Amber Archive Jul 2006: by subject

[Fwd: AMBER: Long line of input]
- Myunggi Yi (Tue Jul 25 2006 - 09:08:27 PDT)
[UCE]AMBER: (no subject)
- Thomas Cheatham (Sun Jul 09 2006 - 16:18:49 PDT)
AMBER:
- Ken Merz (Sat Jul 29 2006 - 08:28:53 PDT)
AMBER: "noimage" option for radial distribution functions
- Ozlem Demir (Sun Jul 16 2006 - 14:14:31 PDT)
AMBER: (no subject)
- David A. Case (Sun Jul 09 2006 - 16:20:30 PDT)
- Andrew Box (Sun Jul 09 2006 - 15:49:02 PDT)
AMBER: 2-D free energy surface using WHAM
- David Mobley (Mon Jul 03 2006 - 07:33:24 PDT)
- Atsutoshi Okabe (Mon Jul 03 2006 - 05:08:01 PDT)
AMBER: about restraint format.
- David A. Case (Mon Jul 10 2006 - 08:10:11 PDT)
- Qingning Shu (Mon Jul 10 2006 - 06:11:16 PDT)
AMBER: Addendum: igb=2 and "bad atom type" conflict
- Evan Kelly (Wed Jul 05 2006 - 12:29:10 PDT)
AMBER: Amber 8 on Rocks 4, Opteron, PGI 6.1
- David A. Case (Fri Jul 14 2006 - 08:00:26 PDT)
- Lars Packschies (Fri Jul 14 2006 - 03:18:08 PDT)
AMBER: Amber 8.0 MM_PBSA Stability : question about methodology
- David A. Case (Mon Jul 24 2006 - 12:36:30 PDT)
- Guillaume Bollot (Mon Jul 17 2006 - 05:18:41 PDT)
AMBER: Amber 8.0 no numerical value and offset for the predicted pKa of many titrable residue!!
- Myunggi Yi (Tue Jul 11 2006 - 09:00:58 PDT)
- Guillaume Bollot (Tue Jul 11 2006 - 04:19:29 PDT)
AMBER: AMBER 8: Problem with MPI_Finalize
- David A. Case (Fri Jul 07 2006 - 14:29:10 PDT)
- jrd (Fri Jul 07 2006 - 11:24:08 PDT)
AMBER: Amber 9 installation issues
- Glass, Kevin A (Fri Jul 14 2006 - 16:18:36 PDT)
AMBER: Amber crashed due to power surge and giving problems..
- Gobind Bisht (Tue Jul 11 2006 - 12:17:46 PDT)
- Carlos Simmerling (Tue Jul 11 2006 - 12:05:48 PDT)
- David A. Case (Tue Jul 11 2006 - 11:55:16 PDT)
- Gobind Bisht (Tue Jul 11 2006 - 10:13:36 PDT)
- Carlos Simmerling (Tue Jul 11 2006 - 08:09:21 PDT)
- Gobind Bisht (Tue Jul 11 2006 - 07:46:54 PDT)
AMBER: Amber8.0 predictied pKa problem for a Lysine!
- Myunggi Yi (Fri Jul 07 2006 - 09:14:42 PDT)
- Guillaume Bollot (Fri Jul 07 2006 - 02:38:08 PDT)
AMBER: amber9
- Piotr Cieplak (Fri Jul 14 2006 - 16:33:00 PDT)
- Ross Walker (Fri Jul 14 2006 - 15:37:19 PDT)
- Thomas Steinbrecher (Fri Jul 14 2006 - 15:12:13 PDT)
- Piotr Cieplak (Fri Jul 14 2006 - 15:02:36 PDT)
AMBER: amber9 compilation problems on EM64T xeon system
- hayden (Mon Jul 10 2006 - 09:57:44 PDT)
- Ross Walker (Thu Jul 06 2006 - 20:06:15 PDT)
- Yong Duan (Thu Jul 06 2006 - 12:38:05 PDT)
- hayden (Thu Jul 06 2006 - 11:11:04 PDT)
AMBER: AMBER9 netcdf trajectory with VMD 1.8.4
- Fabian Boes (Mon Jul 24 2006 - 01:01:46 PDT)
AMBER: analysis of atoms in a range during simulation
- pkb bioinfo (Wed Jul 05 2006 - 05:41:58 PDT)
AMBER: analysis of ATOMs in ´certain range distance during simulation
