:18:45 CDT)
[AMBER] Is iwrap mapping water molecules to my protein cavity?
- Carlos Simmerling (Mon Oct 12 2009 - 14:28:12 CDT)
- Bill Ross (Mon Oct 12 2009 - 14:12:19 CDT)
- ben rodriguez (Mon Oct 12 2009 - 13:55:23 CDT)
[AMBER] Large File Support
- Ross Walker (Thu Oct 15 2009 - 13:14:01 CDT)
- Beale, John (Thu Oct 15 2009 - 07:40:27 CDT)
[AMBER] Lennard Jones Potential A and B coefficients in Topology file
- Crowley, Michael (Sat Oct 31 2009 - 12:32:12 CDT)
- Peter Schmidtke (Sat Oct 31 2009 - 10:10:12 CDT)
- Tom Joseph (Sat Oct 31 2009 - 09:59:14 CDT)
- Tom Joseph (Sat Oct 31 2009 - 00:23:03 CDT)
- Peter Schmidtke (Fri Oct 30 2009 - 19:09:46 CDT)
- Tom Joseph (Fri Oct 30 2009 - 17:04:43 CDT)
- Peter Schmidtke (Fri Oct 30 2009 - 13:32:32 CDT)
[AMBER] LES and NEB problem
- Carlos Simmerling (Thu Oct 15 2009 - 13:09:34 CDT)
- Jason Swails (Thu Oct 15 2009 - 13:09:14 CDT)
- Rima Chaudhuri (Thu Oct 15 2009 - 12:53:41 CDT)
- Carlos Simmerling (Thu Oct 15 2009 - 11:54:18 CDT)
- Rima Chaudhuri (Thu Oct 15 2009 - 11:50:08 CDT)
- Carlos Simmerling (Wed Oct 14 2009 - 09:14:04 CDT)
- Rima Chaudhuri (Tue Oct 13 2009 - 14:35:37 CDT)
[AMBER] Ligand covalent bonds appear to be broken
- Thomas Cheatham (Fri Oct 30 2009 - 10:48:07 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 08:43:25 CDT)
- Jason Swails (Fri Oct 30 2009 - 08:11:03 CDT)
- Tom Joseph (Fri Oct 30 2009 - 06:53:44 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Fri Oct 30 2009 - 01:32:39 CDT)
[AMBER] ligand exiting a protein cavity
- moitrayee_at_mbu.iisc.ernet.in (Thu Oct 29 2009 - 07:27:58 CDT)
[AMBER] man pages?
- Jason Swails (Tue Oct 20 2009 - 16:28:56 CDT)
- Louis-Frédéric Feuillette (Tue Oct 20 2009 - 15:17:52 CDT)
- Ben Roberts (Tue Oct 20 2009 - 12:33:16 CDT)
- Louis-Frédéric Feuillette (Tue Oct 20 2009 - 12:09:09 CDT)
[AMBER] mean square displacment
- Bill Ross (Tue Oct 13 2009 - 19:09:49 CDT)
- Nancy (Tue Oct 13 2009 - 18:59:15 CDT)
[AMBER] method used to determine partial charges?
