Amber Archive Oct 2008: by subject

[Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files
- Robert Hanson (Thu Oct 09 2008 - 16:12:52 PDT)
AMBER: 2'-5'-branched RNA
- Volodymyr Zloy (Mon Oct 27 2008 - 09:10:00 PDT)
AMBER: about SASA and AMBER
- Carlos Simmerling (Mon Oct 20 2008 - 10:17:42 PDT)
- Lachele Foley (Lists) (Mon Oct 20 2008 - 10:07:06 PDT)
- Yunierkis Perez Castillo (Mon Oct 20 2008 - 08:58:06 PDT)
AMBER: Ac-Co Parameters for Amber
- suhaib sh (Thu Oct 02 2008 - 02:34:08 PDT)
- FyD (Wed Oct 01 2008 - 14:26:54 PDT)
- suhaib sh (Wed Oct 01 2008 - 02:05:31 PDT)
- FyD (Tue Sep 30 2008 - 23:14:39 PDT)
AMBER: AddIons approach
- David A. Case (Fri Oct 10 2008 - 04:52:52 PDT)
- parul sharma (Fri Oct 10 2008 - 04:44:41 PDT)
- Germain Vallverdu (Fri Oct 10 2008 - 04:23:00 PDT)
- Carlos Simmerling (Fri Oct 10 2008 - 04:17:08 PDT)
- parul sharma (Fri Oct 10 2008 - 04:13:51 PDT)
AMBER: Addions in GB Mode?
- Carlos Simmerling (Mon Oct 20 2008 - 03:12:52 PDT)
- parul sharma (Mon Oct 20 2008 - 02:25:22 PDT)
- Rogelio Hernández (Sun Oct 19 2008 - 10:04:32 PDT)
AMBER: Again: Installation problem of AMBER on cluster
- Dmitri Nilov (Sat Oct 25 2008 - 05:30:43 PDT)
- Ross Walker (Tue Oct 21 2008 - 09:49:50 PDT)
- Dmitri Nilov (Tue Oct 21 2008 - 09:31:52 PDT)
AMBER: Amber dipole printout.
- Ross Walker (Tue Oct 14 2008 - 13:05:38 PDT)
- Dave Rogers (Tue Oct 14 2008 - 11:14:21 PDT)
- Zhao, Zhen (zhaozh) (Tue Oct 14 2008 - 10:25:40 PDT)
AMBER: AMBER force field for glycolipid
- Stephane Abel (Thu Oct 09 2008 - 07:08:49 PDT)
- Matthew Tessier (Thu Oct 09 2008 - 06:57:59 PDT)
- Stephane Abel (Wed Oct 08 2008 - 05:25:12 PDT)
AMBER: Amber heme parameters
- Shaikh Abdul R S Ramaju (Tue Oct 07 2008 - 23:38:59 PDT)
- sobereva (Tue Oct 07 2008 - 07:02:12 PDT)
- Shaikh Abdul R S Ramaju (Mon Oct 06 2008 - 23:31:34 PDT)
AMBER: amber10 installation on sgi_mips
- Atro Tossavainen (Thu Oct 02 2008 - 12:39:33 PDT)
- Bill Ross (Thu Oct 02 2008 - 10:05:17 PDT)
- Rima Chaudhuri (Thu Oct 02 2008 - 09:42:25 PDT)
- Atro Tossavainen (Thu Oct 02 2008 - 02:59:34 PDT)
- Rima Chaudhuri (Wed Oct 01 2008 - 19:31:06 PDT)
- Bill Ross (Wed Oct 01 2008 - 15:11:08 PDT)
- Rima Chaudhuri (Wed Oct 01 2008 - 13:47:14 PDT)
- David A. Case (Wed Oct 01 2008 - 12:24:56 PDT)
- Rima Chaudhuri (Wed Oct 01 2008 - 12:05:06 PDT)
AMBER: amber10 installation problem in cygwin
- Ross Walker (Tue Oct 14 2008 - 09:32:06 PDT)
- Gustavo Seabra (Tue Oct 14 2008 - 08:56:20 PDT)
- vijayaraj.clri.res.in (Tue Oct 14 2008 - 08:21:19 PDT)
AMBER: amber10 on SiCortex hardware
- Peter Varnai (Fri Oct 03 2008 - 09:27:21 PDT)
AMBER: Amber10: Problem with tgtmd and ncsu testing
- Dmitri Nilov (Wed Oct 15 2008 - 06:00:11 PDT)
AMBER: amber: parameters for 5' nucleotide monophosphates
- FyD (Mon Oct 13 2008 - 12:44:47 PDT)
- Jeff Schwinefus (Mon Oct 13 2008 - 10:52:55 PDT)
AMBER: ANAL
- Madhumalar Arumugam (Wed Oct 29 2008 - 01:44:57 PDT)
AMBER: antechamber
- Marcela Madrid (Tue Oct 21 2008 - 10:02:54 PDT)
- David A. Case (Thu Oct 16 2008 - 14:25:17 PDT)
- Marcela Madrid (Thu Oct 16 2008 - 13:37:07 PDT)
- David A. Case (Mon Oct 13 2008 - 15:43:00 PDT)
- dipti lele (Sat Oct 11 2008 - 21:43:33 PDT)
AMBER: antechamber bug? produces incorrect NEWPDB.PDB file
- Robert Hanson (Wed Oct 29 2008 - 04:50:35 PDT)