- Myunggi Yi (Thu Jul 06 2006 - 15:03:12 PDT)
- Scott Pendley (Thu Jul 06 2006 - 14:47:57 PDT)
- pkb bioinfo (Wed Jul 05 2006 - 20:37:46 PDT)
AMBER: Antechamber 1.26 is released
- Junmei Wang (Wed Jul 12 2006 - 16:42:32 PDT)
AMBER: Antechamber RESP charges do not sum to zero even with -nc 0 flag
- David A. Case (Fri Jul 07 2006 - 14:06:34 PDT)
- Bob Johnson (Fri Jul 07 2006 - 10:35:59 PDT)
- Junmei Wang (Fri Jul 07 2006 - 10:04:00 PDT)
- Bob Johnson (Fri Jul 07 2006 - 07:55:32 PDT)
AMBER: applying restraints on pre-defined planes
- David A. Case (Tue Jul 11 2006 - 16:34:52 PDT)
- Vlad Cojocaru (Tue Jul 11 2006 - 08:34:07 PDT)
AMBER: Building an RNA - Proflavin Complex
- sethl.gatech.edu (Mon Jul 24 2006 - 13:05:49 PDT)
AMBER: calculating dihedral angles, radius of gyration
- madhumalar.bii-sg.org (Fri Jul 07 2006 - 02:57:14 PDT)
AMBER: Calculating energy for specific part of system
- Adam Pelzer (Tue Jul 18 2006 - 15:32:34 PDT)
AMBER: Can you use VMD to measure bond angles/lengths
- Mark Williamson (Tue Jul 04 2006 - 09:06:59 PDT)
- Andreas Svrcek-Seiler (Tue Jul 04 2006 - 09:09:21 PDT)
- sethl.gatech.edu (Tue Jul 04 2006 - 08:24:49 PDT)
AMBER: Can't open xleap
- Bill Ross (Thu Jul 27 2006 - 10:21:39 PDT)
- David A. Case (Thu Jul 27 2006 - 06:53:16 PDT)
- Jahidul Islam (Thu Jul 27 2006 - 04:57:30 PDT)
- Chng Choon-Peng (Thu Jul 27 2006 - 03:45:58 PDT)
- Jahidul Islam (Thu Jul 27 2006 - 03:16:08 PDT)
AMBER: center molecule using iwrap=1?
- Gustavo Seabra (Thu Jul 13 2006 - 12:49:39 PDT)
- Carlos Simmerling (Thu Jul 13 2006 - 12:43:37 PDT)
- Gustavo Seabra (Thu Jul 13 2006 - 12:07:40 PDT)
- Carlos Simmerling (Thu Jul 13 2006 - 12:00:59 PDT)
- Gustavo Seabra (Thu Jul 13 2006 - 11:21:17 PDT)
AMBER: change atom in a DNA double strand
- Carra, Claudio \(JSC-SK\)[USRA] (Mon Jul 10 2006 - 12:24:02 PDT)
- David A. Case (Thu Jul 06 2006 - 09:57:12 PDT)
- Carra, Claudio \(JSC-SK\)[USRA] (Wed Jul 05 2006 - 14:09:23 PDT)
AMBER: combining different versions of AMBER
- Atro Tossavainen (Sun Jul 23 2006 - 22:44:10 PDT)
- Ross Walker (Fri Jul 21 2006 - 13:11:44 PDT)
- Melissa Foley (Fri Jul 21 2006 - 12:25:35 PDT)
AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux
- David A. Case (Thu Jul 06 2006 - 09:43:36 PDT)
- frustrated modeller (Wed Jul 05 2006 - 17:29:52 PDT)
- David A. Case (Wed Jul 05 2006 - 15:22:42 PDT)
- frustrated modeller (Mon Jul 03 2006 - 11:40:50 PDT)
- David LeBard (Mon Jul 03 2006 - 11:15:50 PDT)
- frustrated modeller (Mon Jul 03 2006 - 10:51:13 PDT)
AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .
- hayden (Mon Jul 03 2006 - 17:28:37 PDT)
- Lwin, ThuZar (Mon Jul 03 2006 - 12:02:31 PDT)
AMBER: compilation of amber8 on Xeon x86_64 x86_64 x86_64 GNU/Linux. .. .
