Amber Archive Oct 2009: by subject

(files attached) RESP with -a and witout -a flag
- Jio M (Fri Oct 30 2009 - 22:17:55 PDT)
[AMBER] "Cannot open file ATOMTYPE.INF, exit" when using antechamber
- case (Wed Oct 14 2009 - 04:37:35 PDT)
- haifeng yuan (Tue Oct 13 2009 - 00:44:55 PDT)
[AMBER] "extra points" incompatibility with pmemd
- mousumi (Wed Oct 21 2009 - 22:20:48 PDT)
- Brent Krueger (Wed Oct 21 2009 - 05:28:58 PDT)
- case (Wed Oct 21 2009 - 05:22:28 PDT)
- Robert Duke (Wed Oct 21 2009 - 05:02:54 PDT)
- mousumi (Wed Oct 21 2009 - 00:57:51 PDT)
[AMBER] (no subject)
- Prakash Patodia (Sat Oct 17 2009 - 00:12:39 PDT)
[AMBER] [amber10] atom groups used in torsion constrain
- Han Zheng (Mon Oct 26 2009 - 11:09:07 PDT)
[AMBER] [Fwd: ligand exiting a protein cavity]
- Jason Swails (Fri Oct 30 2009 - 09:23:29 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Oct 30 2009 - 06:42:57 PDT)
- Jason Swails (Fri Oct 30 2009 - 06:07:17 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 22:43:22 PDT)
- Jason Swails (Thu Oct 29 2009 - 08:17:40 PDT)
- Kshatresh Dutta Dubey (Thu Oct 29 2009 - 07:44:28 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 05:36:13 PDT)
[AMBER] [Fwd: problem with minimization]
- Bill Ross (Fri Oct 23 2009 - 10:40:57 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Oct 22 2009 - 11:53:11 PDT)
- Bill Ross (Thu Oct 22 2009 - 09:49:45 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Oct 22 2009 - 05:46:32 PDT)
[AMBER] A bug in LEaP ?
- FyD (Sun Oct 11 2009 - 05:08:37 PDT)
[AMBER] A bug in LEaP II ?
- FyD (Sun Oct 25 2009 - 05:58:36 PDT)
[AMBER] Add the hydrogen to the carboxyl of the GLU residue?
- Carlos Simmerling (Wed Oct 14 2009 - 06:49:00 PDT)
- FyD (Wed Oct 14 2009 - 06:40:09 PDT)
- Andrew Purkiss-Trew (Wed Oct 14 2009 - 05:19:43 PDT)
- xuemeiwang1103 (Wed Oct 14 2009 - 05:05:48 PDT)
[AMBER] AMBER 11.
- case (Thu Oct 15 2009 - 09:52:51 PDT)
- Peter Winn (Thu Oct 15 2009 - 09:27:39 PDT)
[AMBER] AMBER FF and NAMD
- FyD (Fri Oct 16 2009 - 12:19:13 PDT)
- Nicolas Sapay (Fri Oct 16 2009 - 07:59:53 PDT)
- Hannes Loeffler (Fri Oct 16 2009 - 07:45:25 PDT)
- stefano_elli\.libero\.it (Fri Oct 16 2009 - 07:26:14 PDT)
[AMBER] amber parallel test fail
- Nahoum Anthony (Fri Oct 23 2009 - 08:12:40 PDT)
- Jason Swails (Fri Oct 23 2009 - 04:58:19 PDT)
- Nahoum Anthony (Fri Oct 23 2009 - 03:20:45 PDT)
[AMBER] amber8 pmemd trajectory coordinates problem
- Robert Duke (Tue Oct 20 2009 - 18:15:56 PDT)
- Robert Duke (Tue Oct 20 2009 - 18:03:37 PDT)
- Sergio Wong (Tue Oct 20 2009 - 17:49:11 PDT)
- Thomas Cheatham (Tue Oct 20 2009 - 17:39:22 PDT)
- wong105.llnl.gov (Tue Oct 20 2009 - 17:32:24 PDT)
[AMBER] Analyzing per-residue decomposition data
- manoj singh (Thu Oct 29 2009 - 13:18:45 PDT)
[AMBER] Any tutorial on the proper way to merge a ligand and protein?
- Scott Brozell (Fri Oct 16 2009 - 12:40:56 PDT)
[AMBER] B-factor
- Cristina Sisu (Sat Oct 17 2009 - 03:58:34 PDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 15:16:35 PDT)
- Cristina Sisu (Thu Oct 15 2009 - 10:04:25 PDT)
[AMBER] binding energy
- steinbrt.rci.rutgers.edu (Fri Oct 16 2009 - 04:27:24 PDT)
- Simon Becker (Fri Oct 16 2009 - 02:28:39 PDT)
[AMBER] building quadruplex with NAB
- case (Tue Oct 27 2009 - 19:23:29 PDT)
- Peter Varnai (Tue Oct 27 2009 - 13:00:09 PDT)
[AMBER] can I run EVB in other ensemble than NVE?
- case (Tue Oct 20 2009 - 10:08:58 PDT)
- Jose Borreguero (Tue Oct 20 2009 - 09:57:04 PDT)
[AMBER] Can I use other ntb options in constant pH simulation
- Jason Swails (Wed Oct 21 2009 - 04:42:42 PDT)
- nicholus bhattacharjee (Wed Oct 21 2009 - 02:26:43 PDT)
[AMBER] Centering and reimaging with ptraj- stop rotating.