- David A. Case (Wed Oct 29 2008 - 03:49:06 PDT)
- FyD (Wed Oct 29 2008 - 00:19:41 PDT)
- David A. Case (Tue Oct 28 2008 - 15:09:38 PDT)
- David A. Case (Tue Oct 28 2008 - 10:57:49 PDT)
- Robert Hanson (Tue Oct 28 2008 - 15:42:19 PDT)
- Robert Hanson (Tue Oct 28 2008 - 09:46:08 PDT)
- Robert Hanson (Tue Oct 28 2008 - 11:21:59 PDT)
- David A. Case (Tue Oct 28 2008 - 10:41:45 PDT)
AMBER: antechamber errors
- David A. Case (Fri Oct 17 2008 - 07:20:51 PDT)
- oguz gurbulak (Fri Oct 17 2008 - 06:07:37 PDT)
AMBER: antechamber test failure
- David A. Case (Thu Oct 16 2008 - 04:04:13 PDT)
- john smith (Wed Oct 15 2008 - 22:53:50 PDT)
- David A. Case (Wed Oct 15 2008 - 06:16:06 PDT)
- john smith (Mon Oct 13 2008 - 22:47:28 PDT)
AMBER: aromatic bent ligand
- Arturas Ziemys (Mon Oct 27 2008 - 19:34:49 PDT)
AMBER: Atom names CL and four characters
- Francesco Pietra (Fri Oct 24 2008 - 15:44:31 PDT)
- David A. Case (Fri Oct 24 2008 - 12:21:51 PDT)
- Francesco Pietra (Fri Oct 24 2008 - 11:55:05 PDT)
AMBER: atom type for carbon and nitrogen atoms
- Gustavo Seabra (Mon Oct 27 2008 - 10:28:31 PDT)
- Catein Catherine (Mon Oct 27 2008 - 01:58:51 PDT)
- Catein Catherine (Mon Oct 27 2008 - 01:56:06 PDT)
AMBER: capping with non charged residues
- Francesco Pietra (Thu Oct 16 2008 - 15:24:44 PDT)
AMBER: changing pdb structure
- Taufik Al-Sarraj (Tue Oct 14 2008 - 13:26:33 PDT)
- Sally Pias (Sat Oct 11 2008 - 22:00:38 PDT)
- Ibrahim Moustafa (Fri Oct 10 2008 - 07:24:30 PDT)
- Sasha Buzko (Thu Oct 09 2008 - 20:48:43 PDT)
- Ross Walker (Thu Oct 09 2008 - 20:29:24 PDT)
- Robert Hanson (Thu Oct 09 2008 - 20:23:48 PDT)
- taufik.alsarraj.utoronto.ca (Thu Oct 09 2008 - 19:35:07 PDT)
AMBER: Clarification re qmmask
- Gustavo Seabra (Thu Oct 16 2008 - 11:22:41 PDT)
- Ross Walker (Thu Oct 16 2008 - 11:14:04 PDT)
- Benjamin Roberts (Thu Oct 16 2008 - 10:24:45 PDT)
AMBER: cnstph test case failure or expected divergence?
- Melinda Layten (Tue Oct 21 2008 - 08:38:31 PDT)
- Ross Walker (Mon Oct 20 2008 - 13:41:27 PDT)
- Melinda Layten (Mon Oct 20 2008 - 13:23:08 PDT)
AMBER: Contacts
- Beale, John (Mon Oct 20 2008 - 07:29:06 PDT)
AMBER: Conversion between truncated octahedron and orthorohombic box
- Gustavo Seabra (Mon Oct 27 2008 - 10:19:59 PDT)
- Ross Walker (Sun Oct 26 2008 - 09:56:50 PDT)
- #NGUYEN CONG TRI# (Sat Oct 25 2008 - 19:36:30 PDT)
AMBER: Differentiating the force constant of distance restraints
- Germain Vallverdu (Thu Oct 16 2008 - 02:07:07 PDT)
- Francesca Poletti (Thu Oct 16 2008 - 01:40:16 PDT)
AMBER: DNA structure analysis
- Bert (Wed Oct 22 2008 - 04:27:38 PDT)
AMBER: Does LEaP understant capping with ACE/NME?
- Francesco Pietra (Tue Oct 21 2008 - 10:31:36 PDT)
- Carlos Simmerling (Tue Oct 21 2008 - 09:02:41 PDT)
- Francesco Pietra (Tue Oct 21 2008 - 08:57:12 PDT)
AMBER: drug/protein interaction modeling setup
- Sean Johnston (Fri Oct 31 2008 - 12:31:56 PDT)
- Bill Ross (Mon Oct 20 2008 - 15:39:04 PDT)
- Barbault Florent (Mon Oct 20 2008 - 13:37:24 PDT)
- Alessandro Nascimento (Mon Oct 20 2008 - 13:21:05 PDT)
- Sean Johnston (Mon Oct 20 2008 - 13:10:52 PDT)
AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2
- Ross Walker (Thu Oct 30 2008 - 10:41:27 PDT)
- John Chodera (Sun Oct 26 2008 - 18:16:48 PDT)
AMBER: energy leakage?