- hayden (Thu Jul 06 2006 - 05:02:13 PDT)
- Lwin, ThuZar (Wed Jul 05 2006 - 16:01:25 PDT)
AMBER: Compiling / Installing Amber 8 on SUSE 10.1
- David A. Case (Mon Jul 17 2006 - 20:00:36 PDT)
- Andreas Svrcek-Seiler (Fri Jul 14 2006 - 03:38:10 PDT)
- hayden (Fri Jul 14 2006 - 03:27:54 PDT)
AMBER: Compiling AMBER 9 on windows XP using cygwin
- Gobind Bisht (Fri Jul 07 2006 - 09:39:31 PDT)
- Emilio Xavier Esposito (Fri Jul 07 2006 - 09:13:40 PDT)
- Gustavo Seabra (Fri Jul 07 2006 - 09:00:36 PDT)
- Gobind Bisht (Fri Jul 07 2006 - 08:48:35 PDT)
- Gustavo Seabra (Fri Jul 07 2006 - 07:36:50 PDT)
- Gobind Bisht (Fri Jul 07 2006 - 07:13:37 PDT)
- Emilio Xavier Esposito (Thu Jul 06 2006 - 09:08:34 PDT)
- Gustavo Seabra (Thu Jul 06 2006 - 08:50:05 PDT)
- Gobind Bisht (Thu Jul 06 2006 - 08:36:28 PDT)
- David A. Case (Thu Jul 06 2006 - 08:16:11 PDT)
- Emilio Xavier Esposito (Thu Jul 06 2006 - 06:40:39 PDT)
- Gobind Bisht (Wed Jul 05 2006 - 22:17:54 PDT)
AMBER: compiling amber9
- nadiav.soton.ac.uk (Tue Jul 04 2006 - 07:31:02 PDT)
- Ross Walker (Mon Jul 03 2006 - 03:48:10 PDT)
- nadiav.soton.ac.uk (Mon Jul 03 2006 - 01:50:44 PDT)
AMBER: Compiling Leap problem
- David A. Case (Fri Jul 14 2006 - 15:57:31 PDT)
- sethl.gatech.edu (Fri Jul 14 2006 - 14:36:38 PDT)
AMBER: Confusion re AMBER SMD output
- Alik Widge (Mon Jul 24 2006 - 13:31:34 PDT)
AMBER: Constant pH simulation : LYS residue
- Guillaume Bollot (Tue Jul 04 2006 - 04:13:00 PDT)
AMBER: convert chemical structure to pdb file
- Gustavo Seabra (Fri Jul 07 2006 - 11:56:37 PDT)
- Baker, Bo-Yang (Fri Jul 07 2006 - 11:44:25 PDT)
AMBER: converting from parm to parm7
- Raffaella D'Auria (Tue Jul 25 2006 - 09:00:50 PDT)
- David A. Case (Sun Jul 23 2006 - 07:47:05 PDT)
- Carlos Simmerling (Sat Jul 22 2006 - 04:27:10 PDT)
- Raffaella D'Auria (Fri Jul 21 2006 - 18:26:55 PDT)
AMBER: converting from parm to parm7 & L-J coeff A and B
- Raffaella D'Auria (Sat Jul 22 2006 - 08:55:56 PDT)
AMBER: Correction on Zinc parameters
- Nitin Bhardwaj (Thu Jul 27 2006 - 09:38:00 PDT)
AMBER: Creating an Intercalation site
- Thomas Cheatham (Mon Jul 17 2006 - 13:13:54 PDT)
- Bill Ross (Mon Jul 17 2006 - 12:49:20 PDT)
AMBER: difficulties with antechamber: tests dont even run
- frustrated modeller (Wed Jul 19 2006 - 16:06:36 PDT)
AMBER: Dihedral analysis
- Thomas Cheatham (Mon Jul 03 2006 - 12:47:42 PDT)
- Claire Zerafa (Mon Jul 03 2006 - 14:25:33 PDT)
AMBER: Distance between two regions
- Baker, Bo-Yang (Mon Jul 31 2006 - 17:16:02 PDT)
AMBER: dummy atoms in MMPBSA
- Ilyas Yildirim (Thu Jul 27 2006 - 05:18:01 PDT)
- Andrea Bortolato (Thu Jul 27 2006 - 01:10:50 PDT)
AMBER: Dynamics and Restraint problem
- David A. Case (Thu Jul 27 2006 - 16:08:16 PDT)
- Andrew Box (Mon Jul 17 2006 - 16:49:51 PDT)
AMBER: Error in loading molecule in tleap
- Gobind Bisht (Fri Jul 07 2006 - 14:18:08 PDT)
- David A. Case (Fri Jul 07 2006 - 14:11:15 PDT)
- Gobind Bisht (Fri Jul 07 2006 - 11:01:45 PDT)
AMBER: Error in running MD in sander
- Ross Walker (Sat Jul 08 2006 - 10:38:15 PDT)
- Gobind Bisht (Sat Jul 08 2006 - 10:20:10 PDT)
AMBER: error on running parallel sander on remote node- amber9
- Chengwen Chen (Wed Jul 05 2006 - 00:46:11 PDT)
AMBER: Etot has downward drift in 'NVE' ensemble
- Thomas Cheatham (Wed Jul 12 2006 - 19:43:11 PDT)
- John S. Zintsmaster (Wed Jul 12 2006 - 19:01:08 PDT)
AMBER: Failure of iwrap in PMEMD
- Ross Walker (Fri Jul 21 2006 - 08:33:53 PDT)
- Myunggi Yi (Fri Jul 21 2006 - 06:57:03 PDT)
- Robert Duke (Fri Jul 21 2006 - 06:34:02 PDT)