- Bill Ross (Mon Oct 19 2009 - 22:14:10 PDT)
- Thomas Cheatham (Mon Oct 19 2009 - 20:47:07 PDT)
- ben rodriguez (Mon Oct 19 2009 - 20:00:26 PDT)
[AMBER] charges for heme-cys in p450
- FyD (Fri Oct 23 2009 - 03:57:43 PDT)
- Jayalakshmi Sridhar (Thu Oct 22 2009 - 09:03:08 PDT)
[AMBER] Circular RNA topology file
- Filip Lankas (Mon Oct 26 2009 - 03:13:46 PDT)
- case (Wed Oct 21 2009 - 12:06:17 PDT)
- Kasprzak, Wojciech (NIH/NCI) [C] (Wed Oct 21 2009 - 11:26:04 PDT)
[AMBER] Combine and rename group of residues in xleap
- case (Fri Oct 09 2009 - 06:32:57 PDT)
- Lili Peng (Wed Oct 07 2009 - 14:49:23 PDT)
[AMBER] Compiling Amber with gfortran-4.5.0 on a mac
- Mengjuei Hsieh (Tue Oct 06 2009 - 19:05:54 PDT)
- Ben Roberts (Fri Oct 02 2009 - 07:20:47 PDT)
- case (Fri Oct 02 2009 - 06:19:11 PDT)
[AMBER] Computing an Hessian matrix using NAB
- Brut Marie (Tue Oct 13 2009 - 12:00:53 PDT)
- Brut Marie (Tue Oct 13 2009 - 11:56:19 PDT)
- case (Tue Oct 13 2009 - 05:13:42 PDT)
- Brut Marie (Mon Oct 12 2009 - 15:12:44 PDT)
[AMBER] contradictive hydrogen bonds using ptraj
- Binbin Liu (Mon Oct 26 2009 - 09:42:20 PDT)
[AMBER] Conversion of Gaussian output file into mol2
- Junmei Wang (Thu Oct 29 2009 - 08:45:27 PDT)
- megha bajaj (Wed Oct 28 2009 - 01:00:35 PDT)
[AMBER] Conversion of Gaussian output file to mol2
- megha bajaj (Wed Oct 28 2009 - 00:49:51 PDT)
[AMBER] cross correlation analysis with ptraj
- Junmei Wang (Thu Oct 15 2009 - 09:49:29 PDT)
[AMBER] decomposing energies
- Beroza, Paul (Thu Oct 01 2009 - 09:15:07 PDT)
[AMBER] decomposition and calculation of entropy
- Qinghua Liao (Fri Oct 09 2009 - 23:13:49 PDT)
[AMBER] DG improper torsion problem, two missing parameters
- Bill Ross (Fri Oct 09 2009 - 10:25:30 PDT)
- case (Fri Oct 09 2009 - 04:46:34 PDT)
- Youn Kyeung Lee (Fri Oct 09 2009 - 00:02:03 PDT)
[AMBER] Different optimized structures with HF and B3LYP
- Karl Kirschner (Fri Oct 02 2009 - 01:07:08 PDT)
- Sanghwa Han (Fri Oct 02 2009 - 00:50:10 PDT)
[AMBER] Different results for different computers
- Robert Duke (Sat Oct 31 2009 - 15:56:28 PDT)
- Jason Swails (Sat Oct 31 2009 - 12:57:34 PDT)
- manoj singh (Sat Oct 31 2009 - 12:47:36 PDT)
[AMBER] Dihedral energy profile in a single molecule
- Jason Swails (Fri Oct 16 2009 - 08:02:35 PDT)
- Frank X. Vázquez (Fri Oct 16 2009 - 07:55:53 PDT)
[AMBER] Dipole moment visualization.
- K.R. (Thu Oct 01 2009 - 14:37:29 PDT)
[AMBER] Distance Replica Exchange
- Steve Seibold (Fri Oct 09 2009 - 07:21:13 PDT)
- Carlos Simmerling (Fri Oct 09 2009 - 06:40:17 PDT)
- Steve Seibold (Fri Oct 09 2009 - 06:18:44 PDT)
[AMBER] DMF solvent box
- FyD (Thu Oct 08 2009 - 21:08:59 PDT)
- Abhishek Banerjee (Thu Oct 08 2009 - 20:41:02 PDT)
- FyD (Wed Oct 07 2009 - 13:34:35 PDT)
- Abhishek Banerjee (Tue Oct 06 2009 - 21:10:22 PDT)
[AMBER] eigenvalues add up to more than trace of matrix
- Hannes Loeffler (Fri Oct 16 2009 - 06:50:50 PDT)
- Jason Swails (Fri Oct 16 2009 - 06:29:13 PDT)
- Yaw Sing TAN (Thu Oct 15 2009 - 20:14:59 PDT)
[AMBER] Energy-from-MM/PBSA-VS-experiment
- Rilei Yu (Sun Oct 11 2009 - 15:51:26 PDT)
- Jason Swails (Sun Oct 11 2009 - 07:54:08 PDT)
- Rilei Yu (Sun Oct 11 2009 - 05:53:00 PDT)
[AMBER] Environment Variables in Cygwin Don't Remain
- Bill Ross (Thu Oct 01 2009 - 11:57:43 PDT)
- Jack Shultz (Thu Oct 01 2009 - 10:12:19 PDT)
- Wallace Kunin (Thu Oct 01 2009 - 09:54:29 PDT)
[AMBER] error in AMBer distance constraint
- Carlos Simmerling (Tue Oct 27 2009 - 04:28:22 PDT)
- xuemeiwang1103 (Mon Oct 26 2009 - 00:35:08 PDT)
- Bill Ross (Sun Oct 25 2009 - 20:03:19 PDT)
- Carlos Simmerling (Sun Oct 25 2009 - 19:38:23 PDT)
- xuemeiwang1103 (Sun Oct 25 2009 - 19:24:09 PDT)
[AMBER] error in distance restraint
- Carlos Simmerling (Thu Oct 29 2009 - 03:20:13 PDT)