- Sally Pias (Thu Oct 23 2008 - 07:47:28 PDT)
- David A. Case (Thu Oct 23 2008 - 04:00:29 PDT)
- Sally Pias (Thu Oct 23 2008 - 00:25:59 PDT)
AMBER: equilibration
- Carlos Simmerling (Tue Oct 21 2008 - 04:30:12 PDT)
- Urszula Uciechowska (Tue Oct 21 2008 - 04:28:17 PDT)
- Carlos Simmerling (Tue Oct 21 2008 - 04:20:13 PDT)
- Urszula Uciechowska (Tue Oct 21 2008 - 04:17:08 PDT)
- Carlos Simmerling (Tue Oct 21 2008 - 04:01:54 PDT)
- Urszula Uciechowska (Tue Oct 21 2008 - 03:44:54 PDT)
AMBER: Error in creating topology file
- Wei Zhang (Mon Oct 20 2008 - 05:34:40 PDT)
- musa özboyacı (Mon Oct 20 2008 - 04:00:48 PDT)
AMBER: error message of xleap
- Ross Walker (Thu Oct 30 2008 - 21:09:47 PDT)
- Catein Catherine (Thu Oct 30 2008 - 20:40:49 PDT)
AMBER: F modified RNA is split in two parts when running sander simulated annealing
- Peter Podbevšek (Thu Oct 02 2008 - 06:08:51 PDT)
- Andreas Svrcek-Seiler (Wed Oct 01 2008 - 02:56:38 PDT)
- Peter Podbevšek (Wed Oct 01 2008 - 02:01:52 PDT)
AMBER: Folate parameters
- Barbault Florent (Thu Oct 30 2008 - 07:03:09 PDT)
- Michael Lerner (Wed Oct 29 2008 - 10:03:06 PDT)
AMBER: Heme cysteine
- Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 19:46:09 PDT)
- Bill Ross (Tue Oct 21 2008 - 09:20:38 PDT)
- Ross Walker (Tue Oct 21 2008 - 08:17:08 PDT)
- Shaikh Abdul R S Ramaju (Tue Oct 21 2008 - 00:16:50 PDT)
AMBER: High Bfactor values for the terminal residues/atoms
- Carlos Simmerling (Tue Oct 14 2008 - 03:25:25 PDT)
- Siddharth Rastogi (Mon Oct 13 2008 - 21:19:52 PDT)
AMBER: HOLD fixed vs restraint mask
- Ross Walker (Tue Oct 21 2008 - 11:33:32 PDT)
- Taufik Al-Sarraj (Tue Oct 21 2008 - 11:02:34 PDT)
AMBER: How to assign /make the ionion bond?
- steinbrt.rci.rutgers.edu (Fri Oct 17 2008 - 16:06:26 PDT)
- Chih-Ying Lin (Fri Oct 17 2008 - 15:30:07 PDT)
AMBER: how to ger resp charge for a residue?
- WJ Ding (Fri Oct 31 2008 - 07:26:48 PDT)
- FyD (Fri Oct 31 2008 - 06:21:13 PDT)
- Francesco Pietra (Fri Oct 31 2008 - 00:59:31 PDT)
- FyD (Thu Oct 30 2008 - 23:33:42 PDT)
- Ross Walker (Thu Oct 30 2008 - 21:46:43 PDT)
- WJ Ding (Thu Oct 30 2008 - 21:20:05 PDT)
AMBER: How to set up a water slab in Amber?
- David A. Case (Wed Oct 01 2008 - 04:51:17 PDT)
AMBER: Huge difference between pbtot and gbtot in mm-pbsa calculations
- David A. Case (Thu Oct 30 2008 - 06:17:12 PDT)
- moitrayee.mbu.iisc.ernet.in (Thu Oct 30 2008 - 05:49:44 PDT)
- David A. Case (Thu Oct 30 2008 - 04:24:12 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Oct 29 2008 - 22:56:51 PDT)
- Ray Luo (Wed Oct 29 2008 - 09:41:38 PDT)
- moitrayee.mbu.iisc.ernet.in (Wed Oct 29 2008 - 06:07:23 PDT)
AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber
- David A. Case (Tue Oct 28 2008 - 15:15:11 PDT)
- John Chodera (Tue Oct 28 2008 - 08:57:42 PDT)
- David A. Case (Tue Oct 28 2008 - 05:57:22 PDT)
- John Chodera (Mon Oct 27 2008 - 15:12:31 PDT)
AMBER: input
- Germain Vallverdu (Tue Oct 21 2008 - 02:36:40 PDT)
- Urszula Uciechowska (Tue Oct 21 2008 - 02:14:28 PDT)
AMBER: Installation Error
- Jagan Mohan (Wed Oct 15 2008 - 07:03:04 PDT)
- David A. Case (Wed Oct 15 2008 - 06:35:19 PDT)
- Gustavo Seabra (Wed Oct 15 2008 - 06:21:14 PDT)
- Ye Mei (Wed Oct 15 2008 - 01:54:57 PDT)
- Jagan Mohan (Wed Oct 15 2008 - 01:51:03 PDT)
- Scott Brozell (Wed Oct 15 2008 - 01:05:48 PDT)
- Jagan Mohan (Wed Oct 15 2008 - 00:50:18 PDT)
AMBER: installing amber on new linux
- Jan Goeman (Sun Oct 26 2008 - 17:25:49 PDT)
- Scott Brozell (Wed Oct 22 2008 - 16:53:50 PDT)
- Jan Goeman (Wed Oct 22 2008 - 14:06:48 PDT)
AMBER: internal energy INT is not zero from MM_GBSA
- sobereva (Tue Oct 07 2008 - 07:22:57 PDT)
- flyanping (Mon Oct 06 2008 - 23:18:49 PDT)
- Fan Yanping (Mon Oct 06 2008 - 23:08:14 PDT)
AMBER: Is it possible to recover the umbrella file in ABMD simulation after hard disk failure?
