Amber Archive Nov 2006: by subject

AMBER:
- David A. Case (Tue Nov 28 2006 - 07:53:48 PST)
- uccadco.ucl.ac.uk (Tue Nov 28 2006 - 06:48:08 PST)
- David A. Case (Thu Nov 09 2006 - 10:11:55 PST)
- Steve Seibold (Thu Nov 09 2006 - 09:03:14 PST)
- Ross Walker (Sat Nov 04 2006 - 09:35:43 PST)
AMBER: <kein Betreff>
- Gustavo Seabra (Mon Nov 13 2006 - 09:52:55 PST)
- Ross Walker (Mon Nov 13 2006 - 08:44:03 PST)
- Michel Becker (Mon Nov 13 2006 - 03:21:58 PST)
AMBER: ab initio terminology query
- Yong Duan (Wed Nov 01 2006 - 15:17:43 PST)
- Ross Walker (Wed Nov 01 2006 - 12:51:43 PST)
- Ilyas Yildirim (Wed Nov 01 2006 - 12:38:58 PST)
- David A. Case (Wed Nov 01 2006 - 12:42:23 PST)
- Hayden Eastwood (Wed Nov 01 2006 - 12:12:49 PST)
- Jiri Sponer (Wed Nov 01 2006 - 11:43:13 PST)
- Adrian Roitberg (Wed Nov 01 2006 - 11:01:38 PST)
- Yong Duan (Wed Nov 01 2006 - 10:53:39 PST)
- Jiri Sponer (Wed Nov 01 2006 - 10:34:57 PST)
- Jiri Sponer (Wed Nov 01 2006 - 10:27:44 PST)
- David A. Case (Wed Nov 01 2006 - 09:30:50 PST)
- Gustavo Seabra (Wed Nov 01 2006 - 08:50:27 PST)
- Ross Walker (Wed Nov 01 2006 - 08:44:22 PST)
- Jiri Sponer (Wed Nov 01 2006 - 03:59:04 PST)
- HL Eastwood (Wed Nov 01 2006 - 03:38:24 PST)
AMBER: Acetone box
- SERGIO MIGUEL FERNANDES DOS SANTOS (Tue Nov 14 2006 - 10:34:24 PST)
AMBER: ACS Chicago potential symposia and OASYS abstracts
- Thomas Cheatham (Sat Nov 04 2006 - 13:04:47 PST)
AMBER: Amber 9 parallel test fail on 4096wat/Run.column_fft
- Yu Chen (Fri Nov 03 2006 - 11:05:55 PST)
- Ross Walker (Fri Nov 03 2006 - 08:39:22 PST)
- Yu Chen (Fri Nov 03 2006 - 07:18:35 PST)
- Ross Walker (Wed Nov 01 2006 - 09:21:02 PST)
- Yu Chen (Wed Nov 01 2006 - 09:02:26 PST)
- David A. Case (Wed Nov 01 2006 - 08:54:06 PST)
- Yu Chen (Wed Nov 01 2006 - 08:22:54 PST)
AMBER: Amber H-bond print?
- Andres Palencia (Thu Nov 09 2006 - 01:07:46 PST)
AMBER: Amber9 installation error
- Ross Walker (Sat Nov 18 2006 - 09:20:39 PST)
- Keerthi Gottipati (Fri Nov 17 2006 - 16:12:53 PST)
AMBER: amber9 parralel compiling
- David A. Case (Thu Nov 30 2006 - 15:54:08 PST)
- Nikola Trbovic (Thu Nov 30 2006 - 09:06:12 PST)
- David A. Case (Thu Nov 30 2006 - 08:50:47 PST)
- Nikola Trbovic (Thu Nov 30 2006 - 08:31:22 PST)
AMBER: Amber9 patch bugfix.all issue on SunOS 5.1
- Michael John Hanby (Tue Nov 28 2006 - 13:43:06 PST)
- Mark Williamson (Tue Nov 28 2006 - 13:04:06 PST)
- Michael John Hanby (Tue Nov 28 2006 - 12:59:48 PST)
- Michael John Hanby (Tue Nov 28 2006 - 10:06:16 PST)
AMBER: amber9 serial compile with pathscale on SuSe10.1/AMD64
- David A. Case (Fri Nov 24 2006 - 16:43:20 PST)
- In Hee Park (Fri Nov 24 2006 - 14:50:54 PST)
AMBER: Amber: disufide bond
- Fenghui Fan (Sun Nov 05 2006 - 06:02:48 PST)
- hayden (Sun Nov 05 2006 - 05:03:23 PST)
- Fenghui Fan (Sat Nov 04 2006 - 20:29:57 PST)
AMBER: ambpdb -pqr
- Ilyas Yildirim (Tue Nov 28 2006 - 13:02:39 PST)
- Carlos Simmerling (Tue Nov 28 2006 - 13:03:18 PST)
- harianto (Tue Nov 28 2006 - 13:03:26 PST)
- Seth Lilavivat (Tue Nov 28 2006 - 12:52:10 PST)
AMBER: ammonia parameters
- Fenghui Fan (Thu Nov 23 2006 - 07:40:05 PST)
- Peter Trodler (Thu Nov 23 2006 - 00:51:39 PST)
AMBER: Antechamber and gaussian questions
- Fenghui Fan (Fri Nov 24 2006 - 14:04:40 PST)
AMBER: antechamber:tutorial
- Fenghui Fan (Thu Nov 09 2006 - 11:10:17 PST)
- Mark Williamson (Thu Nov 09 2006 - 11:06:24 PST)
- Lwin, ThuZar (Thu Nov 09 2006 - 10:48:58 PST)
AMBER: antechamber:tutorial. .