- xuemeiwang1103 (Wed Oct 28 2009 - 20:43:55 PDT)
- Carlos Simmerling (Wed Oct 28 2009 - 13:48:13 PDT)
- Adrian Roitberg (Wed Oct 28 2009 - 07:01:07 PDT)
- xuemeiwang1103 (Wed Oct 28 2009 - 06:56:48 PDT)
[AMBER] error message from iAPBS
- Oliver Kuhn (Mon Oct 19 2009 - 04:47:32 PDT)
[AMBER] Error: unable to find mopac charges in mopac.out
- case (Tue Oct 20 2009 - 04:45:59 PDT)
- Rilei Yu (Tue Oct 20 2009 - 00:12:19 PDT)
- Ross Walker (Mon Oct 19 2009 - 22:50:17 PDT)
- Rilei Yu (Mon Oct 19 2009 - 22:34:34 PDT)
[AMBER] ff03 parameter for GDP and GTP
- FyD (Sun Oct 11 2009 - 04:42:25 PDT)
- Carlos Simmerling (Sat Oct 10 2009 - 04:36:35 PDT)
- FyD (Fri Oct 09 2009 - 22:52:27 PDT)
- FyD (Fri Oct 09 2009 - 13:38:08 PDT)
- mmg8.ualberta.ca (Fri Oct 09 2009 - 07:30:46 PDT)
- Carlos Simmerling (Fri Oct 09 2009 - 06:09:32 PDT)
- case (Fri Oct 09 2009 - 06:03:02 PDT)
- Carlos Simmerling (Fri Oct 09 2009 - 05:45:04 PDT)
- FyD (Fri Oct 09 2009 - 03:37:40 PDT)
- mmg8.ualberta.ca (Thu Oct 08 2009 - 18:05:18 PDT)
[AMBER] File format for reading in charges in antechamber
- Dean Cuebas (Sun Oct 04 2009 - 13:20:42 PDT)
[AMBER] Fwd: Group specification
- Bill Ross (Thu Oct 08 2009 - 13:22:54 PDT)
- Bill Ross (Thu Oct 08 2009 - 13:15:44 PDT)
- Carlos Simmerling (Thu Oct 08 2009 - 11:35:43 PDT)
- Pavan G (Thu Oct 08 2009 - 11:30:09 PDT)
[AMBER] GAFF parameter
- Ross Walker (Tue Oct 20 2009 - 11:50:18 PDT)
- Jason Swails (Tue Oct 20 2009 - 07:57:09 PDT)
- stefano_elli\.libero\.it (Tue Oct 20 2009 - 06:26:26 PDT)
[AMBER] Gaussian log file error
- megha bajaj (Sat Oct 31 2009 - 06:10:22 PDT)
[AMBER] HBOND analysis
- Marcin Krol (Tue Oct 20 2009 - 08:42:35 PDT)
[AMBER] How create PRMTOP and INCPRD for surface?
- rrd (Sat Oct 17 2009 - 19:40:02 PDT)
[AMBER] How to add a hydrogen to the residue?
- case (Wed Oct 14 2009 - 04:51:08 PDT)
- xuemeiwang1103 (Tue Oct 13 2009 - 20:57:53 PDT)
[AMBER] How to create FF for diamond.
- rrd (Mon Oct 19 2009 - 23:16:07 PDT)
[AMBER] how to get hold of older versions of MKL ?
- Ross Walker (Mon Oct 19 2009 - 09:58:54 PDT)
- Jason Swails (Mon Oct 19 2009 - 03:54:45 PDT)
- Nahoum Anthony (Mon Oct 19 2009 - 01:59:57 PDT)
[AMBER] How to introduce the second protein molecule into simulation box?
- Jason Swails (Fri Oct 16 2009 - 06:15:57 PDT)
- Siddharth Rastogi (Fri Oct 16 2009 - 00:00:03 PDT)
[AMBER] How to prepare the acetate ion file in leap?
- Balazs Jojart (Tue Oct 13 2009 - 00:36:03 PDT)
- xuemeiwang1103 (Tue Oct 13 2009 - 00:05:57 PDT)
[AMBER] iAPBS - how to set the right grid dimensions
- Robert Konecny (Wed Oct 14 2009 - 06:21:07 PDT)
- Oliver Kuhn (Wed Oct 14 2009 - 06:16:28 PDT)
- Robert Konecny (Tue Oct 13 2009 - 10:12:04 PDT)
- Oliver Kuhn (Tue Oct 13 2009 - 08:17:06 PDT)
- Robert Konecny (Tue Oct 13 2009 - 07:42:12 PDT)
- Oliver Kuhn (Tue Oct 13 2009 - 01:36:27 PDT)
[AMBER] inhibitor prepin not recognized in xleap
- Bill Ross (Fri Oct 23 2009 - 11:32:03 PDT)
- Jayalakshmi Sridhar (Fri Oct 23 2009 - 09:05:46 PDT)
- Jayalakshmi Sridhar (Fri Oct 23 2009 - 08:56:40 PDT)
[AMBER] installation of Amber on OSX
- Jason Swails (Wed Oct 14 2009 - 15:41:31 PDT)
- case (Wed Oct 14 2009 - 15:10:04 PDT)
- David Watson (Wed Oct 14 2009 - 15:03:51 PDT)
- Ramgopal Mettu (Wed Oct 14 2009 - 14:46:59 PDT)
[AMBER] Is it the way to do simulation in vacuum
- Ross Walker (Fri Oct 30 2009 - 12:15:01 PDT)
- Carlos Simmerling (Fri Oct 30 2009 - 09:10:22 PDT)
- Jason Swails (Fri Oct 30 2009 - 09:06:14 PDT)
- Carlos Simmerling (Fri Oct 30 2009 - 06:26:20 PDT)
- case (Fri Oct 30 2009 - 05:49:46 PDT)
- nicholus bhattacharjee (Fri Oct 30 2009 - 04:11:03 PDT)
- Carlos Simmerling (Fri Oct 30 2009 - 03:21:49 PDT)
- nicholus bhattacharjee (Fri Oct 30 2009 - 03:18:45 PDT)
[AMBER] Is iwrap mapping water molecules to my protein cavity?