- Ye Mei (Sat Oct 25 2008 - 05:32:25 PDT)
AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files
- FyD (Thu Oct 09 2008 - 09:57:07 PDT)
- Robert Hanson (Thu Oct 09 2008 - 09:30:32 PDT)
- Robert Hanson (Thu Oct 09 2008 - 06:59:20 PDT)
- Robert Hanson (Wed Oct 08 2008 - 13:55:26 PDT)
- FyD (Wed Oct 08 2008 - 12:00:33 PDT)
- Robert Hanson (Wed Oct 08 2008 - 11:16:55 PDT)
AMBER: large number of solvent molecules were added for protein with 221 AA residues
- Carlos Simmerling (Tue Oct 14 2008 - 03:21:46 PDT)
- Siddharth Rastogi (Mon Oct 13 2008 - 21:34:58 PDT)
AMBER: Leap atoms CL and OXT do not have a type
- Bill Ross (Thu Oct 02 2008 - 13:09:53 PDT)
- Francesco Pietra (Thu Oct 02 2008 - 12:15:54 PDT)
- Bill Ross (Thu Oct 02 2008 - 10:36:58 PDT)
- Francesco Pietra (Thu Oct 02 2008 - 08:47:31 PDT)
AMBER: LEaP problem with LEU first residue?
- David A. Case (Mon Oct 20 2008 - 04:00:09 PDT)
- KazuoOhta (Sun Oct 19 2008 - 20:04:38 PDT)
- David A. Case (Wed Oct 15 2008 - 06:18:58 PDT)
- Francesco Pietra (Tue Oct 14 2008 - 06:42:55 PDT)
- Carlos Simmerling (Tue Oct 14 2008 - 03:41:01 PDT)
- Francesco Pietra (Tue Oct 14 2008 - 03:26:25 PDT)
AMBER: LEU as first residue
- Francesco Pietra (Mon Oct 13 2008 - 09:20:00 PDT)
AMBER: Lone pairs in antechamber
- David A. Case (Thu Oct 30 2008 - 07:27:31 PDT)
- Diddo Diddens (Thu Oct 30 2008 - 06:25:35 PDT)
AMBER: Metal parameter values
- musa özboyacı (Thu Oct 23 2008 - 12:09:35 PDT)
- Bill Ross (Thu Oct 23 2008 - 11:23:08 PDT)
- musa özboyacı (Thu Oct 23 2008 - 04:59:13 PDT)
AMBER: minimization
- Ross Walker (Fri Oct 31 2008 - 08:44:49 PDT)
- Jacopo Sgrignani (Fri Oct 31 2008 - 01:52:12 PDT)
- Ross Walker (Thu Oct 30 2008 - 11:48:11 PDT)
- Jacopo Sgrignani (Thu Oct 30 2008 - 11:03:29 PDT)
AMBER: MM-PBSA -energy decomposition error
- Cristina Sisu (Wed Oct 22 2008 - 15:07:43 PDT)
AMBER: MM-PBSA error in Amber10: possible bug?