- FyD (Thu Oct 01 2009 - 23:27:13 CDT)
- Jihang Wang (Thu Oct 01 2009 - 17:42:38 CDT)
- Carlos Simmerling (Thu Oct 01 2009 - 17:30:21 CDT)
- Jihang Wang (Thu Oct 01 2009 - 17:26:24 CDT)
- Bill Ross (Thu Oct 01 2009 - 17:18:01 CDT)
- Jihang Wang (Thu Oct 01 2009 - 16:28:45 CDT)
- Bill Ross (Thu Oct 01 2009 - 16:19:29 CDT)
- Jihang Wang (Thu Oct 01 2009 - 15:36:31 CDT)
- Paul Brandt (Thu Oct 01 2009 - 15:25:54 CDT)
[AMBER] minimization error
- case (Fri Oct 02 2009 - 07:00:52 CDT)
- balaji nagarajan (Fri Oct 02 2009 - 06:42:54 CDT)
[AMBER] Missing X11 Libraries
- Bill Ross (Fri Oct 09 2009 - 19:24:47 CDT)
- FyD (Fri Oct 09 2009 - 16:06:20 CDT)
- Thomas Patko (Fri Oct 09 2009 - 15:53:14 CDT)
- FyD (Fri Oct 09 2009 - 15:35:59 CDT)
- case (Fri Oct 09 2009 - 15:02:06 CDT)
- Wallace Kunin (Fri Oct 09 2009 - 14:20:00 CDT)
- Bill Ross (Fri Oct 09 2009 - 12:52:01 CDT)
- Thomas Patko (Fri Oct 09 2009 - 12:13:22 CDT)
- Wallace Kunin (Fri Oct 09 2009 - 12:03:51 CDT)
- Wallace Kunin (Fri Oct 09 2009 - 11:59:06 CDT)
- Thomas Patko (Thu Oct 08 2009 - 12:26:26 CDT)
- Bill Ross (Thu Oct 08 2009 - 12:25:32 CDT)
- Wallace Kunin (Thu Oct 08 2009 - 12:09:55 CDT)
- Bill Ross (Wed Oct 07 2009 - 17:28:34 CDT)
- Thomas Patko (Wed Oct 07 2009 - 16:14:15 CDT)
- Wallace Kunin (Wed Oct 07 2009 - 16:10:34 CDT)
- FyD (Wed Oct 07 2009 - 15:45:34 CDT)
- Mengjuei Hsieh (Wed Oct 07 2009 - 15:19:20 CDT)
- Wallace Kunin (Wed Oct 07 2009 - 13:04:39 CDT)
- Wallace Kunin (Sat Oct 03 2009 - 12:02:05 CDT)
- Wallace Kunin (Fri Oct 02 2009 - 14:57:49 CDT)
- case (Fri Oct 02 2009 - 13:56:34 CDT)
- Wallace Kunin (Fri Oct 02 2009 - 11:43:59 CDT)
[AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out
- Rubben Torella (Tue Oct 06 2009 - 02:56:18 CDT)
- Jeff Yeo (Mon Oct 05 2009 - 18:22:53 CDT)
[AMBER] MM_PBSA decomposition pair question
- Rubben Torella (Fri Oct 02 2009 - 06:09:38 CDT)
[AMBER] mm_pbsa- Decomposition: bad atom type
- Antonija TomiÄ‡ (Tue Oct 06 2009 - 08:53:25 CDT)
[AMBER] MM_PBSA: abnormal VDW interaction energy
- LIU Huanxiang (Tue Oct 06 2009 - 21:54:49 CDT)
- steinbrt_at_rci.rutgers.edu (Tue Oct 06 2009 - 03:09:27 CDT)
- LIU Huanxiang (Mon Oct 05 2009 - 21:43:21 CDT)
[AMBER] MMPBSA: No radius found for F
- Jeff Yeo (Sun Oct 04 2009 - 19:10:12 CDT)
[AMBER] MMTSB cluster analysis versus ptraj cluster analysis
- Cenk \(Jenk\) Andac (Mon Oct 19 2009 - 16:44:42 CDT)
- Jianyin Shao (Mon Oct 19 2009 - 13:16:47 CDT)
- Cenk \(Jenk\) Andac (Sat Oct 17 2009 - 02:02:20 CDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 10:33:22 CDT)
- Cenk \(Jenk\) Andac (Fri Oct 16 2009 - 07:19:24 CDT)
[AMBER] nab normal mode analysis has imaginary frequencies
- case (Wed Oct 14 2009 - 13:34:05 CDT)
- Junmei Wang (Wed Oct 14 2009 - 11:05:06 CDT)
[AMBER] nasty memory bug in calculatePrincipalAxis
- Scott Brozell (Mon Oct 12 2009 - 16:38:06 CDT)
[AMBER] new process_mdout.pl script????