- Carlos Simmerling (Mon Oct 12 2009 - 12:28:12 PDT)
- Bill Ross (Mon Oct 12 2009 - 12:12:19 PDT)
- ben rodriguez (Mon Oct 12 2009 - 11:55:23 PDT)
[AMBER] Large File Support
- Ross Walker (Thu Oct 15 2009 - 11:14:01 PDT)
- Beale, John (Thu Oct 15 2009 - 05:40:27 PDT)
[AMBER] Lennard Jones Potential A and B coefficients in Topology file
- Crowley, Michael (Sat Oct 31 2009 - 10:32:12 PDT)
- Peter Schmidtke (Sat Oct 31 2009 - 08:10:12 PDT)
- Tom Joseph (Sat Oct 31 2009 - 07:59:14 PDT)
- Tom Joseph (Fri Oct 30 2009 - 22:23:03 PDT)
- Peter Schmidtke (Fri Oct 30 2009 - 17:09:46 PDT)
- Tom Joseph (Fri Oct 30 2009 - 15:04:43 PDT)
- Peter Schmidtke (Fri Oct 30 2009 - 11:32:32 PDT)
[AMBER] LES and NEB problem
- Carlos Simmerling (Thu Oct 15 2009 - 11:09:34 PDT)
- Jason Swails (Thu Oct 15 2009 - 11:09:14 PDT)
- Rima Chaudhuri (Thu Oct 15 2009 - 10:53:41 PDT)
- Carlos Simmerling (Thu Oct 15 2009 - 09:54:18 PDT)
- Rima Chaudhuri (Thu Oct 15 2009 - 09:50:08 PDT)
- Carlos Simmerling (Wed Oct 14 2009 - 07:14:04 PDT)
- Rima Chaudhuri (Tue Oct 13 2009 - 12:35:37 PDT)
[AMBER] Ligand covalent bonds appear to be broken
- Thomas Cheatham (Fri Oct 30 2009 - 08:48:07 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Oct 30 2009 - 06:43:25 PDT)
- Jason Swails (Fri Oct 30 2009 - 06:11:03 PDT)
- Tom Joseph (Fri Oct 30 2009 - 04:53:44 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 23:32:39 PDT)
[AMBER] ligand exiting a protein cavity
- moitrayee.mbu.iisc.ernet.in (Thu Oct 29 2009 - 05:27:58 PDT)
[AMBER] man pages?
- Jason Swails (Tue Oct 20 2009 - 14:28:56 PDT)
- Louis-Frédéric Feuillette (Tue Oct 20 2009 - 13:17:52 PDT)
- Ben Roberts (Tue Oct 20 2009 - 10:33:16 PDT)
- Louis-Frédéric Feuillette (Tue Oct 20 2009 - 10:09:09 PDT)
[AMBER] mean square displacment
- Bill Ross (Tue Oct 13 2009 - 17:09:49 PDT)
- Nancy (Tue Oct 13 2009 - 16:59:15 PDT)
[AMBER] method used to determine partial charges?
- FyD (Thu Oct 01 2009 - 21:27:13 PDT)
- Jihang Wang (Thu Oct 01 2009 - 15:42:38 PDT)
- Carlos Simmerling (Thu Oct 01 2009 - 15:30:21 PDT)
- Jihang Wang (Thu Oct 01 2009 - 15:26:24 PDT)
- Bill Ross (Thu Oct 01 2009 - 15:18:01 PDT)
- Jihang Wang (Thu Oct 01 2009 - 14:28:45 PDT)
- Bill Ross (Thu Oct 01 2009 - 14:19:29 PDT)
- Jihang Wang (Thu Oct 01 2009 - 13:36:31 PDT)
- Paul Brandt (Thu Oct 01 2009 - 13:25:54 PDT)
[AMBER] minimization error
- case (Fri Oct 02 2009 - 05:00:52 PDT)
- balaji nagarajan (Fri Oct 02 2009 - 04:42:54 PDT)
[AMBER] Missing X11 Libraries
- Bill Ross (Fri Oct 09 2009 - 17:24:47 PDT)
- FyD (Fri Oct 09 2009 - 14:06:20 PDT)
- Thomas Patko (Fri Oct 09 2009 - 13:53:14 PDT)
- FyD (Fri Oct 09 2009 - 13:35:59 PDT)
- case (Fri Oct 09 2009 - 13:02:06 PDT)
- Wallace Kunin (Fri Oct 09 2009 - 12:20:00 PDT)
- Bill Ross (Fri Oct 09 2009 - 10:52:01 PDT)
- Thomas Patko (Fri Oct 09 2009 - 10:13:22 PDT)
- Wallace Kunin (Fri Oct 09 2009 - 10:03:51 PDT)
- Wallace Kunin (Fri Oct 09 2009 - 09:59:06 PDT)
- Thomas Patko (Thu Oct 08 2009 - 10:26:26 PDT)
- Bill Ross (Thu Oct 08 2009 - 10:25:32 PDT)
- Wallace Kunin (Thu Oct 08 2009 - 10:09:55 PDT)
- Bill Ross (Wed Oct 07 2009 - 15:28:34 PDT)
- Thomas Patko (Wed Oct 07 2009 - 14:14:15 PDT)
- Wallace Kunin (Wed Oct 07 2009 - 14:10:34 PDT)
- FyD (Wed Oct 07 2009 - 13:45:34 PDT)
- Mengjuei Hsieh (Wed Oct 07 2009 - 13:19:20 PDT)
- Wallace Kunin (Wed Oct 07 2009 - 11:04:39 PDT)
- Wallace Kunin (Sat Oct 03 2009 - 10:02:05 PDT)
- Wallace Kunin (Fri Oct 02 2009 - 12:57:49 PDT)
- case (Fri Oct 02 2009 - 11:56:34 PDT)
- Wallace Kunin (Fri Oct 02 2009 - 09:43:59 PDT)
[AMBER] MM/PBSA: NaN, Infinity and ************* in snapshot_com.all.out
- Rubben Torella (Tue Oct 06 2009 - 00:56:18 PDT)
- Jeff Yeo (Mon Oct 05 2009 - 16:22:53 PDT)
[AMBER] MM_PBSA decomposition pair question
- Rubben Torella (Fri Oct 02 2009 - 04:09:38 PDT)
[AMBER] mm_pbsa- Decomposition: bad atom type
- Antonija Tomić (Tue Oct 06 2009 - 06:53:25 PDT)
[AMBER] MM_PBSA: abnormal VDW interaction energy
- LIU Huanxiang (Tue Oct 06 2009 - 19:54:49 PDT)
- steinbrt.rci.rutgers.edu (Tue Oct 06 2009 - 01:09:27 PDT)
- LIU Huanxiang (Mon Oct 05 2009 - 19:43:21 PDT)
[AMBER] MMPBSA: No radius found for F
- Jeff Yeo (Sun Oct 04 2009 - 17:10:12 PDT)
[AMBER] MMTSB cluster analysis versus ptraj cluster analysis
- Cenk \(Jenk\) Andac (Mon Oct 19 2009 - 14:44:42 PDT)
- Jianyin Shao (Mon Oct 19 2009 - 11:16:47 PDT)
- Cenk \(Jenk\) Andac (Sat Oct 17 2009 - 00:02:20 PDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 08:33:22 PDT)
- Cenk \(Jenk\) Andac (Fri Oct 16 2009 - 05:19:24 PDT)
[AMBER] nab normal mode analysis has imaginary frequencies
- case (Wed Oct 14 2009 - 11:34:05 PDT)
- Junmei Wang (Wed Oct 14 2009 - 09:05:06 PDT)
[AMBER] nasty memory bug in calculatePrincipalAxis
- Scott Brozell (Mon Oct 12 2009 - 14:38:06 PDT)
[AMBER] new process_mdout.pl script????