- Pablo Englebienne (Fri Oct 31 2008 - 20:38:15 PDT)
AMBER: MM-PBSA problem : Use of uninitialized value in multiplicatiom with Amber10
- Carra, Claudio (JSC-SK)[USRA] (Wed Oct 01 2008 - 10:05:55 PDT)
AMBER: MM_PBSA binding error
- Ray Luo (Fri Oct 31 2008 - 15:16:41 PDT)
- Larry Layne (Fri Oct 31 2008 - 05:56:42 PDT)
- Ray Luo (Thu Oct 30 2008 - 12:35:36 PDT)
- Larry Layne (Thu Oct 30 2008 - 11:54:24 PDT)
AMBER: MM_PBSA doesn't terminate
- Khaled Barakat (Wed Oct 22 2008 - 08:27:55 PDT)
- Khaled Barakat (Tue Oct 21 2008 - 09:58:12 PDT)
AMBER: MM_PBSA problems in AMBER9
- 欧阳德方 (Mon Oct 06 2008 - 22:19:54 PDT)
- Alessandro Nascimento (Mon Oct 06 2008 - 06:04:37 PDT)
- Ray Luo (Sun Oct 05 2008 - 20:20:01 PDT)
- 欧阳德方 (Sun Oct 05 2008 - 14:30:12 PDT)
AMBER: mm_pbsa_statistics / 3 traj
- Arturas Ziemys (Mon Oct 20 2008 - 09:18:26 PDT)
AMBER: NAD+ parameters problem using tleap
- Ross Walker (Fri Oct 17 2008 - 11:16:41 PDT)
- Dmitri Nilov (Fri Oct 17 2008 - 09:24:50 PDT)
AMBER: Non bond list error
- neville forlemu (Fri Oct 24 2008 - 12:40:08 PDT)
- Robert Duke (Fri Oct 24 2008 - 12:04:53 PDT)
- Robert Duke (Fri Oct 24 2008 - 11:47:33 PDT)
- neville forlemu (Fri Oct 24 2008 - 11:12:58 PDT)
- Robert Duke (Fri Oct 24 2008 - 09:40:24 PDT)
- neville forlemu (Fri Oct 24 2008 - 09:34:44 PDT)
- Robert Duke (Fri Oct 24 2008 - 06:20:29 PDT)
- Ross Walker (Thu Oct 23 2008 - 23:12:20 PDT)
- neville forlemu (Thu Oct 23 2008 - 22:13:13 PDT)
- Ross Walker (Thu Oct 23 2008 - 21:56:32 PDT)
- neville forlemu (Thu Oct 23 2008 - 21:48:01 PDT)
- Wang,Ying (Thu Oct 23 2008 - 14:58:06 PDT)
- Robert Duke (Thu Oct 23 2008 - 13:44:29 PDT)
- Robert Duke (Thu Oct 23 2008 - 13:14:13 PDT)
- Wang,Ying (Thu Oct 23 2008 - 12:26:26 PDT)
- Ross Walker (Thu Oct 23 2008 - 11:38:09 PDT)
- Wang,Ying (Thu Oct 23 2008 - 10:19:49 PDT)
AMBER: nscm code
- Andreas Svrcek-Seiler (Fri Oct 10 2008 - 04:37:09 PDT)
- Carlos Simmerling (Fri Oct 10 2008 - 03:32:25 PDT)
- Naser Alijabbari (Thu Oct 09 2008 - 22:05:59 PDT)
AMBER: Oct 6 deadline for ACS computational chemistry awards
- Carlos Simmerling (Thu Oct 02 2008 - 10:45:35 PDT)
AMBER: Once again, with feeling --- Support for intel mpi in pmemd 10; better support for intel MKL
- David A. Case (Tue Oct 07 2008 - 14:05:07 PDT)
- Robert Duke (Tue Oct 07 2008 - 10:02:51 PDT)
AMBER: Optimal compiling of amber on XT3
- Carlos Simmerling (Thu Oct 30 2008 - 03:22:35 PDT)
- Robert Duke (Wed Oct 29 2008 - 22:59:21 PDT)
- Ross Walker (Wed Oct 29 2008 - 22:33:35 PDT)
- Robert Duke (Wed Oct 29 2008 - 22:31:49 PDT)
- Patrick McCarren (Wed Oct 29 2008 - 21:30:56 PDT)
AMBER: Origin of periodic box
- Gustavo Seabra (Thu Oct 16 2008 - 06:24:50 PDT)
- Ross Walker (Wed Oct 15 2008 - 18:57:47 PDT)
- Naser Alijabbari (Wed Oct 15 2008 - 18:34:00 PDT)
AMBER: Packing density calculation
- Siddharth Rastogi (Thu Oct 30 2008 - 03:41:58 PDT)
AMBER: pairwise interaction energies
- Alessandro Nascimento (Mon Oct 13 2008 - 03:35:39 PDT)
- Thomas Leonard (Sun Oct 12 2008 - 23:12:11 PDT)
AMBER: Parameters for alkali cations and halogen anions
- Francesco Pietra (Sun Oct 05 2008 - 00:29:45 PDT)
AMBER: PDB standards
- Francesco Pietra (Mon Oct 13 2008 - 01:18:23 PDT)
AMBER: pdb structure is only half the molecule.