- Myunggi Yi (Thu Jul 20 2006 - 17:24:34 PDT)
- Robert Duke (Thu Jul 20 2006 - 14:35:58 PDT)
- Myunggi Yi (Thu Jul 20 2006 - 08:04:31 PDT)
- Robert Duke (Thu Jul 20 2006 - 07:40:48 PDT)
- darden (Thu Jul 20 2006 - 07:34:47 PDT)
- Myunggi Yi (Thu Jul 20 2006 - 07:01:07 PDT)
AMBER: FIX conformation of a ligand
- David A. Case (Thu Jul 06 2006 - 07:30:01 PDT)
- a a (Wed Jul 05 2006 - 19:17:23 PDT)
AMBER: fixing residues
- Prabhakar. G. (Wed Jul 05 2006 - 20:57:38 PDT)
- a a (Mon Jul 03 2006 - 19:47:08 PDT)
- Prabhakar. G. (Mon Jul 03 2006 - 05:16:46 PDT)
AMBER: For different ligand conformation
- David Mobley (Mon Jul 31 2006 - 15:29:40 PDT)
- pkb bioinfo (Mon Jul 31 2006 - 06:53:45 PDT)
AMBER: Free energy calculated from mm_pbsa
- gtg549i.mail.gatech.edu (Thu Jul 13 2006 - 00:26:44 PDT)
AMBER: from traj to crd
- Fabián Alejandro Rodríguez (Mon Jul 31 2006 - 17:58:19 PDT)
AMBER: Fwd: ADL: peptide simulation before docking
- jitrayut jitonnom (Sun Jul 09 2006 - 02:26:59 PDT)
AMBER: Fwd: difficulties with antechamber: tests dont even run
- Junmei Wang (Tue Jul 25 2006 - 16:00:04 PDT)
- David A. Case (Tue Jul 25 2006 - 08:11:22 PDT)
- frustrated modeller (Wed Jul 19 2006 - 16:30:07 PDT)
AMBER: Gb Na+ ions DNA
- Andreas Svrcek-Seiler (Fri Jul 21 2006 - 02:22:21 PDT)
- Conn O'Rourke (Thu Jul 20 2006 - 08:16:05 PDT)
AMBER: GB tutorials and disulphide bonds
- Abhilash (Mon Jul 31 2006 - 13:41:30 PDT)
AMBER: Harmonic restraint along z-axis
- Carlos Simmerling (Thu Jul 27 2006 - 09:15:18 PDT)
- David A. Case (Thu Jul 27 2006 - 07:32:52 PDT)
- Myunggi Yi (Wed Jul 26 2006 - 17:26:02 PDT)
AMBER: Having trouble with Nucgen for generating pdb more than 16 bps
- Bill Ross (Mon Jul 31 2006 - 11:53:11 PDT)
- amit.mbu.iisc.ernet.in (Sun Jul 30 2006 - 11:51:05 PDT)
AMBER: hbond analysis
- Thomas Cheatham (Mon Jul 03 2006 - 12:19:57 PDT)
- Claire Zerafa (Mon Jul 03 2006 - 14:06:22 PDT)
AMBER: hbond analysis2
- Claire Zerafa (Tue Jul 04 2006 - 07:00:35 PDT)
AMBER: How to calculate binding free energy using MM-PBSA
- Xioling Chuang (Fri Jun 30 2006 - 21:39:09 PDT)
AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap
- David A. Case (Wed Jul 26 2006 - 10:44:58 PDT)
- Lwin, ThuZar (Tue Jul 25 2006 - 17:39:32 PDT)
AMBER: how to mutate in amber 8 for thermodynamic integration without using xleap. .
- David A. Case (Fri Jul 28 2006 - 07:27:44 PDT)
- Lwin, ThuZar (Thu Jul 27 2006 - 18:35:19 PDT)
AMBER: How to resume remaining simulation
- Guanglei Cui (Mon Jul 24 2006 - 08:19:56 PDT)
- pkb bioinfo (Mon Jul 24 2006 - 03:05:23 PDT)
AMBER: Hybridization in leap
- David A. Case (Tue Jul 25 2006 - 13:37:30 PDT)
- opitz.che.udel.edu (Tue Jul 25 2006 - 11:23:12 PDT)
AMBER: igb=2 and "bad atom type" conflict
- David A. Case (Fri Jul 07 2006 - 14:42:09 PDT)
- Evan Kelly (Thu Jul 06 2006 - 15:01:39 PDT)
- Evan Kelly (Thu Jul 06 2006 - 09:21:06 PDT)
- Evan Kelly (Thu Jul 06 2006 - 08:45:10 PDT)
- Scott Pendley (Wed Jul 05 2006 - 13:22:43 PDT)
- Evan Kelly (Wed Jul 05 2006 - 12:25:16 PDT)
AMBER: iso command and a cubic box
- David A. Case (Wed Jul 12 2006 - 12:00:25 PDT)
- Patricia Hunt (Wed Jul 12 2006 - 00:03:03 PDT)
AMBER: leap error
- David A. Case (Thu Jul 27 2006 - 07:34:17 PDT)
- AYTUG TUNCEL (Wed Jul 26 2006 - 16:29:35 PDT)
AMBER: library for 8oxoguanine
- FyD (Tue Jul 25 2006 - 05:39:27 PDT)
- Carlos Simmerling (Mon Jul 24 2006 - 14:12:38 PDT)
- M. L. Dodson (Mon Jul 24 2006 - 13:07:17 PDT)
- Carra, Claudio \(JSC-SK\)[USRA] (Mon Jul 24 2006 - 12:50:59 PDT)
AMBER: loading torsion parameters