- Ross Walker (Mon Oct 05 2009 - 11:38:17 PDT)
- Dean Cuebas (Mon Oct 05 2009 - 11:11:49 PDT)
[AMBER] NMR restraint
- Sally Pias (Tue Oct 27 2009 - 21:32:33 PDT)
- xuemeiwang1103 (Tue Oct 27 2009 - 19:31:39 PDT)
[AMBER] OpenMP
- michael (Tue Oct 13 2009 - 07:43:09 PDT)
- Ross Walker (Mon Oct 12 2009 - 11:29:45 PDT)
- Ben Roberts (Mon Oct 12 2009 - 10:35:35 PDT)
[AMBER] pairwise per-residue decomposition
- manoj singh (Fri Oct 30 2009 - 11:26:14 PDT)
- Tom Joseph (Fri Oct 30 2009 - 11:18:52 PDT)
- manoj singh (Thu Oct 29 2009 - 22:46:22 PDT)
- Tom Joseph (Thu Oct 29 2009 - 22:15:40 PDT)
- Tom Joseph (Thu Oct 29 2009 - 17:30:51 PDT)
- manoj singh (Thu Oct 29 2009 - 10:32:38 PDT)
- Carlos Simmerling (Thu Oct 29 2009 - 03:20:55 PDT)
- manoj singh (Wed Oct 28 2009 - 21:34:32 PDT)
[AMBER] Parallel sander & polarisability
- case (Thu Oct 29 2009 - 10:02:28 PDT)
- Ross Walker (Thu Oct 29 2009 - 10:00:13 PDT)
- Thomas Taylor (Thu Oct 29 2009 - 09:19:14 PDT)
[AMBER] parameters for O2 molecule
- Jeffrey (Thu Oct 29 2009 - 06:01:44 PDT)
- Jason Swails (Thu Oct 22 2009 - 07:19:51 PDT)
- Jeffrey (Thu Oct 22 2009 - 06:32:07 PDT)
[AMBER] part of the protein escaped from the water box
- Jason Swails (Thu Oct 15 2009 - 04:43:00 PDT)
- case (Thu Oct 15 2009 - 04:40:53 PDT)
- Carlos Simmerling (Thu Oct 15 2009 - 04:39:40 PDT)
- qiaoyan (Thu Oct 15 2009 - 04:33:00 PDT)
[AMBER] PEMD
- Tom Joseph (Mon Oct 26 2009 - 16:03:26 PDT)
- Cristina Sisu (Mon Oct 26 2009 - 14:44:42 PDT)
[AMBER] pmemd ifort problem
- Robert Duke (Fri Oct 23 2009 - 08:33:27 PDT)
- Sel Ercan (Fri Oct 23 2009 - 07:57:59 PDT)
[AMBER] Possible bug in "com" group torsion angle constrain? Thanks!
- Carlos Simmerling (Tue Oct 27 2009 - 16:22:43 PDT)
- Han Zheng (Tue Oct 27 2009 - 15:47:20 PDT)
- Seetin, Matthew (Tue Oct 27 2009 - 14:17:41 PDT)
- Han Zheng (Tue Oct 27 2009 - 10:28:16 PDT)
[AMBER] Preparing distance restraints
- case (Mon Oct 26 2009 - 14:26:26 PDT)
- Yunjie Zhao (Mon Oct 26 2009 - 01:44:58 PDT)
[AMBER] probelm-APBS
- Rilei Yu (Sun Oct 04 2009 - 17:51:10 PDT)
- Robert Konecny (Sun Oct 04 2009 - 17:20:18 PDT)
- Rilei Yu (Fri Oct 02 2009 - 22:41:07 PDT)
[AMBER] Problem with memory in nmode analysis
- Alireza Shaneh (Tue Oct 06 2009 - 08:23:55 PDT)
[AMBER] problem with minimization
- moitrayee.mbu.iisc.ernet.in (Thu Oct 22 2009 - 04:01:14 PDT)
[AMBER] Problem with running anal module in amber
- moitrayee.mbu.iisc.ernet.in (Tue Oct 20 2009 - 23:47:17 PDT)
[AMBER] Protein and charged surface
- rrd (Thu Oct 01 2009 - 20:49:18 PDT)
[AMBER] ptraj and prmtop
- Carlos Simmerling (Wed Oct 14 2009 - 06:41:04 PDT)
- Beale, John (Wed Oct 14 2009 - 05:46:11 PDT)
[AMBER] Ptraj Segmentation Fault
- Katrina Hill (Wed Oct 21 2009 - 19:15:31 PDT)
[AMBER] pucker calculation for six member rings
- Ganesh Kamath (Mon Oct 05 2009 - 11:03:15 PDT)
[AMBER] Question about distance restraint ?