- Taufik Al-Sarraj (Fri Oct 24 2008 - 16:15:52 PDT)
- Florian Haberl (Fri Oct 24 2008 - 03:18:45 PDT)
- Ye Mei (Thu Oct 23 2008 - 20:21:59 PDT)
- Gustavo Seabra (Thu Oct 23 2008 - 13:19:05 PDT)
- Joel Tyndall (Thu Oct 23 2008 - 13:18:36 PDT)
- Taufik Al-Sarraj (Thu Oct 23 2008 - 12:42:24 PDT)
AMBER: peptide MD
- Carlos Simmerling (Mon Oct 27 2008 - 11:07:11 PDT)
- Gustavo Seabra (Mon Oct 27 2008 - 10:52:25 PDT)
- Beale, John (Mon Oct 27 2008 - 10:47:42 PDT)
- Gustavo Seabra (Mon Oct 27 2008 - 10:36:35 PDT)
- Carlos Simmerling (Mon Oct 27 2008 - 10:35:57 PDT)
- Beale, John (Mon Oct 27 2008 - 10:13:47 PDT)
- Carlos Simmerling (Mon Oct 27 2008 - 10:05:00 PDT)
- Beale, John (Mon Oct 27 2008 - 08:38:48 PDT)
AMBER: Problem installing PMEMD with intel mpi, ifort
- Rupesh Nanjunda (Thu Oct 30 2008 - 08:07:56 PDT)
- Rupesh Nanjunda (Wed Oct 29 2008 - 10:57:06 PDT)
- Robert Duke (Tue Oct 28 2008 - 18:12:17 PDT)
- Ross Walker (Tue Oct 28 2008 - 17:41:39 PDT)
- Rupesh Nanjunda (Tue Oct 28 2008 - 14:07:01 PDT)
AMBER: problem with amber8 installation
- David A. Case (Sat Oct 25 2008 - 06:30:30 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 23:36:27 PDT)
- Ross Walker (Fri Oct 24 2008 - 07:57:52 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 05:22:40 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 05:20:17 PDT)
AMBER: problem with Dihedral angle potentials
- Carlos Simmerling (Thu Oct 30 2008 - 15:07:27 PDT)
- aneesh cna (Thu Oct 30 2008 - 09:35:00 PDT)
- Carlos Simmerling (Thu Oct 30 2008 - 03:20:59 PDT)
- aneesh cna (Thu Oct 30 2008 - 02:11:48 PDT)
- Carlos Simmerling (Wed Oct 29 2008 - 03:09:15 PDT)
- aneesh cna (Wed Oct 29 2008 - 02:23:57 PDT)
AMBER: problem with running mm-pbsa
- moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 23:30:11 PDT)
- Ray Luo (Fri Oct 24 2008 - 09:24:59 PDT)
- moitrayee.mbu.iisc.ernet.in (Fri Oct 24 2008 - 00:14:49 PDT)
AMBER: problem with zMatrix in tleap
- WJ Ding (Fri Oct 31 2008 - 08:48:27 PDT)
- David A. Case (Fri Oct 31 2008 - 07:37:11 PDT)
- WJ Ding (Fri Oct 31 2008 - 07:23:45 PDT)
- David A. Case (Fri Oct 31 2008 - 05:33:44 PDT)
- WJ Ding (Thu Oct 30 2008 - 21:40:59 PDT)
AMBER: ptraj
- John Bennett (Tue Oct 21 2008 - 07:32:07 PDT)
AMBER: ptraj - closest command
- sobereva (Wed Oct 08 2008 - 19:49:46 PDT)
- Ryan Pavlovicz (Wed Oct 08 2008 - 13:49:08 PDT)
- Jianyin Shao (Wed Oct 08 2008 - 12:50:29 PDT)
- Ryan Pavlovicz (Wed Oct 08 2008 - 10:36:17 PDT)
AMBER: ptraj average structure
- Ross Walker (Sat Oct 04 2008 - 07:55:51 PDT)
- Carlos Simmerling (Sat Oct 04 2008 - 06:55:31 PDT)
- Yunierkis Perez Castillo (Sat Oct 04 2008 - 06:25:42 PDT)
AMBER: Ptraj pucker for pyranose
- Neha Gandhi (Mon Oct 13 2008 - 02:43:33 PDT)
AMBER: Query on restart file
- Neha Gandhi (Thu Oct 30 2008 - 19:22:49 PDT)
- Robert Duke (Thu Oct 30 2008 - 19:14:40 PDT)
- Carlos Simmerling (Thu Oct 30 2008 - 19:03:53 PDT)
- Neha Gandhi (Thu Oct 30 2008 - 18:49:30 PDT)
AMBER: question about pression
- Yunierkis Perez Castillo (Mon Oct 13 2008 - 08:33:45 PDT)
- David A. Case (Mon Oct 13 2008 - 07:55:57 PDT)
- Yunierkis Perez Castillo (Mon Oct 13 2008 - 07:45:38 PDT)
AMBER: Question about resp charges for a charged molecule...