- Lwin, ThuZar (Thu Nov 09 2006 - 12:02:28 PST)
AMBER: Atom Exclusion
- Nitin Bhardwaj (Tue Nov 07 2006 - 21:44:30 PST)
AMBER: big bond energy change from minimization and md (heating)
- Rachel (Wed Nov 08 2006 - 08:40:12 PST)
AMBER: Biomolecular Simulation 2007
- Angelo (Thu Nov 09 2006 - 08:03:43 PST)
AMBER: bond command between Zn and a CYM residue in one chain of a protein complex
- Fenghui Fan (Fri Nov 10 2006 - 21:25:01 PST)
AMBER: bond information
- Junmei Wang (Tue Nov 28 2006 - 14:16:03 PST)
- Fenghui Fan (Sun Nov 26 2006 - 20:10:42 PST)
AMBER: bondtype problem
- Fenghui Fan (Fri Nov 24 2006 - 16:22:23 PST)
AMBER: building a box
- kepa koldo burusco (Wed Nov 08 2006 - 04:08:32 PST)
- Fenghui Fan (Tue Nov 07 2006 - 09:49:54 PST)
- kepa koldo burusco (Tue Nov 07 2006 - 08:52:28 PST)
AMBER: Building Library
- Steve Seibold (Thu Nov 09 2006 - 11:40:30 PST)
- Fenghui Fan (Thu Nov 09 2006 - 10:21:57 PST)
- Steve Seibold (Thu Nov 09 2006 - 08:52:08 PST)
AMBER: Can we use the distance restraint in Replica-exchange simulation with AMBER8
- Carlos Simmerling (Thu Nov 02 2006 - 12:28:33 PST)
- wenfei Li (Thu Nov 02 2006 - 04:44:18 PST)
AMBER: Charge fitting in Amber
- FyD (Tue Nov 28 2006 - 23:16:38 PST)
- Changge Ji (Tue Nov 28 2006 - 08:50:20 PST)
AMBER: Closest(closest water)
- Sergey Samsonov (Wed Nov 01 2006 - 00:38:55 PST)
AMBER: Combine amber-force field and gaff94 for one molecule?
- Jiri Sponer (Sun Nov 05 2006 - 14:01:27 PST)
- M. L. Dodson (Sun Nov 05 2006 - 12:47:22 PST)
- Fenghui Fan (Sun Nov 05 2006 - 12:13:57 PST)
- M. L. Dodson (Sun Nov 05 2006 - 11:35:34 PST)
- Fenghui Fan (Sun Nov 05 2006 - 10:30:27 PST)
- Michel Becker (Sun Nov 05 2006 - 09:45:05 PST)
AMBER: Combining Residues in LEaP for Lipid Bilayers
- kepa koldo burusco (Fri Nov 24 2006 - 03:38:06 PST)
- David A. Case (Tue Nov 21 2006 - 08:16:06 PST)
- Bill Ross (Mon Nov 20 2006 - 10:58:11 PST)
- Matthew Tessier (Mon Nov 20 2006 - 09:48:32 PST)
- David A. Case (Mon Nov 20 2006 - 09:35:04 PST)
- Matthew Tessier (Mon Nov 20 2006 - 09:09:13 PST)
AMBER: compile amber8 on IBM-sp4
- Rachel (Thu Nov 23 2006 - 09:45:04 PST)
- Martin Peters (Thu Nov 23 2006 - 09:22:06 PST)
- Rachel (Thu Nov 23 2006 - 08:37:18 PST)
- Xuebin Qiao (Thu Nov 23 2006 - 06:23:36 PST)
- Rachel (Thu Nov 23 2006 - 05:14:09 PST)
- Xuebin Qiao (Thu Nov 23 2006 - 04:21:07 PST)
- Xuebin Qiao (Thu Nov 23 2006 - 04:26:12 PST)
- Rachel (Thu Nov 23 2006 - 01:56:53 PST)
- Xuebin Qiao (Wed Nov 22 2006 - 19:51:57 PST)
- Rachel (Wed Nov 22 2006 - 10:34:19 PST)
- Ross Walker (Wed Nov 22 2006 - 09:55:45 PST)
- Rachel (Wed Nov 22 2006 - 02:08:42 PST)
- Scott Brozell (Tue Nov 21 2006 - 10:38:49 PST)
- Rachel (Tue Nov 21 2006 - 09:56:13 PST)
AMBER: Confusion about PBC
- Thomas Steinbrecher (Wed Nov 29 2006 - 08:40:05 PST)
- anna.schrey.gmx.de (Wed Nov 29 2006 - 08:26:04 PST)
AMBER: Did Antechamber support tertiary amines? How can I get the prepin file for it?
- a a (Mon Nov 27 2006 - 00:50:12 PST)
AMBER: dihedral angle equation
- Igor Schapiro (Fri Nov 17 2006 - 06:24:29 PST)
- Igor Schapiro (Fri Nov 17 2006 - 06:15:47 PST)
- Vitor Manuel Sousa F?x (Fri Nov 17 2006 - 04:41:25 PST)
AMBER: DNA helix end stable?