- Carlos Simmerling (Fri Oct 23 2009 - 03:56:24 PDT)
- xuemeiwang1103 (Fri Oct 23 2009 - 03:07:47 PDT)
[AMBER] question with hbond in carnal
- Bill Ross (Tue Oct 20 2009 - 09:32:56 PDT)
- Ganesh Kamath (Tue Oct 20 2009 - 06:58:36 PDT)
[AMBER] question with pucker in six member ring
- Bill Ross (Mon Oct 19 2009 - 10:54:03 PDT)
- Ganesh Kamath (Mon Oct 19 2009 - 10:42:17 PDT)
- Bill Ross (Fri Oct 16 2009 - 12:48:04 PDT)
- Ganesh Kamath (Fri Oct 16 2009 - 12:31:31 PDT)
- Bill Ross (Fri Oct 16 2009 - 11:43:56 PDT)
- Ganesh Kamath (Fri Oct 16 2009 - 11:36:41 PDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 11:23:05 PDT)
- Nicolas Sapay (Fri Oct 16 2009 - 08:04:24 PDT)
- Ganesh Kamath (Thu Oct 15 2009 - 12:55:45 PDT)
[AMBER] R.E.D.-III.3 tools release - q4md-forcefieldtools.org
- FyD (Sun Oct 04 2009 - 07:37:06 PDT)
[AMBER] RDC and alignment tensor
- Eliana Asciutto (Fri Oct 23 2009 - 12:19:00 PDT)
- case (Tue Oct 20 2009 - 05:24:45 PDT)
- Eliana Asciutto (Mon Oct 19 2009 - 12:03:43 PDT)
- case (Mon Oct 19 2009 - 10:36:16 PDT)
- Eliana Asciutto (Mon Oct 19 2009 - 09:50:31 PDT)
- Thomas Cheatham III (Fri Oct 16 2009 - 13:45:25 PDT)
- Eliana Asciutto (Fri Oct 16 2009 - 13:21:34 PDT)
[AMBER] red problem
- FyD (Thu Oct 01 2009 - 21:48:57 PDT)
- James Moore (Thu Oct 01 2009 - 18:52:46 PDT)
[AMBER] RESP charges with -a and without -a flag
- Jio M (Fri Oct 30 2009 - 22:13:03 PDT)
- Junmei Wang (Fri Oct 30 2009 - 09:49:00 PDT)
- Jio M (Fri Oct 30 2009 - 06:36:43 PDT)
[AMBER] resp_problem
- FyD (Sat Oct 24 2009 - 23:12:31 PDT)
- Ross Walker (Sat Oct 24 2009 - 15:39:01 PDT)
- vhakkim boy (Sat Oct 24 2009 - 03:16:22 PDT)
[AMBER] rms fit of mutant with respect to wild type structure
- Carlos Simmerling (Thu Oct 29 2009 - 07:03:35 PDT)
- Siddharth Rastogi (Thu Oct 29 2009 - 06:55:12 PDT)
[AMBER] RMSD vs time and RMSD vs residues
- Sally Pias (Fri Oct 02 2009 - 12:16:33 PDT)
- case (Fri Oct 02 2009 - 12:12:23 PDT)
- Luis Gracia (Fri Oct 02 2009 - 11:07:10 PDT)
- Olotu Odunayo (Fri Oct 02 2009 - 10:40:40 PDT)
[AMBER] S-S problem-in protein
- Rilei Yu (Mon Oct 12 2009 - 15:14:02 PDT)
- Jason Swails (Mon Oct 12 2009 - 04:23:25 PDT)
- Rilei Yu (Mon Oct 12 2009 - 02:16:15 PDT)
- Rilei Yu (Sun Oct 11 2009 - 23:28:14 PDT)
- Jason Swails (Sun Oct 11 2009 - 21:24:51 PDT)
- Jason Swails (Sun Oct 11 2009 - 19:15:10 PDT)
- Rilei Yu (Sun Oct 11 2009 - 18:53:24 PDT)
[AMBER] Salt bridge time scale
- Mannan (Sun Oct 25 2009 - 18:57:20 PDT)
[AMBER] Simulated annealing
- Carlos Simmerling (Wed Oct 28 2009 - 03:51:41 PDT)
- Shaikh Abdul R S Ramaju (Tue Oct 27 2009 - 22:44:33 PDT)
- Carlos Simmerling (Thu Oct 15 2009 - 04:43:56 PDT)
- waleed zalloum (Thu Oct 15 2009 - 03:59:29 PDT)
[AMBER] Simulating transmembrane protein.