- FyD (Fri Oct 10 2008 - 06:37:48 PDT)
- Germain Vallverdu (Fri Oct 10 2008 - 04:20:45 PDT)
- Alberto Sergio Garay (Fri Oct 10 2008 - 03:54:22 PDT)
AMBER: question about simulation box
- Adrien Delmont (Tue Oct 21 2008 - 06:43:24 PDT)
- Gustavo Seabra (Mon Oct 20 2008 - 06:09:03 PDT)
- Adrien Delmont (Sun Oct 19 2008 - 14:04:24 PDT)
AMBER: Question on AMBER MD Implications
- Carlos Simmerling (Fri Oct 31 2008 - 09:51:21 PDT)
- Campbell, Patrick (Fri Oct 31 2008 - 09:27:41 PDT)
AMBER: Question on Urea box
- Antonios Samiotakis (Tue Oct 07 2008 - 12:31:44 PDT)
AMBER: Radius of Gyration
- Carlos Simmerling (Fri Oct 10 2008 - 04:48:21 PDT)
- Beale, John (Fri Oct 10 2008 - 04:27:22 PDT)
AMBER: REDvIII_I_lack_of_charges_in_mol2
- FyD (Wed Oct 22 2008 - 08:15:15 PDT)
- Karol Kaszuba (Sun Oct 19 2008 - 06:00:35 PDT)
- FyD (Sun Oct 19 2008 - 01:12:03 PDT)
- Karol Kaszuba (Sat Oct 18 2008 - 23:57:23 PDT)
- FyD (Sat Oct 18 2008 - 14:30:33 PDT)
- Karol Kaszuba (Sat Oct 18 2008 - 09:32:58 PDT)
- FyD (Sat Oct 18 2008 - 04:54:56 PDT)
- Karol Kaszuba (Sat Oct 18 2008 - 04:08:53 PDT)
AMBER: regarding rigid molecules
- Gustavo Seabra (Thu Oct 16 2008 - 08:16:39 PDT)
- Ross Walker (Thu Oct 16 2008 - 07:53:29 PDT)
- Gustavo Seabra (Thu Oct 16 2008 - 06:34:56 PDT)
- Steven Winfield (Thu Oct 16 2008 - 04:30:31 PDT)
- David A. Case (Thu Oct 16 2008 - 04:06:42 PDT)
- Germain Vallverdu (Thu Oct 16 2008 - 04:02:49 PDT)
- aneesh cna (Thu Oct 16 2008 - 02:34:36 PDT)
AMBER: Regarding sleap - documentation and output behavior
- Keith Van Nostrand (Fri Oct 24 2008 - 08:26:58 PDT)
AMBER: removing COM and rotation in explicit solvation
- David A. Case (Sun Oct 12 2008 - 14:32:54 PDT)
- Naser Alijabbari (Sun Oct 12 2008 - 13:02:22 PDT)
AMBER: Restraining with PMEMD 10
- Francesco Pietra (Sat Oct 25 2008 - 11:57:40 PDT)
- Ross Walker (Sat Oct 25 2008 - 10:25:08 PDT)
- Robert Duke (Sat Oct 25 2008 - 10:12:20 PDT)
- Francesco Pietra (Sat Oct 25 2008 - 09:33:57 PDT)
- Robert Duke (Sat Oct 25 2008 - 05:57:03 PDT)
- Francesco Pietra (Sat Oct 25 2008 - 02:32:39 PDT)
AMBER: Restricting the system to simulate
- Francesco Pietra (Fri Oct 17 2008 - 09:00:50 PDT)
AMBER: Ring flips
- David Watson (Fri Oct 10 2008 - 10:36:36 PDT)
- David Watson (Fri Oct 10 2008 - 10:30:37 PDT)
- Beale, John (Fri Oct 10 2008 - 10:09:52 PDT)
AMBER: saveamberparm error
- Shaikh Abdul R S Ramaju (Thu Oct 09 2008 - 03:53:35 PDT)
- Wei Zhang (Thu Oct 09 2008 - 03:22:45 PDT)
- Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 19:24:58 PDT)
- Ross Walker (Wed Oct 08 2008 - 08:23:12 PDT)
- Shaikh Abdul R S Ramaju (Wed Oct 08 2008 - 04:33:31 PDT)
AMBER: scyld beowulf --amber10--openmpi
- Gustavo Seabra (Mon Oct 20 2008 - 19:56:35 PDT)
- Rima Chaudhuri (Mon Oct 20 2008 - 18:46:13 PDT)
- Ross Walker (Mon Oct 20 2008 - 18:38:04 PDT)
- Rima Chaudhuri (Mon Oct 20 2008 - 17:00:27 PDT)
AMBER: Segmentation fault
- Ross Walker (Tue Oct 14 2008 - 07:53:08 PDT)
- hklwatergod (Mon Oct 13 2008 - 23:52:36 PDT)
AMBER: Setting GROUP for pmemd
- Francesco Pietra (Thu Oct 30 2008 - 23:25:44 PDT)
- Robert Duke (Thu Oct 30 2008 - 19:02:05 PDT)
- Francesco Pietra (Thu Oct 30 2008 - 16:28:37 PDT)
- Robert Duke (Thu Oct 30 2008 - 15:30:07 PDT)
- Francesco Pietra (Thu Oct 30 2008 - 14:56:27 PDT)
- Robert Duke (Thu Oct 30 2008 - 12:29:27 PDT)
- Francesco Pietra (Thu Oct 30 2008 - 12:10:39 PDT)
AMBER: shake the molecule
- David A. Case (Fri Oct 03 2008 - 09:28:32 PDT)
- amit jain (Thu Oct 02 2008 - 22:26:33 PDT)
AMBER: something puzzled with mm_pbsa
- Ray Luo (Mon Oct 27 2008 - 09:56:54 PDT)
- TaoPaul (Fri Oct 24 2008 - 19:08:50 PDT)
- Ray Luo (Fri Oct 24 2008 - 09:21:59 PDT)