- Carlos Simmerling (Wed Nov 29 2006 - 04:24:14 PST)
- a a (Tue Nov 28 2006 - 19:35:11 PST)
AMBER: energy minimizations in amber8 vs. amber9
- Seongeun Yang (Mon Nov 27 2006 - 23:43:35 PST)
AMBER: erroneous placement of TER card
- Bill Ross (Thu Nov 16 2006 - 11:06:25 PST)
- David A. Case (Thu Nov 16 2006 - 10:59:28 PST)
- Bill Ross (Thu Nov 16 2006 - 10:54:50 PST)
- Robert Duke (Thu Nov 16 2006 - 08:47:23 PST)
- David A. Case (Thu Nov 16 2006 - 08:20:32 PST)
- Robert Duke (Thu Nov 16 2006 - 05:56:11 PST)
- Gregory Sandala (Thu Nov 16 2006 - 01:12:43 PST)
AMBER: error about the number of snapshots
- AYTUG TUNCEL (Tue Nov 07 2006 - 13:11:24 PST)
AMBER: Error in compliling LEAP on Fedora 5
- David A. Case (Wed Nov 15 2006 - 17:24:34 PST)
- Steven Winfield (Wed Nov 15 2006 - 16:10:33 PST)
- Pankaj Daga (Wed Nov 15 2006 - 14:56:58 PST)
AMBER: error in tleap test
- Christian Roth (Wed Nov 15 2006 - 10:18:07 PST)
- Scott Brozell (Wed Nov 15 2006 - 09:55:07 PST)
- Christian Roth (Tue Nov 14 2006 - 16:40:24 PST)
AMBER: Ethanol
- FyD (Wed Nov 22 2006 - 04:22:28 PST)
- Rita Cassia (Wed Nov 22 2006 - 01:33:24 PST)
- FyD (Fri Nov 17 2006 - 06:19:15 PST)
- Rita Cassia (Fri Nov 17 2006 - 04:13:14 PST)
AMBER: failure in testing amber8 parallel parts on IBM-SP4 machines
- Xuebin Qiao (Fri Nov 24 2006 - 20:55:14 PST)
- Rachel (Fri Nov 24 2006 - 11:53:29 PST)
- Nicolas Lux Fawzi (Fri Nov 24 2006 - 11:16:01 PST)
- Rachel (Fri Nov 24 2006 - 09:58:53 PST)
AMBER: ff03 GLY HAs atom type
- mahdi fathi (Tue Nov 21 2006 - 21:46:22 PST)
- Yong Duan (Tue Nov 21 2006 - 09:41:17 PST)
- Sandro Fornili (Tue Nov 21 2006 - 08:21:01 PST)
AMBER: Flag for removal of translational and rotational center-of-mass (COM) motion
- David A. Case (Wed Nov 08 2006 - 08:35:24 PST)
- Rajesh Murarka (Wed Nov 08 2006 - 07:59:36 PST)
AMBER: Format of the prmtop file (NUMBER_EXCLUDED_ATOMS) & (EXCLUDED_ATOMS_LIST)
- David A. Case (Tue Nov 07 2006 - 17:51:48 PST)
- Nitin Bhardwaj (Tue Nov 07 2006 - 13:08:42 PST)
AMBER: GBSA implicit chloroform
- Adrian Roitberg (Wed Nov 01 2006 - 09:22:14 PST)
- nadiav.soton.ac.uk (Wed Nov 01 2006 - 09:13:22 PST)
- David A. Case (Wed Nov 01 2006 - 08:56:07 PST)
- nadiav.soton.ac.uk (Wed Nov 01 2006 - 08:41:18 PST)
AMBER: gfortran and amber9 success on FreeBSD
- M. L. Dodson (Sat Nov 18 2006 - 14:02:16 PST)
AMBER: gfortran/gcc versus ifort/icc
- Lachele Foley (Lists) (Thu Nov 16 2006 - 12:49:23 PST)
- Jordi Camps (Thu Nov 16 2006 - 08:22:55 PST)
- Luis Gracia (Wed Nov 15 2006 - 10:34:36 PST)
- Jordi Camps (Wed Nov 15 2006 - 09:50:54 PST)
- Lachele Foley (Lists) (Wed Nov 15 2006 - 07:37:27 PST)
- Fenghui Fan (Tue Nov 14 2006 - 09:40:13 PST)
- Lachele Foley (Lists) (Tue Nov 14 2006 - 06:35:21 PST)
AMBER: GLYCAM and ff98 atom-types
- Fenghui Fan (Thu Nov 16 2006 - 11:16:34 PST)
- Gabbar S. Daaku (Thu Nov 16 2006 - 10:11:05 PST)
AMBER: GLYCAM and ff98 atom-types]
- Austin B. Yongye (Thu Nov 16 2006 - 11:53:03 PST)
AMBER: grid output
- Sergey Samsonov (Tue Nov 07 2006 - 08:46:07 PST)
- Thomas Cheatham (Tue Nov 07 2006 - 08:25:39 PST)
- Sergey Samsonov (Tue Nov 07 2006 - 00:35:28 PST)
- Thomas Cheatham (Mon Nov 06 2006 - 20:30:25 PST)
- Sergey Samsonov (Wed Nov 01 2006 - 08:31:34 PST)
AMBER: H-bond analysis (Ptraj)
- Esther Brugger (Thu Nov 30 2006 - 17:28:10 PST)
AMBER: H-Bond Terms in amber force field
- Jiri Sponer (Wed Nov 15 2006 - 16:30:48 PST)
- Ilyas Yildirim (Wed Nov 15 2006 - 16:05:13 PST)
- Thomas Cheatham (Wed Nov 15 2006 - 15:51:36 PST)
- Jiri Sponer (Wed Nov 15 2006 - 15:20:18 PST)
- Ilyas Yildirim (Wed Nov 15 2006 - 11:28:06 PST)
AMBER: helices in GB simulations
- Ilyas Yildirim (Mon Nov 27 2006 - 14:09:04 PST)
- Carlos Simmerling (Mon Nov 27 2006 - 10:12:02 PST)
- Marie-Pierre Durrieu (Mon Nov 27 2006 - 09:43:41 PST)
AMBER: how can i treat with long "mask" in ptraj analysis.
- Changge Ji (Sun Nov 26 2006 - 08:22:00 PST)
AMBER: How the ensemble average calculated in Gibbs, AMBER7?
- David A. Case (Sun Nov 05 2006 - 19:26:02 PST)
- Yongmei Pan (Wed Nov 01 2006 - 14:06:09 PST)
AMBER: How to apply a force to some atom in a residues?
- Carlos Simmerling (Thu Nov 30 2006 - 04:13:42 PST)
- a a (Wed Nov 29 2006 - 22:45:04 PST)
- Carlos Simmerling (Wed Nov 29 2006 - 04:26:19 PST)
- a a (Tue Nov 28 2006 - 19:36:15 PST)
AMBER: how to choose the parameter for the production/sampling run after the equilibration run
- hbluo (Fri Nov 03 2006 - 17:57:01 PST)
AMBER: how to get complete prepin file
- Fenghui Fan (Sat Nov 25 2006 - 21:02:20 PST)
AMBER: How to recompile sander for single-processor use in AMBER 8?
- David A. Case (Thu Nov 30 2006 - 15:19:10 PST)
- Peter Anderson (Thu Nov 30 2006 - 13:41:27 PST)
AMBER: how to remove the rotation of system in periodic condition?
- David A. Case (Wed Nov 15 2006 - 08:34:01 PST)
- 张勇 (Tue Nov 14 2006 - 04:10:22 PST)
AMBER: How to run MD simulation of a silicon containing complex with AMBER9?