- Bill Ross (Mon Jul 31 2006 - 13:49:38 PDT)
- Nitin Bhardwaj (Mon Jul 31 2006 - 13:35:18 PDT)
- Ross Walker (Mon Jul 31 2006 - 13:25:08 PDT)
- Wei Zhang (Mon Jul 31 2006 - 13:13:57 PDT)
- Nitin Bhardwaj (Mon Jul 31 2006 - 12:47:19 PDT)
AMBER: Long line of input
- David A. Case (Mon Jul 24 2006 - 12:37:20 PDT)
- Myunggi Yi (Wed Jul 19 2006 - 19:03:11 PDT)
- hornak.csb.sunysb.edu (Wed Jul 19 2006 - 13:37:29 PDT)
- Myunggi Yi (Wed Jul 19 2006 - 13:13:26 PDT)
AMBER: manual/prmtop/missing bonds section
- David A. Case (Wed Jul 05 2006 - 09:09:06 PDT)
AMBER: Minimization problem: coordinates out of virtual box
- Zu Thur Yew (Mon Jul 24 2006 - 05:53:19 PDT)
AMBER: MM-PBSA: Problem when Generating Snapshots
- Zu Thur Yew (Tue Jul 04 2006 - 00:20:39 PDT)
AMBER: MM/PBSA
- Wei Chen (Sat Jul 08 2006 - 11:29:06 PDT)
- Ray Luo (Fri Jul 07 2006 - 17:26:28 PDT)
- Wei Chen (Fri Jul 07 2006 - 14:20:47 PDT)
AMBER: Modelling dsDNA less than 10bp
- Lena Dolghih (Fri Jul 21 2006 - 06:15:16 PDT)
AMBER: multiple "restraint_wt" in sander
- Viktor Hornak (Mon Jul 03 2006 - 07:43:44 PDT)
- kanazta1.yahoo.co.jp (Mon Jul 03 2006 - 07:12:21 PDT)
AMBER: Myrinet or Gigabit ethernet?
- Robert Duke (Thu Jul 20 2006 - 07:45:45 PDT)
- Mingfeng Yang (Thu Jul 20 2006 - 06:35:08 PDT)
AMBER: NAMOT
- Andreas Svrcek-Seiler (Mon Jul 03 2006 - 04:02:57 PDT)
AMBER: Namot on AMD 64 possible
- Andreas Svrcek-Seiler (Wed Jul 05 2006 - 11:08:44 PDT)
- sethl.gatech.edu (Wed Jul 05 2006 - 10:05:26 PDT)
AMBER: New (small) Topology without solvent from previous one (big) with solvent
- Petr Kulhanek (Fri Jul 14 2006 - 02:24:26 PDT)
- j j (Fri Jul 14 2006 - 01:48:33 PDT)
- j j (Fri Jul 14 2006 - 01:40:10 PDT)
- Petr Kulhanek (Fri Jul 14 2006 - 00:44:09 PDT)
- David A. Case (Thu Jul 13 2006 - 11:14:20 PDT)
- j j (Thu Jul 13 2006 - 10:59:00 PDT)
- Thomas Cheatham (Thu Jul 13 2006 - 09:34:00 PDT)
- j j (Thu Jul 13 2006 - 03:47:15 PDT)
- j j (Thu Jul 13 2006 - 03:50:55 PDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
- Ray Luo (Wed Jul 05 2006 - 10:45:49 PDT)
AMBER: Obtaining LCPO parameters for F and Fe
- zachary hartman (Mon Jul 17 2006 - 11:16:54 PDT)
AMBER: parallel installation of amber8 on HP cluster
- David A. Case (Thu Jul 27 2006 - 08:57:41 PDT)
- Michael Crowley (Wed Jul 26 2006 - 11:52:09 PDT)
- Manish Datt (Wed Jul 26 2006 - 10:54:51 PDT)
- David A. Case (Wed Jul 26 2006 - 08:00:53 PDT)
- michael crowley (Wed Jul 26 2006 - 07:42:19 PDT)
- Manish Datt (Wed Jul 26 2006 - 03:00:30 PDT)
AMBER: PDB from .rst?
- priya priya (Thu Jul 20 2006 - 20:24:08 PDT)
- Ilyas Yildirim (Thu Jul 20 2006 - 14:08:20 PDT)
- Wei Zhang (Thu Jul 20 2006 - 14:04:58 PDT)
- Evan Kelly (Thu Jul 20 2006 - 13:51:09 PDT)
AMBER: peptide simulation before docking
- jitrayut jitonnom (Sat Jul 08 2006 - 13:45:28 PDT)
AMBER: PhosphoThreonine Parms for use with ff03
- Carlos Simmerling (Tue Jul 18 2006 - 04:28:20 PDT)
- FyD (Tue Jul 18 2006 - 00:57:24 PDT)
- Zu Thur Yew (Mon Jul 17 2006 - 22:19:15 PDT)
AMBER: PMEMD with NMR restraint and position restraint
- Robert Duke (Tue Jul 18 2006 - 21:34:35 PDT)
- Robert Duke (Tue Jul 18 2006 - 19:03:42 PDT)
- Robert Duke (Tue Jul 18 2006 - 13:49:05 PDT)
- Ting Wang (Tue Jul 18 2006 - 13:12:41 PDT)
- Robert Duke (Mon Jul 17 2006 - 20:03:29 PDT)
- Ting Wang (Mon Jul 17 2006 - 16:18:31 PDT)
AMBER: pmemd9 issue
- Robert Duke (Sun Jul 02 2006 - 04:46:21 PDT)
- Robert Duke (Sun Jul 02 2006 - 04:12:11 PDT)
- Brent Krueger (Sat Jul 01 2006 - 20:45:11 PDT)
AMBER: problem about Distance Restraints.