- Ross Walker (Mon Oct 05 2009 - 13:38:17 CDT)
- Dean Cuebas (Mon Oct 05 2009 - 13:11:49 CDT)
[AMBER] NMR restraint
- Sally Pias (Tue Oct 27 2009 - 23:32:33 CDT)
- xuemeiwang1103 (Tue Oct 27 2009 - 21:31:39 CDT)
[AMBER] OpenMP
- michael (Tue Oct 13 2009 - 09:43:09 CDT)
- Ross Walker (Mon Oct 12 2009 - 13:29:45 CDT)
- Ben Roberts (Mon Oct 12 2009 - 12:35:35 CDT)
[AMBER] pairwise per-residue decomposition
- manoj singh (Sat Oct 31 2009 - 23:59:38 CDT)
- manoj singh (Fri Oct 30 2009 - 13:26:14 CDT)
- Tom Joseph (Fri Oct 30 2009 - 13:18:52 CDT)
- manoj singh (Fri Oct 30 2009 - 00:46:22 CDT)
- Tom Joseph (Fri Oct 30 2009 - 00:15:40 CDT)
- Tom Joseph (Thu Oct 29 2009 - 19:30:51 CDT)
- manoj singh (Thu Oct 29 2009 - 12:32:38 CDT)
- Carlos Simmerling (Thu Oct 29 2009 - 05:20:55 CDT)
- manoj singh (Wed Oct 28 2009 - 23:34:32 CDT)
[AMBER] Parallel sander & polarisability
- case (Thu Oct 29 2009 - 12:02:28 CDT)
- Ross Walker (Thu Oct 29 2009 - 12:00:13 CDT)
- Thomas Taylor (Thu Oct 29 2009 - 11:19:14 CDT)
[AMBER] parameters for O2 molecule
- Jeffrey (Thu Oct 29 2009 - 08:01:44 CDT)
- Jason Swails (Thu Oct 22 2009 - 09:19:51 CDT)
- Jeffrey (Thu Oct 22 2009 - 08:32:07 CDT)
[AMBER] part of the protein escaped from the water box
- Jason Swails (Thu Oct 15 2009 - 06:43:00 CDT)
- case (Thu Oct 15 2009 - 06:40:53 CDT)
- Carlos Simmerling (Thu Oct 15 2009 - 06:39:40 CDT)
- qiaoyan (Thu Oct 15 2009 - 06:33:00 CDT)
[AMBER] PEMD
- Tom Joseph (Mon Oct 26 2009 - 18:03:26 CDT)
- Cristina Sisu (Mon Oct 26 2009 - 16:44:42 CDT)
[AMBER] pmemd ifort problem
- Robert Duke (Fri Oct 23 2009 - 10:33:27 CDT)
- Sel Ercan (Fri Oct 23 2009 - 09:57:59 CDT)
[AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
- Carlos Simmerling (Tue Oct 27 2009 - 18:22:43 CDT)
- Han Zheng (Tue Oct 27 2009 - 17:47:20 CDT)
- Seetin, Matthew (Tue Oct 27 2009 - 16:17:41 CDT)
- Han Zheng (Tue Oct 27 2009 - 12:28:16 CDT)
[AMBER] Preparing distance restraints
- case (Mon Oct 26 2009 - 16:26:26 CDT)
- Yunjie Zhao (Mon Oct 26 2009 - 03:44:58 CDT)
[AMBER] probelm-APBS
- Rilei Yu (Sun Oct 04 2009 - 19:51:10 CDT)
- Robert Konecny (Sun Oct 04 2009 - 19:20:18 CDT)
- Rilei Yu (Sat Oct 03 2009 - 00:41:07 CDT)
[AMBER] Problem with memory in nmode analysis
- Alireza Shaneh (Tue Oct 06 2009 - 10:23:55 CDT)
[AMBER] problem with minimization
- moitrayee_at_mbu.iisc.ernet.in (Thu Oct 22 2009 - 06:01:14 CDT)
[AMBER] Problem with running anal module in amber
- moitrayee_at_mbu.iisc.ernet.in (Wed Oct 21 2009 - 01:47:17 CDT)
[AMBER] Protein and charged surface
- rrd (Thu Oct 01 2009 - 22:49:18 CDT)
[AMBER] ptraj and prmtop
- Carlos Simmerling (Wed Oct 14 2009 - 08:41:04 CDT)
- Beale, John (Wed Oct 14 2009 - 07:46:11 CDT)
[AMBER] Ptraj Segmentation Fault
- Katrina Hill (Wed Oct 21 2009 - 21:15:31 CDT)
[AMBER] pucker calculation for six member rings
- Ganesh Kamath (Mon Oct 05 2009 - 13:03:15 CDT)
[AMBER] Question about distance restraint ?