- Chengwen Chen (Wed Nov 29 2006 - 23:06:54 PST)
AMBER: How to run QM/MM simulation of DNA duplex bound with platinum moietes
- Gustavo Seabra (Thu Nov 30 2006 - 07:20:00 PST)
- Chengwen Chen (Thu Nov 30 2006 - 00:07:28 PST)
AMBER: How to specify a box with few walls rigid and others with periodic boundary conditions and then apply a pressure gradient across it?
- Gobind Singh Bisht (Wed Nov 29 2006 - 23:34:28 PST)
AMBER: How to specify user defined force fields or its parameters in amber??
- Gustavo Seabra (Thu Nov 30 2006 - 07:46:42 PST)
- Gobind Singh Bisht (Tue Nov 28 2006 - 08:40:53 PST)
- Gustavo Seabra (Tue Nov 28 2006 - 07:18:49 PST)
- Gobind Singh Bisht (Tue Nov 28 2006 - 06:34:36 PST)
- Carlos Simmerling (Tue Nov 28 2006 - 06:07:18 PST)
- Gobind Singh Bisht (Tue Nov 28 2006 - 05:56:10 PST)
- Carlos Simmerling (Tue Nov 28 2006 - 04:11:51 PST)
- Gobind Singh Bisht (Tue Nov 28 2006 - 03:51:30 PST)
AMBER: How to start a Simulation of a peptide in bilayer
- nur avneet (Wed Nov 01 2006 - 01:28:31 PST)
AMBER: I got the error meassage in testcase of QMMM
- Lee Kyung-koo (Fri Nov 03 2006 - 21:33:44 PST)
AMBER: Interaction Energy Calculation
- Varsha Goyal (Thu Nov 02 2006 - 15:04:12 PST)
- Vitor Manuel Sousa F?x (Thu Nov 02 2006 - 14:08:01 PST)
- Varsha Goyal (Thu Nov 02 2006 - 13:34:28 PST)
AMBER: klambda for TI method.
- David A. Case (Tue Nov 07 2006 - 08:06:21 PST)
- Biswa Ranjan Meher (Tue Nov 07 2006 - 04:59:15 PST)
AMBER: Langevin temperature control vs berendson heat bath
- Carlos Simmerling (Thu Nov 30 2006 - 04:23:24 PST)
- Andreas Svrcek-Seiler (Thu Nov 30 2006 - 04:06:22 PST)
- Hayden Eastwood (Thu Nov 30 2006 - 03:23:37 PST)
- Carlos Simmerling (Wed Nov 29 2006 - 11:02:20 PST)
- Hayden Eastwood (Wed Nov 29 2006 - 10:12:16 PST)
AMBER: leap - compilation error
- David A. Case (Tue Nov 07 2006 - 18:25:37 PST)
- Tomas Kubar (Tue Nov 07 2006 - 01:47:33 PST)
AMBER: leap usage
- Angelo (Thu Nov 02 2006 - 08:39:57 PST)
- Mark Williamson (Thu Nov 02 2006 - 07:26:42 PST)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Nov 02 2006 - 01:41:34 PST)
AMBER: Mass weights
- Sergey Samsonov (Tue Nov 07 2006 - 00:06:14 PST)
- Thomas Cheatham (Mon Nov 06 2006 - 20:58:54 PST)
- Sergey Samsonov (Wed Nov 01 2006 - 00:41:33 PST)
AMBER: matrix correl
- Jardas sucuriba (Tue Nov 21 2006 - 05:05:41 PST)
AMBER: minimization of Hydrogens with xLeaP
- David A. Case (Mon Nov 27 2006 - 18:19:48 PST)
- rebeca.mmb.pcb.ub.es (Mon Nov 27 2006 - 10:38:04 PST)
AMBER: MM_PBSA
- Thomas Steinbrecher (Thu Nov 16 2006 - 08:21:55 PST)
- Varsha Goyal (Wed Nov 15 2006 - 18:27:15 PST)
AMBER: mm_pbsa does not terminate
- Holly Freedman (Wed Nov 01 2006 - 11:34:17 PST)
- Holly Freedman (Wed Nov 01 2006 - 09:56:28 PST)
AMBER: Modifying a Force Field
- Seth Lilavivat (Tue Nov 28 2006 - 07:27:08 PST)
AMBER: Mutual exclusion of atoms
- Nitin Bhardwaj (Mon Nov 06 2006 - 14:27:49 PST)
- Thomas Steinbrecher (Mon Nov 06 2006 - 14:02:47 PST)
- Nitin Bhardwaj (Mon Nov 06 2006 - 13:40:50 PST)
- Nitin Bhardwaj (Sun Nov 05 2006 - 21:59:38 PST)
AMBER: NAD ??
- Cenk Andac (Mon Nov 13 2006 - 06:46:47 PST)
- Urszula Uciechowska (Mon Nov 13 2006 - 01:08:45 PST)
- Cenk Andac (Fri Nov 10 2006 - 15:27:35 PST)
- Cenk Andac (Fri Nov 10 2006 - 15:20:53 PST)
- Urszula Uciechowska (Fri Nov 10 2006 - 01:36:15 PST)
- David A. Case (Wed Nov 08 2006 - 06:49:31 PST)
- Urszula Uciechowska (Wed Nov 08 2006 - 05:40:15 PST)
AMBER: NEWPDB.PDB from antechamber
- Junmei Wang (Wed Nov 01 2006 - 11:42:42 PST)
- Esther Brugger (Wed Nov 01 2006 - 11:10:20 PST)
- Junmei Wang (Wed Nov 01 2006 - 09:19:27 PST)
- Esther Brugger (Wed Nov 01 2006 - 08:59:29 PST)
AMBER: nmode output with ptraj
- a a (Tue Nov 28 2006 - 19:18:32 PST)
- David A. Case (Tue Nov 28 2006 - 18:36:33 PST)
- nadiav.soton.ac.uk (Tue Nov 28 2006 - 07:59:02 PST)
AMBER: no g77 in Fedora Core 5. how to get around with this problem in Fedora Core 5?