- David A. Case (Wed Jul 12 2006 - 16:33:54 PDT)
- Qingning Shu (Tue Jul 11 2006 - 20:38:48 PDT)
AMBER: Problem with bcc flag of antechamber
- Junmei Wang (Thu Jul 06 2006 - 10:53:37 PDT)
- Gobind Bisht (Thu Jul 06 2006 - 10:00:49 PDT)
AMBER: Problem with bcc flag of antechamber..continued
- amit.mbu.iisc.ernet.in (Fri Jul 07 2006 - 03:09:32 PDT)
- Gobind Bisht (Thu Jul 06 2006 - 10:08:45 PDT)
AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities
- Thomas Steinbrecher (Thu Jul 06 2006 - 16:02:19 PDT)
AMBER: problem with saving the parameters file
- Bill Ross (Wed Jul 05 2006 - 11:23:05 PDT)
- David A. Case (Wed Jul 05 2006 - 11:09:12 PDT)
- amere swathi (Wed Jul 05 2006 - 01:50:40 PDT)
AMBER: problems about compiling a parallel version of AMBER 9
- David A. Case (Wed Jul 05 2006 - 11:06:08 PDT)
- Chengwen Chen (Tue Jul 04 2006 - 21:29:38 PDT)
AMBER: problems of running sander.MPI of amber9 on remote node
- Chengwen Chen (Sun Jul 23 2006 - 23:29:20 PDT)
AMBER: process_mdout.perl's output is empty
- Alik Widge (Tue Jul 25 2006 - 08:19:44 PDT)
- Chng Choon-Peng (Mon Jul 24 2006 - 18:02:57 PDT)
- Prashanth Athri (Mon Jul 24 2006 - 13:53:04 PDT)
AMBER: program to calculate net charge of a ligand for Antechamber
- David Mobley (Mon Jul 10 2006 - 21:18:36 PDT)
- Christophe Guilbert (Mon Jul 10 2006 - 18:30:39 PDT)
AMBER: ptraj help - amber7 failed, amber8 read prmtop file incorrectly...
- fine wu (Thu Jul 20 2006 - 08:55:55 PDT)
AMBER: PTRAJ OUTPUT
- Bill Ross (Wed Jul 05 2006 - 16:43:57 PDT)
- Cporteli (Wed Jul 05 2006 - 16:02:47 PDT)
AMBER: Ptraj: Hbond time series
- Chng Choon-Peng (Tue Jul 11 2006 - 16:56:20 PDT)
- Zu Thur Yew (Tue Jul 11 2006 - 08:19:34 PDT)
AMBER: QMMM simulation
- amit.mbu.iisc.ernet.in (Thu Jul 13 2006 - 11:38:48 PDT)
AMBER: Question about Energy calculation using MM-PBSA scripts & Imaging
- David A. Case (Wed Jul 05 2006 - 10:50:52 PDT)
- Zu Thur Yew (Wed Jul 05 2006 - 10:03:13 PDT)
AMBER: Question about NSCM
- David A. Case (Tue Jul 11 2006 - 08:02:11 PDT)
- Xiaowei (David) Li (Tue Jul 11 2006 - 01:25:48 PDT)
AMBER: R.E.D II
- Franck Vendeix (Wed Jul 05 2006 - 07:56:24 PDT)
- FyD (Tue Jul 04 2006 - 23:55:13 PDT)
- Franck_Vendeix.ncsu.edu (Tue Jul 04 2006 - 21:33:21 PDT)
- FyD (Tue Jul 04 2006 - 09:33:46 PDT)
- Franck_Vendeix.ncsu.edu (Tue Jul 04 2006 - 07:29:59 PDT)
- FyD (Tue Jul 04 2006 - 00:47:51 PDT)
- Franck_Vendeix.ncsu.edu (Mon Jul 03 2006 - 23:23:22 PDT)
- FyD (Mon Jul 03 2006 - 03:03:19 PDT)
- a a (Mon Jul 03 2006 - 02:35:35 PDT)
- FyD (Sun Jul 02 2006 - 23:39:20 PDT)
- Franck_Vendeix.ncsu.edu (Sun Jul 02 2006 - 19:11:39 PDT)
AMBER: Replica Exchange
- Adrian Roitberg (Fri Jul 21 2006 - 06:37:26 PDT)
- Austin B. Yongye (Fri Jul 21 2006 - 06:29:08 PDT)
- Carlos Simmerling (Thu Jul 20 2006 - 19:51:19 PDT)
- Austin B. Yongye (Thu Jul 20 2006 - 19:07:46 PDT)
- Carlos Simmerling (Thu Jul 20 2006 - 05:32:07 PDT)
- Guanglei Cui (Wed Jul 19 2006 - 11:24:55 PDT)
- Austin B. Yongye (Wed Jul 19 2006 - 10:23:47 PDT)
- Carlos Simmerling (Wed Jul 19 2006 - 09:29:33 PDT)
- Austin B. Yongye (Wed Jul 19 2006 - 08:04:44 PDT)
- Austin B. Yongye (Mon Jul 17 2006 - 15:22:51 PDT)