- Bill Ross (Mon Oct 12 2009 - 15:37:50 PDT)
- case (Mon Oct 12 2009 - 14:55:42 PDT)
- Jayalakshmi Sridhar (Mon Oct 12 2009 - 12:57:02 PDT)
- Bill Ross (Mon Oct 12 2009 - 12:04:36 PDT)
- Jayalakshmi Sridhar (Mon Oct 12 2009 - 11:42:11 PDT)
[AMBER] simulation blown up
- Robert Duke (Tue Oct 20 2009 - 20:55:39 PDT)
- Jason Swails (Tue Oct 20 2009 - 19:58:47 PDT)
- moitrayee.mbu.iisc.ernet.in (Tue Oct 20 2009 - 10:41:29 PDT)
[AMBER] six member pucker calculation
- Ganesh Kamath (Wed Oct 14 2009 - 07:27:24 PDT)
[AMBER] software to hydrate protein pockets
- Hannes Kopitz (Fri Oct 23 2009 - 06:11:26 PDT)
- Alessandro Nascimento (Fri Oct 23 2009 - 05:50:05 PDT)
- Vlad Cojocaru (Fri Oct 23 2009 - 05:23:54 PDT)
[AMBER] solvent accessible surface area
- Ray Luo (Thu Oct 08 2009 - 11:17:09 PDT)
- Siddharth Rastogi (Thu Oct 08 2009 - 03:02:20 PDT)
- Siddharth Rastogi (Thu Oct 08 2009 - 02:54:01 PDT)
[AMBER] Some queries about pH simulation
- nicholus bhattacharjee (Fri Oct 09 2009 - 22:07:21 PDT)
- Carlos Simmerling (Fri Oct 09 2009 - 11:59:17 PDT)
- Jason Swails (Fri Oct 09 2009 - 11:48:44 PDT)
- nicholus bhattacharjee (Thu Oct 08 2009 - 21:36:56 PDT)
[AMBER] some queries on -states flag in constant pH simulation
- Jason Swails (Sat Oct 31 2009 - 05:28:22 PDT)
- nicholus bhattacharjee (Fri Oct 30 2009 - 23:31:31 PDT)
- Jason Swails (Fri Oct 30 2009 - 06:00:37 PDT)
- nicholus bhattacharjee (Thu Oct 29 2009 - 21:21:27 PDT)
[AMBER] SPC/E HOH angle
- Carlos Simmerling (Fri Oct 30 2009 - 06:47:18 PDT)
- case (Fri Oct 30 2009 - 05:51:41 PDT)
- Hemant Kumar (Fri Oct 30 2009 - 03:36:55 PDT)
[AMBER] stacking clusters
- Shaikh Abdul R S Ramaju (Thu Oct 29 2009 - 19:44:59 PDT)
[AMBER] surface binding protein
- Jason Swails (Sat Oct 31 2009 - 05:35:44 PDT)
- sadaf iqbal (Fri Oct 30 2009 - 22:28:22 PDT)
[AMBER] The -c option in Sander
- case (Fri Oct 09 2009 - 18:54:05 PDT)
- phani ghanakota (Fri Oct 09 2009 - 17:47:18 PDT)
[AMBER] the criterion of equilibrium
- Adrian Roitberg (Sat Oct 24 2009 - 11:22:25 PDT)
- Bill Ross (Sat Oct 24 2009 - 10:19:09 PDT)
- qiaoyan (Fri Oct 23 2009 - 19:19:58 PDT)
[AMBER] The hydrophobic contribution
- case (Thu Oct 08 2009 - 05:41:28 PDT)
- Rilei Yu (Wed Oct 07 2009 - 22:48:32 PDT)
[AMBER] Thermodynamic Integration calculation on an artificial anion receptor
- steinbrt.rci.rutgers.edu (Thu Oct 29 2009 - 03:35:24 PDT)
- Huifang (Wed Oct 28 2009 - 21:38:05 PDT)
[AMBER] Time scale of the Protein domain motion ?
- Chih-Ying Lin (Sat Oct 17 2009 - 12:46:37 PDT)
- Carlos Simmerling (Sat Oct 17 2009 - 12:42:01 PDT)
- Chih-Ying Lin (Sat Oct 17 2009 - 12:36:18 PDT)
- Carlos Simmerling (Sat Oct 17 2009 - 12:23:34 PDT)
- Chih-Ying Lin (Sat Oct 17 2009 - 12:18:34 PDT)
[AMBER] TiO2 modeling
- stefano_elli.libero.it (Mon Oct 05 2009 - 09:00:59 PDT)
[AMBER] too many undefined parameters in frcmod
- xueqin pang (Thu Oct 29 2009 - 06:06:24 PDT)
- Junmei Wang (Mon Oct 26 2009 - 07:45:04 PDT)
- Jason Swails (Thu Oct 22 2009 - 04:59:55 PDT)
- FyD (Thu Oct 22 2009 - 02:37:46 PDT)
- xueqin pang (Thu Oct 22 2009 - 01:52:57 PDT)
[AMBER] translate multiple residues
- Bill Ross (Wed Oct 21 2009 - 15:40:51 PDT)
- Taufik Al-Sarraj (Wed Oct 21 2009 - 14:32:30 PDT)
- Bill Ross (Wed Oct 21 2009 - 13:53:20 PDT)
- Taufik Al-Sarraj (Wed Oct 21 2009 - 13:33:12 PDT)
[AMBER] trouble using iAPBS
- Robert Konecny (Thu Oct 01 2009 - 10:27:42 PDT)
- Oliver Kuhn (Thu Oct 01 2009 - 04:31:51 PDT)
[AMBER] Unable to correctly identify element when running QM/MM in amber10
- Ross Walker (Thu Oct 22 2009 - 12:03:40 PDT)
- Jifeng Wang (Thu Oct 22 2009 - 09:20:30 PDT)
[AMBER] unit converter for force constants
- GÜL ALTINBAŞ (Mon Oct 12 2009 - 05:22:00 PDT)
[AMBER] unit convertion for force constants
- vhakkim boy (Mon Oct 12 2009 - 06:26:05 PDT)
- GÜL ALTINBAŞ (Mon Oct 12 2009 - 05:47:42 PDT)
[AMBER] units of measures
- case (Thu Oct 22 2009 - 05:42:11 PDT)
- lorenzo (Thu Oct 22 2009 - 04:20:26 PDT)
[AMBER] Using idecomp=3 with igb=10 (PB)
- Chris Whittleston (Tue Oct 13 2009 - 03:02:17 PDT)
- Hannes Kopitz (Mon Oct 12 2009 - 12:51:23 PDT)
- Chris Whittleston (Mon Oct 12 2009 - 08:56:06 PDT)
- Hannes Kopitz (Sun Oct 11 2009 - 14:13:45 PDT)
- Chris Whittleston (Fri Oct 09 2009 - 08:16:53 PDT)
- Hannes Kopitz (Thu Oct 08 2009 - 13:30:19 PDT)
- Chris Whittleston (Thu Oct 08 2009 - 03:47:22 PDT)
- Chris Whittleston (Wed Oct 07 2009 - 09:57:25 PDT)
[AMBER] using RESP program
- FyD (Wed Oct 07 2009 - 13:04:38 PDT)
- Ganesh Kamath (Wed Oct 07 2009 - 03:36:13 PDT)
- gunajyoti das (Wed Oct 07 2009 - 03:30:27 PDT)
[AMBER] vlimit
- Ross Walker (Wed Oct 28 2009 - 15:35:15 PDT)
- Taufik Al-Sarraj (Wed Oct 28 2009 - 15:02:43 PDT)
- Bill Ross (Wed Oct 28 2009 - 14:55:55 PDT)
- Ross Walker (Wed Oct 28 2009 - 14:29:21 PDT)
- Taufik Al-Sarraj (Wed Oct 28 2009 - 14:16:32 PDT)
[AMBER] why is TAUTP scaled by "e" ?