- Scott Pendley (Mon Nov 06 2006 - 09:28:48 PST)
- Scott Pendley (Mon Nov 06 2006 - 09:20:43 PST)
- Andreas Svrcek-Seiler (Mon Nov 06 2006 - 09:13:37 PST)
- Margaret S. Cheung (Mon Nov 06 2006 - 07:23:29 PST)
- Andreas Svrcek-Seiler (Mon Nov 06 2006 - 01:17:11 PST)
- Fenghui Fan (Sun Nov 05 2006 - 16:22:26 PST)
- Peter Gannett (Sun Nov 05 2006 - 15:40:18 PST)
- Margaret S. Cheung (Sun Nov 05 2006 - 15:16:34 PST)
AMBER: NONB values adjusted?
- Dave S Walker (Tue Nov 28 2006 - 11:48:36 PST)
- Thomas Steinbrecher (Tue Nov 28 2006 - 08:31:33 PST)
- Dave S Walker (Mon Nov 27 2006 - 23:37:28 PST)
AMBER: NTR for implicit solvent? How to defin restrain for two disconnected sequences?
- a a (Fri Nov 24 2006 - 01:29:26 PST)
- David A. Case (Thu Nov 23 2006 - 23:02:21 PST)
- a a (Thu Nov 23 2006 - 22:13:38 PST)
AMBER: NTR for implicit solvent? How to defin restrain for two disconnectedsequences?
- a a (Mon Nov 27 2006 - 02:29:42 PST)
- David A. Case (Sat Nov 25 2006 - 00:51:06 PST)
- a a (Fri Nov 24 2006 - 18:27:26 PST)
- cristian obiol (Fri Nov 24 2006 - 02:24:28 PST)
AMBER: ntt=1 in simulated annealing
- David A. Case (Wed Nov 15 2006 - 08:46:58 PST)
- kepa koldo burusco (Wed Nov 15 2006 - 03:53:27 PST)
- Sergey Samsonov (Tue Nov 14 2006 - 23:09:15 PST)
- Tanya Johannsen (Tue Nov 14 2006 - 15:59:04 PST)
- Steven Winfield (Tue Nov 07 2006 - 03:26:28 PST)
- Ross Walker (Fri Nov 03 2006 - 18:04:08 PST)
- Tanya Johannsen (Fri Nov 03 2006 - 16:38:38 PST)
- Carlos Simmerling (Fri Nov 03 2006 - 03:48:06 PST)
- Tanya Johannsen (Thu Nov 02 2006 - 19:44:19 PST)
AMBER: opls_aa in amber
- Vitor Manuel Sousa F?x (Thu Nov 16 2006 - 06:29:45 PST)
AMBER: optimatized structure is so much different from the original pdb structure
- Gabbar S. Daaku (Fri Nov 17 2006 - 09:13:04 PST)
- emilia wu (Thu Nov 16 2006 - 21:38:18 PST)
AMBER: parameters for beta peptides
- yipinl.umich.edu (Thu Nov 16 2006 - 11:29:08 PST)
AMBER: parameters for silicon atom
- Chengwen Chen (Sun Nov 19 2006 - 23:45:07 PST)
AMBER: PCA and projections
- Miguel Ferreira (Wed Nov 01 2006 - 06:11:57 PST)
AMBER: PCA results with explicit Vs Implicit solvation
- Angelo (Mon Nov 06 2006 - 09:14:47 PST)
- Keerthi Gottipati (Mon Nov 06 2006 - 08:32:16 PST)
AMBER: Performing Interactive Essential Dynamics in Ptraj
- hbluo (Thu Nov 30 2006 - 16:58:11 PST)
AMBER: Periodic simulations with net charge
- David A. Case (Tue Nov 28 2006 - 18:03:22 PST)
- Jennie Thomas (Tue Nov 28 2006 - 16:47:32 PST)
AMBER: phantom sander8 in dmesg
- Lachele Foley (Lists) (Mon Nov 27 2006 - 13:25:57 PST)
AMBER: pmemd installation problem
- Robert Duke (Fri Nov 03 2006 - 11:09:52 PST)
- Ed Pate (Fri Nov 03 2006 - 10:51:36 PST)
AMBER: Potential Energy Calculation
- Mingfeng Yang (Mon Nov 06 2006 - 13:06:18 PST)
- Hayden Eastwood (Mon Nov 06 2006 - 04:47:00 PST)
- Carlos Simmerling (Mon Nov 06 2006 - 04:32:35 PST)
- sangeeta (Mon Nov 06 2006 - 04:11:30 PST)
AMBER: pqr file
- David A. Case (Thu Nov 16 2006 - 08:53:46 PST)
- Seth Lilavivat (Thu Nov 16 2006 - 08:43:55 PST)
AMBER: prepin file nan
- Junmei Wang (Tue Nov 28 2006 - 13:47:03 PST)
- Fenghui Fan (Tue Nov 28 2006 - 06:48:33 PST)
- linfu (Tue Nov 28 2006 - 01:00:30 PST)
- Fenghui Fan (Mon Nov 27 2006 - 19:28:16 PST)
AMBER: Probelm with running Amber 9 parallelly
- Rafi Ahmad (Thu Nov 09 2006 - 04:59:56 PST)