- Carlos Simmerling (Fri Oct 23 2009 - 05:56:24 CDT)
- xuemeiwang1103 (Fri Oct 23 2009 - 05:07:47 CDT)
[AMBER] question with hbond in carnal
- Bill Ross (Tue Oct 20 2009 - 11:32:56 CDT)
- Ganesh Kamath (Tue Oct 20 2009 - 08:58:36 CDT)
[AMBER] question with pucker in six member ring
- Bill Ross (Mon Oct 19 2009 - 12:54:03 CDT)
- Ganesh Kamath (Mon Oct 19 2009 - 12:42:17 CDT)
- Bill Ross (Fri Oct 16 2009 - 14:48:04 CDT)
- Ganesh Kamath (Fri Oct 16 2009 - 14:31:31 CDT)
- Bill Ross (Fri Oct 16 2009 - 13:43:56 CDT)
- Ganesh Kamath (Fri Oct 16 2009 - 13:36:41 CDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 13:23:05 CDT)
- Nicolas Sapay (Fri Oct 16 2009 - 10:04:24 CDT)
- Ganesh Kamath (Thu Oct 15 2009 - 14:55:45 CDT)
[AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org
- FyD (Sun Oct 04 2009 - 09:37:06 CDT)
[AMBER] RDC and alignment tensor
- Eliana Asciutto (Fri Oct 23 2009 - 14:19:00 CDT)
- case (Tue Oct 20 2009 - 07:24:45 CDT)
- Eliana Asciutto (Mon Oct 19 2009 - 14:03:43 CDT)
- case (Mon Oct 19 2009 - 12:36:16 CDT)
- Eliana Asciutto (Mon Oct 19 2009 - 11:50:31 CDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 15:45:25 CDT)
- Eliana Asciutto (Fri Oct 16 2009 - 15:21:34 CDT)
[AMBER] red problem
- FyD (Thu Oct 01 2009 - 23:48:57 CDT)
- James Moore (Thu Oct 01 2009 - 20:52:46 CDT)
[AMBER] RESP charges with -a and without -a flag
- Jio M (Sat Oct 31 2009 - 00:13:03 CDT)
- Junmei Wang (Fri Oct 30 2009 - 11:49:00 CDT)
- Jio M (Fri Oct 30 2009 - 08:36:43 CDT)
[AMBER] resp_problem
- FyD (Sun Oct 25 2009 - 01:12:31 CDT)
- Ross Walker (Sat Oct 24 2009 - 17:39:01 CDT)
- vhakkim boy (Sat Oct 24 2009 - 05:16:22 CDT)
[AMBER] rms fit of mutant with respect to wild type structure
- Carlos Simmerling (Thu Oct 29 2009 - 09:03:35 CDT)
- Siddharth Rastogi (Thu Oct 29 2009 - 08:55:12 CDT)
[AMBER] RMSD vs time and RMSD vs residues
- Sally Pias (Fri Oct 02 2009 - 14:16:33 CDT)
- case (Fri Oct 02 2009 - 14:12:23 CDT)
- Luis Gracia (Fri Oct 02 2009 - 13:07:10 CDT)
- Olotu Odunayo (Fri Oct 02 2009 - 12:40:40 CDT)
[AMBER] S-S problem-in protein
- Rilei Yu (Mon Oct 12 2009 - 17:14:02 CDT)
- Jason Swails (Mon Oct 12 2009 - 06:23:25 CDT)
- Rilei Yu (Mon Oct 12 2009 - 04:16:15 CDT)
- Rilei Yu (Mon Oct 12 2009 - 01:28:14 CDT)
- Jason Swails (Sun Oct 11 2009 - 23:24:51 CDT)
- Jason Swails (Sun Oct 11 2009 - 21:15:10 CDT)
- Rilei Yu (Sun Oct 11 2009 - 20:53:24 CDT)
[AMBER] Salt bridge time scale
- Mannan (Sun Oct 25 2009 - 20:57:20 CDT)
[AMBER] Simulated annealing
- Carlos Simmerling (Wed Oct 28 2009 - 05:51:41 CDT)
- Shaikh Abdul R S Ramaju (Wed Oct 28 2009 - 00:44:33 CDT)
- Carlos Simmerling (Thu Oct 15 2009 - 06:43:56 CDT)
- waleed zalloum (Thu Oct 15 2009 - 05:59:29 CDT)
[AMBER] Simulating transmembrane protein.