- Jose Borreguero (Fri Oct 16 2009 - 12:13:42 PDT)
- case (Fri Oct 16 2009 - 06:30:53 PDT)
- Ross Walker (Thu Oct 15 2009 - 15:08:52 PDT)
- Jose Borreguero (Thu Oct 15 2009 - 13:49:18 PDT)
[AMBER] Why the calculation ofen stop with the calculation process not end?
- xuemeiwang1103 (Wed Oct 21 2009 - 07:04:57 PDT)
[AMBER] xleap editing window icons inactive
- Jayalakshmi Sridhar (Wed Oct 21 2009 - 11:32:46 PDT)
- Niel Henriksen (Wed Oct 21 2009 - 11:21:54 PDT)
- Jayalakshmi Sridhar (Wed Oct 21 2009 - 11:20:01 PDT)
[AMBER] xleap not reconizing inhibitor prepin
- Junmei Wang (Mon Oct 26 2009 - 07:51:41 PDT)
- Bill Ross (Fri Oct 23 2009 - 11:33:44 PDT)
- Jayalakshmi Sridhar (Fri Oct 23 2009 - 09:21:07 PDT)
[AMBER] xleap problem !
- balaji nagarajan (Wed Sep 30 2009 - 11:40:58 PDT)
[AMBER] xleap-does not work
- Rilei Yu (Sun Oct 11 2009 - 04:01:07 PDT)
- Jason Swails (Sat Oct 10 2009 - 10:08:08 PDT)
- case (Sat Oct 10 2009 - 06:53:57 PDT)
- Rilei Yu (Sat Oct 10 2009 - 06:35:53 PDT)
- case (Sat Oct 10 2009 - 05:27:01 PDT)
- Rilei Yu (Sat Oct 10 2009 - 01:30:06 PDT)
[AMBER] xleap-does not work(Being solved!)
- Rilei Yu (Sat Oct 10 2009 - 07:13:28 PDT)
[AMBER] XServe cluster
- Jim Paugh (Thu Oct 22 2009 - 14:10:49 PDT)
- Richard Owczarzy (Thu Oct 22 2009 - 13:02:24 PDT)
- Abdul Rehman Gani (Thu Oct 22 2009 - 12:40:11 PDT)
- Jim Paugh (Thu Oct 22 2009 - 12:24:37 PDT)
- Abdul Rehman Gani (Thu Oct 22 2009 - 12:14:36 PDT)
[Amber]AMBER: MM_PBSA problems in AMBER10
- Ray Luo (Wed Oct 14 2009 - 09:48:48 PDT)
- He Hongqing (Tue Oct 13 2009 - 20:43:57 PDT)
AMBER: periodic bondary condition
- Markus Kaukonen (Mon Oct 26 2009 - 01:14:48 PDT)
- case (Fri Oct 16 2009 - 06:13:49 PDT)
- Markus Kaukonen (Fri Oct 16 2009 - 00:38:03 PDT)
AW: [AMBER] Add the hydrogen to the carboxyl of the GLU residue?
- Aust, Susanne (Mon Oct 19 2009 - 02:01:27 PDT)
Help required in Amber10 Installation
- Bill Ross (Thu Oct 15 2009 - 09:28:26 PDT)
- Abhishek Banerjee (Thu Oct 15 2009 - 08:51:56 PDT)
- case (Thu Oct 15 2009 - 06:45:42 PDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 06:30:25 PDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 06:13:27 PDT)
- Jason Swails (Thu Oct 15 2009 - 06:01:38 PDT)
- Jason Swails (Thu Oct 15 2009 - 05:55:31 PDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 05:53:42 PDT)
- Nicolas Sapay (Thu Oct 15 2009 - 05:34:28 PDT)
- Sudeep Narayan Banerjee (Thu Oct 15 2009 - 05:11:01 PDT)
- Chris Whittleston (Wed Oct 07 2009 - 10:48:18 PDT)
- Bill Ross (Wed Oct 07 2009 - 09:59:21 PDT)
- David Watson (Wed Oct 07 2009 - 08:53:26 PDT)
- Sudeep Narayan Banerjee (Wed Oct 07 2009 - 08:48:02 PDT)
Missing X11 Libraries
- Wallace Kunin (Fri Oct 02 2009 - 09:55:34 PDT)
RDC and alignment tensor
- case (Mon Oct 19 2009 - 11:22:47 PDT)
- Eliana Asciutto (Mon Oct 19 2009 - 10:51:50 PDT)
VDW and TI for free energy
- Qicun Shi (Sat Oct 10 2009 - 21:05:20 PDT)
- steinbrt.rci.rutgers.edu (Sat Oct 10 2009 - 01:44:31 PDT)
- Qicun Shi (Fri Oct 09 2009 - 19:00:08 PDT)
- Ross Walker (Thu Oct 08 2009 - 17:43:48 PDT)
回复： [Amber]AMBER: MM_PBSA problems in AMBER10
- Rilei Yu (Wed Oct 14 2009 - 01:18:34 PDT)
- He Hongqing (Wed Oct 14 2009 - 00:32:25 PDT)
- Rilei Yu (Tue Oct 13 2009 - 22:47:02 PDT)
回复： [Amber]AMBER: MM_PBSA problemsin AMBER10
- Bill Ross (Wed Oct 14 2009 - 09:56:41 PDT)
- Qinghua Liao (Wed Oct 14 2009 - 02:22:41 PDT)
- He Hongqing (Wed Oct 14 2009 - 01:39:33 PDT)

Amber Archive Oct 2009 by subject