AMBER: Problem about dummy atoms when running antechamber
- Junmei Wang (Tue Nov 28 2006 - 13:54:42 PST)
- 한 민우 (Mon Nov 27 2006 - 19:30:27 PST)
AMBER: problem in calculating EGB using sander for ligand containing F atom
- David A. Case (Thu Nov 09 2006 - 08:14:06 PST)
- VANDANA KUMARI (Wed Nov 08 2006 - 19:36:52 PST)
AMBER: Problem Installing Amber in SGI Irix 6.5
- trudy.uoguelph.ca (Thu Nov 30 2006 - 07:31:02 PST)
- trudy.uoguelph.ca (Wed Nov 29 2006 - 06:50:51 PST)
- Joe Nolan (Wed Nov 29 2006 - 04:40:58 PST)
- trudy.uoguelph.ca (Tue Nov 28 2006 - 07:41:07 PST)
- David A. Case (Mon Nov 27 2006 - 17:56:14 PST)
- trudy.uoguelph.ca (Mon Nov 27 2006 - 12:29:53 PST)
AMBER: problem installing amber9 with g95 gcc on a fc5 m/c
- Sayandeep Purkayasth (Wed Nov 01 2006 - 22:48:03 PST)
AMBER: Problem of QM/MM calculation with amber 9 parallel version
- Ross Walker (Thu Nov 02 2006 - 09:17:42 PST)
- Ross Walker (Thu Nov 02 2006 - 09:05:38 PST)
- Rafi Ahmad (Thu Nov 02 2006 - 01:51:18 PST)
- Lee Kyung-koo (Thu Nov 02 2006 - 00:53:53 PST)
- Ross Walker (Wed Nov 01 2006 - 16:04:28 PST)
- Lee Kyung-koo (Wed Nov 01 2006 - 15:25:25 PST)
- Ross Walker (Wed Nov 01 2006 - 13:36:17 PST)
- Lee Kyung-koo (Wed Nov 01 2006 - 11:50:28 PST)
AMBER: problem of the REMD with nmr constraints
- wenfei Li (Sat Nov 25 2006 - 17:56:05 PST)
- Carlos Simmerling (Fri Nov 24 2006 - 06:35:25 PST)
- wenfei Li (Wed Nov 22 2006 - 17:57:32 PST)
AMBER: Problem with mask when using distance in ptraj
- Christopher Gaughan (Sun Nov 26 2006 - 06:28:29 PST)
- Thomas Cheatham (Wed Nov 22 2006 - 13:17:12 PST)
- David A. Case (Wed Nov 22 2006 - 13:07:29 PST)
- Christopher Gaughan (Wed Nov 22 2006 - 11:36:23 PST)
AMBER: problem with NAD+ parameters
- Cenk Andac (Mon Nov 06 2006 - 14:05:52 PST)
- Urszula Uciechowska (Mon Nov 06 2006 - 06:27:16 PST)
AMBER: Problems amber mask in distance?
- Sergey Samsonov (Wed Nov 08 2006 - 08:57:20 PST)
- Viktor Hornak (Wed Nov 08 2006 - 08:50:59 PST)
- Sergey Samsonov (Wed Nov 08 2006 - 08:39:18 PST)
AMBER: Problems with equilibrating the starting density
- Ross Walker (Fri Nov 03 2006 - 11:41:55 PST)
- Markus Weingarth (Fri Nov 03 2006 - 09:32:20 PST)
AMBER: problems with saving self-built molecules parameters
- Bill Ross (Mon Nov 20 2006 - 10:55:00 PST)
- Rachel (Mon Nov 20 2006 - 10:42:10 PST)
- Fenghui Fan (Mon Nov 20 2006 - 10:10:21 PST)
- David A. Case (Mon Nov 20 2006 - 09:33:25 PST)
- Rachel (Mon Nov 20 2006 - 09:18:00 PST)
- Fenghui Fan (Mon Nov 20 2006 - 07:06:53 PST)
- Rachel (Mon Nov 20 2006 - 06:23:30 PST)
- Fenghui Fan (Mon Nov 20 2006 - 05:57:10 PST)
- Rachel (Mon Nov 20 2006 - 04:59:07 PST)
AMBER: protonated phosphate
- Einar Uggerud (Mon Nov 27 2006 - 23:11:46 PST)
AMBER: ptraj and mdvel question
- Thomas Cheatham (Wed Nov 15 2006 - 15:37:13 PST)
- Jianhui (Wed Nov 15 2006 - 11:07:06 PST)
AMBER: ptraj grid
- Hannes Loeffler (Sun Nov 26 2006 - 20:05:05 PST)
AMBER: PTRAJ RMS: dumping RMSd vs time data
- r. a. (Mon Nov 06 2006 - 23:41:35 PST)
- David A. Case (Mon Nov 06 2006 - 23:26:13 PST)
- r. a. (Mon Nov 06 2006 - 22:44:35 PST)
- Thomas Cheatham (Mon Nov 06 2006 - 20:18:20 PST)
- Fenghui Fan (Sat Nov 04 2006 - 22:31:25 PST)
- Adrian Roitberg (Sat Nov 04 2006 - 05:00:40 PST)
- r. a. (Sat Nov 04 2006 - 00:58:25 PST)
- r. a. (Sat Nov 04 2006 - 00:45:25 PST)
AMBER: Ptraj syntax change Amber8->Amber9 ?