- Bill Ross (Mon Oct 12 2009 - 17:37:50 CDT)
- case (Mon Oct 12 2009 - 16:55:42 CDT)
- Jayalakshmi Sridhar (Mon Oct 12 2009 - 14:57:02 CDT)
- Bill Ross (Mon Oct 12 2009 - 14:04:36 CDT)
- Jayalakshmi Sridhar (Mon Oct 12 2009 - 13:42:11 CDT)
[AMBER] simulation blown up
- Robert Duke (Tue Oct 20 2009 - 22:55:39 CDT)
- Jason Swails (Tue Oct 20 2009 - 21:58:47 CDT)
- moitrayee_at_mbu.iisc.ernet.in (Tue Oct 20 2009 - 12:41:29 CDT)
[AMBER] six member pucker calculation
- Ganesh Kamath (Wed Oct 14 2009 - 09:27:24 CDT)
[AMBER] software to hydrate protein pockets
- Hannes Kopitz (Fri Oct 23 2009 - 08:11:26 CDT)
- Alessandro Nascimento (Fri Oct 23 2009 - 07:50:05 CDT)
- Vlad Cojocaru (Fri Oct 23 2009 - 07:23:54 CDT)
[AMBER] solvent accessible surface area
- Ray Luo (Thu Oct 08 2009 - 13:17:09 CDT)
- Siddharth Rastogi (Thu Oct 08 2009 - 05:02:20 CDT)
- Siddharth Rastogi (Thu Oct 08 2009 - 04:54:01 CDT)
[AMBER] Some queries about pH simulation
- nicholus bhattacharjee (Sat Oct 10 2009 - 00:07:21 CDT)
- Carlos Simmerling (Fri Oct 09 2009 - 13:59:17 CDT)
- Jason Swails (Fri Oct 09 2009 - 13:48:44 CDT)
- nicholus bhattacharjee (Thu Oct 08 2009 - 23:36:56 CDT)
[AMBER] some queries on -states flag in constant pH simulation
- Jason Swails (Sat Oct 31 2009 - 07:28:22 CDT)
- nicholus bhattacharjee (Sat Oct 31 2009 - 01:31:31 CDT)
- Jason Swails (Fri Oct 30 2009 - 08:00:37 CDT)
- nicholus bhattacharjee (Thu Oct 29 2009 - 23:21:27 CDT)
[AMBER] SPC/E HOH angle
- Carlos Simmerling (Fri Oct 30 2009 - 08:47:18 CDT)
- case (Fri Oct 30 2009 - 07:51:41 CDT)
- Hemant Kumar (Fri Oct 30 2009 - 05:36:55 CDT)
[AMBER] stacking clusters
- Shaikh Abdul R S Ramaju (Thu Oct 29 2009 - 21:44:59 CDT)
[AMBER] surface binding protein
- Jason Swails (Sat Oct 31 2009 - 07:35:44 CDT)
- sadaf iqbal (Sat Oct 31 2009 - 00:28:22 CDT)
[AMBER] The -c option in Sander
- case (Fri Oct 09 2009 - 20:54:05 CDT)
- phani ghanakota (Fri Oct 09 2009 - 19:47:18 CDT)
[AMBER] the criterion of equilibrium
- Adrian Roitberg (Sat Oct 24 2009 - 13:22:25 CDT)
- Bill Ross (Sat Oct 24 2009 - 12:19:09 CDT)
- qiaoyan (Fri Oct 23 2009 - 21:19:58 CDT)
[AMBER] The hydrophobic contribution
- case (Thu Oct 08 2009 - 07:41:28 CDT)
- Rilei Yu (Thu Oct 08 2009 - 00:48:32 CDT)
[AMBER] Thermodynamic Integration calculation on an artificial anion receptor
- steinbrt_at_rci.rutgers.edu (Thu Oct 29 2009 - 05:35:24 CDT)
- Huifang (Wed Oct 28 2009 - 23:38:05 CDT)
[AMBER] Time scale of the Protein domain motion ?