- Carlos Simmerling (Mon Jul 17 2006 - 07:44:55 PDT)
- Guanglei Cui (Mon Jul 17 2006 - 07:18:57 PDT)
- Austin B. Yongye (Mon Jul 17 2006 - 05:31:09 PDT)
- Carlos Simmerling (Wed Jul 12 2006 - 07:25:14 PDT)
- Atsutoshi Okabe (Tue Jul 11 2006 - 21:13:38 PDT)
- Carlos Simmerling (Tue Jul 11 2006 - 05:49:20 PDT)
- Atsutoshi Okabe (Mon Jul 10 2006 - 19:43:17 PDT)
- Carlos Simmerling (Mon Jul 10 2006 - 05:13:48 PDT)
- Atsutoshi Okabe (Mon Jul 10 2006 - 04:38:17 PDT)
AMBER: Replica exchange with Amber9
- Atsutoshi Okabe (Wed Jul 19 2006 - 09:22:49 PDT)
- Atsutoshi Okabe (Mon Jul 17 2006 - 01:20:25 PDT)
- Adrian Roitberg (Fri Jul 14 2006 - 06:00:14 PDT)
- Atsutoshi Okabe (Thu Jul 13 2006 - 23:20:21 PDT)
AMBER: residue and atom number
- David A. Case (Mon Jul 10 2006 - 08:09:29 PDT)
- Andrea Bortolato (Mon Jul 10 2006 - 05:57:05 PDT)
AMBER: Ring of dna
- f m (Tue Jul 18 2006 - 07:30:03 PDT)
- Bill Ross (Mon Jul 17 2006 - 12:19:49 PDT)
- Bill Ross (Mon Jul 17 2006 - 12:15:10 PDT)
- M. L. Dodson (Mon Jul 17 2006 - 07:56:03 PDT)
- f m (Mon Jul 17 2006 - 06:48:33 PDT)
- f m (Mon Jul 17 2006 - 04:32:01 PDT)
- Bill Ross (Sat Jul 15 2006 - 10:55:07 PDT)
- f m (Sat Jul 15 2006 - 09:37:59 PDT)
- Bill Ross (Fri Jul 14 2006 - 10:23:07 PDT)
- j j (Fri Jul 14 2006 - 07:25:59 PDT)
- f m (Fri Jul 14 2006 - 06:27:03 PDT)
AMBER: Ringof dna
- f m (Thu Jul 13 2006 - 10:00:48 PDT)
- David A. Case (Thu Jul 13 2006 - 09:54:07 PDT)
- Flora Mactavish (Thu Jul 13 2006 - 06:14:22 PDT)
AMBER: RMS & PCA
- Zu Thur Yew (Mon Jul 17 2006 - 22:12:35 PDT)
- Guanglei Cui (Mon Jul 17 2006 - 11:22:56 PDT)
- Zu Thur Yew (Mon Jul 17 2006 - 07:55:12 PDT)
AMBER: saltcon variable
- David A. Case (Mon Jul 24 2006 - 12:38:53 PDT)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jul 20 2006 - 12:00:01 PDT)
AMBER: Sander NOE violations
- David A. Case (Thu Jul 06 2006 - 18:41:28 PDT)
- Andrew Box (Thu Jul 06 2006 - 18:32:21 PDT)
- David A. Case (Thu Jul 06 2006 - 18:01:19 PDT)
- Andrew Box (Thu Jul 06 2006 - 16:55:59 PDT)
AMBER: script to extract data from minimization .out file
- Ross Walker (Sat Jul 08 2006 - 08:47:17 PDT)
- sangeeta.bioinfo.ernet.in (Sat Jul 08 2006 - 03:41:44 PDT)
- sangeeta.bioinfo.ernet.in (Sat Jul 08 2006 - 03:23:52 PDT)
- Gustavo Seabra (Fri Jul 07 2006 - 10:35:32 PDT)
- Tanya Johannsen (Fri Jul 07 2006 - 09:55:44 PDT)
AMBER: Silicon related parameters
- hbluo (Sat Jul 22 2006 - 10:52:17 PDT)
AMBER: simulate a self-assemble process in vacuum
- Eric Hu (Thu Jul 20 2006 - 14:43:35 PDT)
- Gustavo Seabra (Thu Jul 13 2006 - 06:22:15 PDT)
- Eric Hu (Wed Jul 12 2006 - 16:22:58 PDT)
AMBER: Simulating an "average" DNA sequence
- David A. Case (Sun Jul 23 2006 - 07:47:15 PDT)
- S. Jamal Rahi (Fri Jul 21 2006 - 20:20:36 PDT)
AMBER: small bug in ambmask (amber9)
- David A. Case (Mon Jul 10 2006 - 08:39:38 PDT)
- Kateryna Miroshnychenko (Mon Jul 10 2006 - 07:53:02 PDT)
AMBER: temperature regulation
- Carlos Simmerling (Tue Jul 18 2006 - 04:41:18 PDT)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Tue Jul 18 2006 - 01:31:04 PDT)
AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.