- David A. Case (Wed Nov 22 2006 - 13:22:37 PST)
- Markus Kaukonen (Wed Nov 22 2006 - 02:35:26 PST)
AMBER: ptraj----radial output files
- Esther Brugger (Wed Nov 29 2006 - 12:03:20 PST)
AMBER: Ptraj: correlation time
- Austin B. Yongye (Tue Nov 21 2006 - 13:05:52 PST)
AMBER: Ptraj: diffusion rate
- Austin B. Yongye (Tue Nov 21 2006 - 13:03:52 PST)
AMBER: Ptraj: radial distribution and correlation coefficient
- Andres Palencia (Tue Nov 14 2006 - 12:13:39 PST)
- Thomas Cheatham (Tue Nov 14 2006 - 11:17:40 PST)
- Austin B. Yongye (Tue Nov 14 2006 - 11:02:27 PST)
- Austin B. Yongye (Tue Nov 14 2006 - 10:50:01 PST)
- Thomas Cheatham (Tue Nov 14 2006 - 10:34:57 PST)
- Austin B. Yongye (Tue Nov 14 2006 - 10:10:39 PST)
AMBER: PTRAJ: radius of gyration
- Bill Ross (Fri Nov 10 2006 - 11:04:06 PST)
- kepa koldo burusco (Fri Nov 10 2006 - 09:05:09 PST)
AMBER: Quantifying pi-pi interactions
- Jiri Sponer (Tue Nov 21 2006 - 08:14:32 PST)
- zachary hartman (Tue Nov 21 2006 - 07:51:30 PST)
AMBER: question about the topology file
- J. Zhang (Sun Nov 12 2006 - 17:42:20 PST)
- Carlos Simmerling (Wed Nov 08 2006 - 04:18:58 PST)
- J. Zhang (Wed Nov 08 2006 - 01:24:10 PST)
AMBER: Radius of gyration
- r. a. (Mon Nov 27 2006 - 20:20:32 PST)
- Elijah Gregory (Fri Nov 24 2006 - 12:33:50 PST)
- Andy Purkiss-Trew (Fri Nov 24 2006 - 11:38:28 PST)
- Andy Purkiss-Trew (Fri Nov 24 2006 - 11:34:52 PST)
- Carles Jaime Cardiel (Fri Nov 24 2006 - 10:25:02 PST)
- kepa koldo burusco (Fri Nov 24 2006 - 09:45:55 PST)
- Andy Purkiss-Trew (Fri Nov 24 2006 - 04:58:53 PST)
- kepa koldo burusco (Fri Nov 24 2006 - 02:27:01 PST)
- r. a. (Wed Nov 22 2006 - 02:11:14 PST)
AMBER: reading psf file
- jojartb.pharm.u-szeged.hu (Sat Nov 18 2006 - 01:40:37 PST)
- jojartb.pharm.u-szeged.hu (Sat Nov 18 2006 - 00:38:26 PST)
- Thomas Cheatham (Fri Nov 17 2006 - 16:28:45 PST)
- jojartb.pharm.u-szeged.hu (Fri Nov 17 2006 - 15:24:24 PST)
AMBER: resp
- Fenghui Fan (Sat Nov 25 2006 - 13:03:00 PST)
AMBER: respin file
- Fenghui Fan (Sun Nov 26 2006 - 16:42:09 PST)
- M. L. Dodson (Sun Nov 26 2006 - 10:05:33 PST)
- Ilyas Yildirim (Sun Nov 26 2006 - 09:45:20 PST)
- Fenghui Fan (Sun Nov 26 2006 - 09:12:01 PST)
- Ilyas Yildirim (Sun Nov 26 2006 - 00:03:33 PST)
- Fenghui Fan (Sat Nov 25 2006 - 19:15:53 PST)
- Ilyas Yildirim (Sat Nov 25 2006 - 18:45:37 PST)
- Fenghui Fan (Sat Nov 25 2006 - 17:49:58 PST)
- Ilyas Yildirim (Sat Nov 25 2006 - 17:07:04 PST)
- Fenghui Fan (Sat Nov 25 2006 - 14:23:46 PST)
- M. L. Dodson (Sat Nov 25 2006 - 06:37:05 PST)
- Fenghui Fan (Fri Nov 24 2006 - 23:06:49 PST)
AMBER: Restarting with new topology
- Sergey Samsonov (Thu Nov 23 2006 - 08:39:53 PST)
AMBER: Restraints of the strand-endings?
- Bill Ross (Tue Nov 14 2006 - 14:19:06 PST)
- Michel Becker (Tue Nov 14 2006 - 12:22:36 PST)
AMBER: saltconc for explicit solvent calculation.
- Carlos Simmerling (Thu Nov 09 2006 - 10:14:21 PST)
- David A. Case (Thu Nov 09 2006 - 10:13:05 PST)
- a a (Thu Nov 09 2006 - 09:51:36 PST)
AMBER: sander error: rst file crash
- jitrayut jitonnom (Sat Nov 11 2006 - 09:22:20 PST)
- David A. Case (Fri Nov 10 2006 - 13:11:15 PST)
- Carlos Simmerling (Fri Nov 10 2006 - 05:26:16 PST)
- jitrayut jitonnom (Fri Nov 10 2006 - 04:52:19 PST)
AMBER: SHAKE problem after minimization
- Rachel (Thu Nov 23 2006 - 10:37:24 PST)
- David A. Case (Wed Nov 22 2006 - 14:24:44 PST)
- Steven Winfield (Wed Nov 22 2006 - 13:53:07 PST)
- Hayden Eastwood (Wed Nov 22 2006 - 12:47:09 PST)
- Hayden Eastwood (Wed Nov 22 2006 - 12:33:17 PST)
- Rachel (Wed Nov 22 2006 - 11:37:15 PST)
- Hayden Eastwood (Wed Nov 22 2006 - 11:13:24 PST)
- Rachel (Wed Nov 22 2006 - 10:43:50 PST)
- Ross Walker (Wed Nov 22 2006 - 09:59:58 PST)
- Rachel (Wed Nov 22 2006 - 07:42:34 PST)
- Rachel (Wed Nov 22 2006 - 03:39:18 PST)
AMBER: simulating a small chain protein in water box
- Carlos Simmerling (Wed Nov 08 2006 - 09:50:59 PST)
- Dave, Sonya (Wed Nov 08 2006 - 08:03:46 PST)
AMBER: Simulation a small chain of amino acids - error in MD simulation
- Dave, Sonya (Fri Nov 03 2006 - 11:20:55 PST)
- Ross Walker (Fri Nov 03 2006 - 10:32:27 PST)
- Carlos Simmerling (Fri Nov 03 2006 - 10:05:22 PST)
- Dave, Sonya (Fri Nov 03 2006 - 09:54:06 PST)
AMBER: Snapshots (pdbs) from a trajectory.
- David A. Case (Thu Nov 23 2006 - 19:58:34 PST)
- Carlos Simmerling (Thu Nov 23 2006 - 09:25:31 PST)
- Jordi Rodrigo De Losada (Thu Nov 23 2006 - 09:11:18 PST)
AMBER: Solvation Energies
- Ivelin Georgiev (Wed Nov 29 2006 - 06:31:13 PST)
AMBER: Some warning !!! during SANDER ?