- Chih-Ying Lin (Sat Oct 17 2009 - 14:46:37 CDT)
- Carlos Simmerling (Sat Oct 17 2009 - 14:42:01 CDT)
- Chih-Ying Lin (Sat Oct 17 2009 - 14:36:18 CDT)
- Carlos Simmerling (Sat Oct 17 2009 - 14:23:34 CDT)
- Chih-Ying Lin (Sat Oct 17 2009 - 14:18:34 CDT)
[AMBER] TiO2 modeling
- stefano_elli_at_libero.it (Mon Oct 05 2009 - 11:00:59 CDT)
[AMBER] too many undefined parameters in frcmod
- xueqin pang (Thu Oct 29 2009 - 08:06:24 CDT)
- Junmei Wang (Mon Oct 26 2009 - 09:45:04 CDT)
- Jason Swails (Thu Oct 22 2009 - 06:59:55 CDT)
- FyD (Thu Oct 22 2009 - 04:37:46 CDT)
- xueqin pang (Thu Oct 22 2009 - 03:52:57 CDT)
[AMBER] translate multiple residues
- Bill Ross (Wed Oct 21 2009 - 17:40:51 CDT)
- Taufik Al-Sarraj (Wed Oct 21 2009 - 16:32:30 CDT)
- Bill Ross (Wed Oct 21 2009 - 15:53:20 CDT)
- Taufik Al-Sarraj (Wed Oct 21 2009 - 15:33:12 CDT)
[AMBER] trouble using iAPBS
- Robert Konecny (Thu Oct 01 2009 - 12:27:42 CDT)
- Oliver Kuhn (Thu Oct 01 2009 - 06:31:51 CDT)
[AMBER] Unable to correctly identify element when running QM/MM in amber10
- Ross Walker (Thu Oct 22 2009 - 14:03:40 CDT)
- Jifeng Wang (Thu Oct 22 2009 - 11:20:30 CDT)
[AMBER] unit converter for force constants
- GÃœL ALTINBAÅž (Mon Oct 12 2009 - 07:22:00 CDT)
[AMBER] unit convertion for force constants
- vhakkim boy (Mon Oct 12 2009 - 08:26:05 CDT)
- GÃœL ALTINBAÅž (Mon Oct 12 2009 - 07:47:42 CDT)
[AMBER] units of measures
- case (Thu Oct 22 2009 - 07:42:11 CDT)
- lorenzo (Thu Oct 22 2009 - 06:20:26 CDT)
[AMBER] Using idecomp=3 with igb=10 (PB)
- Chris Whittleston (Tue Oct 13 2009 - 05:02:17 CDT)
- Hannes Kopitz (Mon Oct 12 2009 - 14:51:23 CDT)
- Chris Whittleston (Mon Oct 12 2009 - 10:56:06 CDT)
- Hannes Kopitz (Sun Oct 11 2009 - 16:13:45 CDT)
- Chris Whittleston (Fri Oct 09 2009 - 10:16:53 CDT)
- Hannes Kopitz (Thu Oct 08 2009 - 15:30:19 CDT)
- Chris Whittleston (Thu Oct 08 2009 - 05:47:22 CDT)
- Chris Whittleston (Wed Oct 07 2009 - 11:57:25 CDT)
[AMBER] using RESP program
- FyD (Wed Oct 07 2009 - 15:04:38 CDT)
- Ganesh Kamath (Wed Oct 07 2009 - 05:36:13 CDT)
- gunajyoti das (Wed Oct 07 2009 - 05:30:27 CDT)
[AMBER] vlimit
- Ross Walker (Wed Oct 28 2009 - 17:35:15 CDT)
- Taufik Al-Sarraj (Wed Oct 28 2009 - 17:02:43 CDT)
- Bill Ross (Wed Oct 28 2009 - 16:55:55 CDT)
- Ross Walker (Wed Oct 28 2009 - 16:29:21 CDT)
- Taufik Al-Sarraj (Wed Oct 28 2009 - 16:16:32 CDT)
[AMBER] why is TAUTP scaled by "e" ?
- Jose Borreguero (Fri Oct 16 2009 - 14:13:42 CDT)
- case (Fri Oct 16 2009 - 08:30:53 CDT)
- Ross Walker (Thu Oct 15 2009 - 17:08:52 CDT)
- Jose Borreguero (Thu Oct 15 2009 - 15:49:18 CDT)
[AMBER] Why the calculation ofen stop with the calculation process not end?
- xuemeiwang1103 (Wed Oct 21 2009 - 09:04:57 CDT)
[AMBER] xleap editing window icons inactive
- Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:32:46 CDT)
- Niel Henriksen (Wed Oct 21 2009 - 13:21:54 CDT)
- Jayalakshmi Sridhar (Wed Oct 21 2009 - 13:20:01 CDT)
[AMBER] xleap not reconizing inhibitor prepin
- Junmei Wang (Mon Oct 26 2009 - 09:51:41 CDT)
- Bill Ross (Fri Oct 23 2009 - 13:33:44 CDT)
- Jayalakshmi Sridhar (Fri Oct 23 2009 - 11:21:07 CDT)
[AMBER] xleap-does not work
- Rilei Yu (Sun Oct 11 2009 - 06:01:07 CDT)
- Jason Swails (Sat Oct 10 2009 - 12:08:08 CDT)
- case (Sat Oct 10 2009 - 08:53:57 CDT)
- Rilei Yu (Sat Oct 10 2009 - 08:35:53 CDT)
- case (Sat Oct 10 2009 - 07:27:01 CDT)
- Rilei Yu (Sat Oct 10 2009 - 03:30:06 CDT)
[AMBER] xleap-does not work(Being solved!)