- TaoPaul (Fri Oct 24 2008 - 03:50:04 PDT)
AMBER: Sources of disruption during NVE
- Bill Ross (Fri Oct 03 2008 - 08:27:37 PDT)
- Gustavo Seabra (Fri Oct 03 2008 - 06:39:05 PDT)
- Naser Alijabbari (Wed Oct 01 2008 - 18:10:43 PDT)
- Gustavo Seabra (Wed Oct 01 2008 - 12:32:06 PDT)
- Naser Alijabbari (Wed Oct 01 2008 - 08:59:29 PDT)
AMBER: SPCFW problems
- Naser Alijabbari (Tue Oct 28 2008 - 10:57:59 PDT)
- David A. Case (Tue Oct 28 2008 - 15:12:02 PDT)
- Naser Alijabbari (Tue Oct 28 2008 - 08:50:49 PDT)
- David A. Case (Tue Oct 28 2008 - 10:25:23 PDT)
- David A. Case (Tue Oct 28 2008 - 03:49:37 PDT)
- Naser Alijabbari (Mon Oct 27 2008 - 19:37:12 PDT)
AMBER: stripping water from a restart file
- Gustavo Seabra (Mon Oct 27 2008 - 10:12:04 PDT)
- Bill Ross (Fri Oct 24 2008 - 08:21:59 PDT)
- CHAMI F. (Fri Oct 24 2008 - 02:58:58 PDT)
- Bill Ross (Thu Oct 23 2008 - 16:48:59 PDT)
- Carlos Simmerling (Thu Oct 23 2008 - 15:05:07 PDT)
- CHAMI F. (Thu Oct 23 2008 - 14:59:03 PDT)
- Bill Ross (Thu Oct 23 2008 - 11:13:43 PDT)
- Carlos Simmerling (Thu Oct 23 2008 - 05:22:00 PDT)
- CHAMI F. (Thu Oct 23 2008 - 04:33:29 PDT)
- CHAMI F. (Thu Oct 23 2008 - 05:45:19 PDT)
- Bill Ross (Wed Oct 22 2008 - 13:38:11 PDT)
- CHAMI F. (Wed Oct 22 2008 - 13:29:45 PDT)
- Bill Ross (Wed Oct 22 2008 - 10:12:29 PDT)
- Carlos Simmerling (Wed Oct 22 2008 - 09:29:32 PDT)
- CHAMI F. (Wed Oct 22 2008 - 09:11:46 PDT)
AMBER: Support for intel mpi in pmemd 10; better support for intel MKL
- Robert Duke (Fri Oct 03 2008 - 08:43:22 PDT)
- Robert Duke (Thu Oct 02 2008 - 15:39:28 PDT)
- Francesco Pietra (Thu Oct 02 2008 - 14:35:45 PDT)
- Robert Duke (Thu Oct 02 2008 - 13:56:07 PDT)
AMBER: Temperature regulation
- julliane Yoneda (Wed Oct 08 2008 - 10:52:52 PDT)
- Carlos Simmerling (Wed Oct 01 2008 - 19:04:36 PDT)
- julliane Yoneda (Wed Oct 01 2008 - 18:10:27 PDT)
- Carlos Simmerling (Wed Oct 01 2008 - 10:49:26 PDT)
- julliane Yoneda (Wed Oct 01 2008 - 10:22:06 PDT)
AMBER: the install problem
- hklwatergod (Tue Oct 14 2008 - 00:19:02 PDT)
AMBER: the question about "RADIOPT" option in mm_pbsa
- TaoPaul (Sat Oct 25 2008 - 04:11:04 PDT)
AMBER: thermodynamic integration with Amber9
- Ross Walker (Thu Oct 02 2008 - 10:10:57 PDT)
- Sadhna Rana (Thu Oct 02 2008 - 09:08:27 PDT)
- Ross Walker (Thu Oct 02 2008 - 08:24:01 PDT)
- Sadhna Rana (Thu Oct 02 2008 - 08:12:47 PDT)
AMBER: Trouble compiling Amber 9 leap programs on SGI Altix system
- Ross Walker (Fri Oct 31 2008 - 11:22:13 PDT)
- John Finke (Fri Oct 31 2008 - 11:05:57 PDT)
AMBER: Using charmm force field in amber
- David A. Case (Thu Oct 16 2008 - 14:51:45 PDT)
- Ross Walker (Thu Oct 16 2008 - 14:44:30 PDT)
- Harry (Yicun) Ni (Thu Oct 16 2008 - 14:20:45 PDT)
AMBER: using ptraj
- Gustavo Seabra (Fri Oct 17 2008 - 18:35:23 PDT)
- Adrien Delmont (Fri Oct 17 2008 - 14:44:16 PDT)
AMBER: velocity-verlet algorithm and ensembles
- David A. Case (Thu Oct 09 2008 - 05:46:08 PDT)
- oguz gurbulak (Wed Oct 08 2008 - 11:59:46 PDT)
AMBER: xleap fails to savemol2
- FyD (Tue Oct 14 2008 - 12:15:48 PDT)
- FyD (Wed Oct 08 2008 - 23:54:05 PDT)
- taufik.alsarraj.utoronto.ca (Wed Oct 08 2008 - 14:57:30 PDT)
AMBER: Zn2+ Bondi radius value
- Enguerran Vanquelef (Wed Oct 08 2008 - 04:55:21 PDT)
- Sergey Samsonov (Tue Oct 07 2008 - 01:50:10 PDT)
Fwd: AMBER: LEaP problem with LEU first residue?
- Francesco Pietra (Tue Oct 14 2008 - 15:58:08 PDT)
- Scott Brozell (Tue Oct 14 2008 - 14:46:36 PDT)
- Francesco Pietra (Tue Oct 14 2008 - 10:58:33 PDT)
Fwd: AMBER: Restricting the system to simulate
- Francesco Pietra (Sat Oct 18 2008 - 00:44:19 PDT)

Amber Archive Oct 2008 by subject