- Ross Walker (Wed Nov 22 2006 - 08:48:55 PST)
- jitrayut jitonnom (Wed Nov 22 2006 - 00:20:36 PST)
AMBER: strange temperature behavior when changing to constant pressure
- Joshua (Thu Nov 09 2006 - 11:52:33 PST)
AMBER: the energy and temperature both increasing during the simulation with NTT=0
- David A. Case (Mon Nov 20 2006 - 22:09:28 PST)
- Xiaowei (David) Li (Mon Nov 20 2006 - 10:50:00 PST)
AMBER: The plc.frcmod file in the old version tutorial
- Ross Walker (Mon Nov 13 2006 - 08:29:26 PST)
- Fenghui Fan (Sun Nov 12 2006 - 18:50:29 PST)
AMBER: too big EEL values in the minimisation output
- Rachel (Fri Nov 03 2006 - 04:09:54 PST)
- darden (Thu Nov 02 2006 - 11:13:29 PST)
- Rachel (Thu Nov 02 2006 - 10:08:00 PST)
- darden (Wed Nov 01 2006 - 10:08:27 PST)
- Rachel (Wed Nov 01 2006 - 09:01:17 PST)
AMBER: top2mol2.c scanf format string bug
- David A. Case (Tue Nov 07 2006 - 08:18:43 PST)
- Chris Moth (Mon Nov 06 2006 - 16:19:36 PST)
AMBER: trajout script
- Thomas Cheatham (Mon Nov 06 2006 - 12:39:04 PST)
- Fenghui Fan (Sun Nov 05 2006 - 08:23:57 PST)
AMBER: Unable to find mopac charges in divcon.out
- Mark Williamson (Fri Nov 24 2006 - 05:54:34 PST)
- Rachel (Thu Nov 23 2006 - 15:22:06 PST)
- Mark Williamson (Thu Nov 23 2006 - 14:06:35 PST)
- Rachel (Thu Nov 23 2006 - 11:31:55 PST)
AMBER: Unable to find solution for an error - "cannot successfully assign bond type"
- Rama krishnan (Sat Nov 04 2006 - 02:06:51 PST)
AMBER: Unit of force
- Kakali Sen (Wed Nov 08 2006 - 05:12:41 PST)
- Adrian Roitberg (Wed Nov 08 2006 - 04:57:00 PST)
- Kakali Sen (Wed Nov 08 2006 - 03:06:16 PST)
AMBER: vlimit exceeded for step 0, vmax = infinity
- Yong Duan (Tue Nov 14 2006 - 15:05:08 PST)
- Rachel (Tue Nov 14 2006 - 14:44:44 PST)
- Yong Duan (Mon Nov 13 2006 - 17:56:29 PST)
- Rachel (Mon Nov 13 2006 - 09:09:22 PST)
- Yong Duan (Fri Nov 10 2006 - 13:55:23 PST)
- David A. Case (Fri Nov 10 2006 - 08:34:45 PST)
- Rachel (Fri Nov 10 2006 - 07:54:26 PST)
- Carlos Simmerling (Fri Nov 10 2006 - 06:58:26 PST)
- Rachel (Fri Nov 10 2006 - 06:42:31 PST)
- David A. Case (Wed Nov 08 2006 - 13:35:10 PST)
- Carlos Simmerling (Wed Nov 08 2006 - 10:35:21 PST)
- Carlos Simmerling (Wed Nov 08 2006 - 09:46:27 PST)
- Rachel (Wed Nov 08 2006 - 09:31:12 PST)
- David A. Case (Wed Nov 08 2006 - 08:48:01 PST)
- Rachel (Wed Nov 08 2006 - 04:59:00 PST)
AMBER: watershell and image commands
- Esther Brugger (Thu Nov 30 2006 - 16:04:04 PST)
- Thomas Cheatham (Thu Nov 30 2006 - 15:22:59 PST)
- Esther Brugger (Thu Nov 30 2006 - 14:37:58 PST)
AMBER: watershell command
- Esther Brugger (Thu Nov 30 2006 - 15:16:52 PST)
AMBER: what to do with the counter ions when minimizing average structure of DNA?
- Chengwen Chen (Tue Nov 14 2006 - 03:09:25 PST)
AMBER: xleap
- David A. Case (Tue Nov 28 2006 - 08:02:13 PST)
- Steve Seibold (Tue Nov 28 2006 - 06:33:48 PST)
AMBER: Xleap woes
- M. L. Dodson (Thu Nov 16 2006 - 12:14:07 PST)
- Fenghui Fan (Thu Nov 16 2006 - 11:22:59 PST)
- David A. Case (Thu Nov 16 2006 - 10:39:39 PST)
- Shozeb Haider (Thu Nov 16 2006 - 15:07:01 PST)
AMBER: Zn metal library
- Carlos Simmerling (Mon Nov 06 2006 - 04:26:52 PST)
- Ross Walker (Sun Nov 05 2006 - 22:08:20 PST)
- Fenghui Fan (Sun Nov 05 2006 - 19:51:19 PST)
AMBER: ZN prepin
- Fenghui Fan (Sun Nov 26 2006 - 14:29:31 PST)
Amber: ZN-complex file
- FyD (Tue Nov 28 2006 - 23:21:19 PST)
- Junmei Wang (Tue Nov 28 2006 - 15:54:56 PST)
- Fenghui Fan (Tue Nov 28 2006 - 15:47:19 PST)
- Junmei Wang (Tue Nov 28 2006 - 15:21:40 PST)
AMBER: ZN-CYS prepin and frcmd file
- Fenghui Fan (Sun Nov 12 2006 - 18:16:37 PST)
antechamber:tutorial
- Lwin, ThuZar (Thu Nov 09 2006 - 11:03:46 PST)
Fluorine and Bromine Parameters in Amber 9
- Philip Cheung (Fri Nov 03 2006 - 11:56:52 PST)
Fwd: AMBER: sander error: rst file crash
- David A. Case (Sun Nov 12 2006 - 18:44:48 PST)
- Carlos Simmerling (Sat Nov 11 2006 - 04:38:52 PST)
- jitrayut jitonnom (Sat Nov 11 2006 - 03:16:37 PST)
- jitrayut jitonnom (Fri Nov 10 2006 - 07:52:00 PST)
I got the error meassage in testcase of QMMM
- Lee Kyung-koo (Tue Nov 07 2006 - 08:59:16 PST)
- Lee Kyung-koo (Tue Nov 07 2006 - 08:46:25 PST)
- Ross Walker (Sat Nov 04 2006 - 10:09:13 PST)
installation instructions
- David A. Case (Wed Nov 22 2006 - 08:48:17 PST)
Unit of force
- Kakali Sen (Tue Nov 07 2006 - 22:41:30 PST)

Amber Archive Nov 2006 by subject