- Rilei Yu (Sat Oct 10 2009 - 09:13:28 CDT)
[AMBER] XServe cluster
- Jim Paugh (Thu Oct 22 2009 - 16:10:49 CDT)
- Richard Owczarzy (Thu Oct 22 2009 - 15:02:24 CDT)
- Abdul Rehman Gani (Thu Oct 22 2009 - 14:40:11 CDT)
- Jim Paugh (Thu Oct 22 2009 - 14:24:37 CDT)
- Abdul Rehman Gani (Thu Oct 22 2009 - 14:14:36 CDT)
[Amber]AMBER: MM_PBSA problems in AMBER10
- Ray Luo (Wed Oct 14 2009 - 11:48:48 CDT)
- He Hongqing (Tue Oct 13 2009 - 22:43:57 CDT)
AMBER: periodic bondary condition
- Markus Kaukonen (Mon Oct 26 2009 - 03:14:48 CDT)
- case (Fri Oct 16 2009 - 08:13:49 CDT)
- Markus Kaukonen (Fri Oct 16 2009 - 02:38:03 CDT)
AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
- Aust, Susanne (Mon Oct 19 2009 - 04:01:27 CDT)
Help required in Amber10 Installation
- Bill Ross (Thu Oct 15 2009 - 11:28:26 CDT)
- Abhishek Banerjee (Thu Oct 15 2009 - 10:51:56 CDT)
- case (Thu Oct 15 2009 - 08:45:42 CDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 08:30:25 CDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 08:13:27 CDT)
- Jason Swails (Thu Oct 15 2009 - 08:01:38 CDT)
- Jason Swails (Thu Oct 15 2009 - 07:55:31 CDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 07:53:42 CDT)
- Nicolas Sapay (Thu Oct 15 2009 - 07:34:28 CDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 07:11:01 CDT)
- Chris Whittleston (Wed Oct 07 2009 - 12:48:18 CDT)
- Bill Ross (Wed Oct 07 2009 - 11:59:21 CDT)
- David Watson (Wed Oct 07 2009 - 10:53:26 CDT)
- Sudeep Narayan Banerjee (Wed Oct 07 2009 - 10:48:02 CDT)
Missing X11 Libraries
- Wallace Kunin (Fri Oct 02 2009 - 11:55:34 CDT)
RDC and alignment tensor
- case (Mon Oct 19 2009 - 13:22:47 CDT)
- Eliana Asciutto (Mon Oct 19 2009 - 12:51:50 CDT)
VDW and TI for free energy
- Qicun Shi (Sat Oct 10 2009 - 23:05:20 CDT)
- steinbrt_at_rci.rutgers.edu (Sat Oct 10 2009 - 03:44:31 CDT)
- Qicun Shi (Fri Oct 09 2009 - 21:00:08 CDT)
- Ross Walker (Thu Oct 08 2009 - 19:43:48 CDT)
å›žå¤ï¼š [Amber]AMBER: MM_PBSA problems in AMBER10
- Rilei Yu (Wed Oct 14 2009 - 03:18:34 CDT)
- He Hongqing (Wed Oct 14 2009 - 02:32:25 CDT)
- Rilei Yu (Wed Oct 14 2009 - 00:47:02 CDT)
å›žå¤ï¼š [Amber]AMBER: MM_PBSA problemsin AMBER10
- Bill Ross (Wed Oct 14 2009 - 11:56:41 CDT)
- Qinghua Liao (Wed Oct 14 2009 - 04:22:41 CDT)
- He Hongqing (Wed Oct 14 2009 - 03:39:33 CDT)

Last message date: Mon Nov 23 2009 - 11:49:36 CST
Archived on: Mon Nov 23 2009 - 11:49:39 CST

482 messages sorted by: [ author ] [ date ] [ thread ]
About this archive