- Christophe Guilbert (Wed Jul 05 2006 - 19:50:24 PDT)
- David A. Case (Wed Jul 05 2006 - 18:54:38 PDT)
- Christophe Guilbert (Wed Jul 05 2006 - 16:55:49 PDT)
- David A. Case (Wed Jul 05 2006 - 14:31:14 PDT)
AMBER: Tutorial 4-section 4 (plc.frcmod)
- Mark Williamson (Mon Jul 03 2006 - 05:46:08 PDT)
- a a (Mon Jul 03 2006 - 02:41:44 PDT)
AMBER: Tutorial 4-section 4 - VDW parameters
- a a (Mon Jul 03 2006 - 02:49:31 PDT)
AMBER: Tutorial 4-section 4 DIHE in frcmod file.
- Ilyas Yildirim (Mon Jul 03 2006 - 20:47:22 PDT)
- a a (Mon Jul 03 2006 - 19:13:04 PDT)
AMBER: Tutorial 8, section 6: best fit before clustering
- sangeeta (Wed Jul 26 2006 - 06:42:47 PDT)
- Ross Walker (Mon Jul 24 2006 - 07:45:59 PDT)
- sangeeta (Mon Jul 24 2006 - 06:18:05 PDT)
AMBER: Units for Leonard-Jones potential parameters
- David A. Case (Thu Jul 06 2006 - 09:45:00 PDT)
- Vanessa Oklejas (Wed Jul 05 2006 - 20:02:59 PDT)
AMBER: Using a trajectory and some PDB files as input for PCA
- Zu Thur Yew (Mon Jul 31 2006 - 03:20:42 PDT)
AMBER: water diffusion
- Thomas Cheatham (Mon Jul 17 2006 - 23:36:36 PDT)
- Sergei Smirnov (Mon Jul 17 2006 - 17:48:59 PDT)
AMBER: Where is the repulsion energy ( part of nonpolar solvation energy) in MM_PBSA ?
- Ray Luo (Thu Jul 13 2006 - 14:21:30 PDT)
- Changge Ji (Tue Jul 11 2006 - 23:03:30 PDT)
AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ?
- Carlos Simmerling (Thu Jul 06 2006 - 18:51:58 PDT)
- David A. Case (Thu Jul 06 2006 - 18:48:12 PDT)
- Christophe Guilbert (Thu Jul 06 2006 - 17:51:49 PDT)
AMBER: working with large strained system
- Bill Ross (Thu Jul 06 2006 - 10:06:57 PDT)
- Robert Duke (Thu Jul 06 2006 - 07:06:48 PDT)
- Carlos Simmerling (Thu Jul 06 2006 - 06:41:39 PDT)
- Tanya Johannsen (Wed Jul 05 2006 - 19:29:58 PDT)
AMBER: xleap
- Chng Choon-Peng (Thu Jul 27 2006 - 03:14:58 PDT)
- Md Jahidul Islam (Thu Jul 27 2006 - 02:49:36 PDT)
AMBER: Xmgr in Windows
- Jahidul Islam (Mon Jul 31 2006 - 20:24:19 PDT)
AMBER: Zinc coordinating CYS
- madhumalar.bii-sg.org (Fri Jul 28 2006 - 02:17:36 PDT)
- Nitin Bhardwaj (Thu Jul 27 2006 - 21:00:45 PDT)
- madhumalar.bii-sg.org (Thu Jul 27 2006 - 17:37:12 PDT)
- Nitin Bhardwaj (Thu Jul 27 2006 - 14:30:45 PDT)
AMBER: Zinc parameters
- Ross Walker (Thu Jul 27 2006 - 10:26:29 PDT)
- Nitin Bhardwaj (Thu Jul 27 2006 - 09:35:57 PDT)
AMBER: Zinc-coordinating histidine protonation state
- David A. Case (Mon Jul 31 2006 - 08:50:16 PDT)
- Nitin Bhardwaj (Thu Jul 27 2006 - 13:01:16 PDT)
Confusion re AMBER SMD output
- Alik Widge (Mon Jul 31 2006 - 15:54:59 PDT)
Strange problems with PMEMD on Intel Xeons with Infiniband
- Robert Duke (Thu Jul 06 2006 - 05:43:24 PDT)
- Fabian Boes (Thu Jul 06 2006 - 01:29:35 PDT)

Amber Archive Jul 2006 by subject