Amber Archive Apr 2008: by subject

amber help
- Ross Walker (Sat Apr 05 2008 - 20:25:19 PDT)
amber tutorial A3
- Ross Walker (Tue Apr 22 2008 - 21:45:29 PDT)
amber8 files in amber9
- Ross Walker (Wed Apr 30 2008 - 09:24:49 PDT)
- Jena M (Wed Apr 30 2008 - 08:55:45 PDT)
AMBER:
- Florian Haberl (Thu Apr 17 2008 - 08:17:24 PDT)
- Da-Wei Li (Thu Apr 17 2008 - 08:18:04 PDT)
- uccabke.ucl.ac.uk (Thu Apr 17 2008 - 08:02:06 PDT)
AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
- Ross Walker (Tue Apr 29 2008 - 13:57:21 PDT)
- Barbault Florent (Tue Apr 29 2008 - 13:56:09 PDT)
- saurabh agrawal (Sat Apr 26 2008 - 07:15:38 PDT)
- saurabh agrawal (Sun Apr 27 2008 - 22:18:50 PDT)
- Ross Walker (Sat Apr 26 2008 - 22:59:57 PDT)
- Barbault Florent (Sat Apr 26 2008 - 06:13:47 PDT)
- saurabh agrawal (Sat Apr 26 2008 - 04:36:13 PDT)
AMBER: 2D-RMSD
- Tom McGrory (Wed Apr 23 2008 - 08:00:57 PDT)
AMBER: about glycam06
- Austin B. Yongye (Wed Apr 30 2008 - 14:47:32 PDT)
- WANG,YING (Wed Apr 30 2008 - 12:49:46 PDT)
- Austin B. Yongye (Wed Apr 30 2008 - 10:26:44 PDT)
- WANG,YING (Wed Apr 30 2008 - 09:00:12 PDT)
AMBER: Accessing Equilibration Results
- dpandit.brandeis.edu (Thu Apr 17 2008 - 06:29:35 PDT)
AMBER: Amber 8 on Redhat 4 X86_64
- yavuzturkm.prc.boun.edu.tr (Mon Mar 31 2008 - 22:30:32 PDT)
AMBER: amber 9 compilation problem on IBM SP5
- David A. Case (Wed Apr 30 2008 - 11:37:11 PDT)
- Andrew Emerson (Wed Apr 30 2008 - 05:44:38 PDT)
AMBER: Amber 9 run error
- Ross Walker (Tue Apr 08 2008 - 14:52:30 PDT)
- Andrew Borgert (Tue Apr 08 2008 - 14:28:07 PDT)
AMBER: AMBER 9 testing
- Taufik Al-Sarraj (Wed Apr 02 2008 - 19:36:57 PDT)
AMBER: Amber installation
- Ross Walker (Fri Apr 11 2008 - 15:45:42 PDT)
- Mengjuei Hsieh (Fri Apr 11 2008 - 14:39:48 PDT)
- Ross Walker (Fri Apr 11 2008 - 11:09:14 PDT)
- jacopo.sgrignani.unifi.it (Fri Apr 11 2008 - 06:23:24 PDT)
AMBER: Amber10 on Leopard with Intel compilers, "Undefined symbols" error
- Yu Chen (Wed Apr 23 2008 - 11:50:54 PDT)
- David A. Case (Wed Apr 23 2008 - 11:34:30 PDT)
- Yu Chen (Wed Apr 23 2008 - 11:03:13 PDT)
AMBER: Amber9 with MPICH2 failure at runtime
- Sasha Buzko (Wed Apr 16 2008 - 21:49:01 PDT)
- Ross Walker (Wed Apr 16 2008 - 21:25:19 PDT)
- Sasha Buzko (Wed Apr 16 2008 - 17:40:09 PDT)
- David A. Case (Wed Apr 16 2008 - 17:26:05 PDT)
- Sasha Buzko (Wed Apr 16 2008 - 17:06:14 PDT)
- Ross Walker (Wed Apr 16 2008 - 16:47:03 PDT)
- Sasha Buzko (Wed Apr 16 2008 - 15:43:12 PDT)
- Ross Walker (Wed Apr 16 2008 - 15:05:26 PDT)
- Sasha Buzko (Wed Apr 16 2008 - 14:43:07 PDT)
AMBER: AmberTools on OS X Leopard with Intel compilers
- David A. Case (Tue Apr 22 2008 - 08:13:38 PDT)
- Mike Summers (Tue Apr 22 2008 - 05:22:18 PDT)
- Mike Summers (Tue Apr 22 2008 - 05:03:53 PDT)
- Yu Chen (Mon Apr 21 2008 - 20:21:34 PDT)
- David A. Case (Mon Apr 21 2008 - 13:55:26 PDT)
- Yu Chen (Mon Apr 21 2008 - 12:52:16 PDT)
- Scott Brozell (Mon Apr 21 2008 - 13:33:49 PDT)
- David A. Case (Mon Apr 21 2008 - 12:05:38 PDT)
- Scott Brozell (Mon Apr 21 2008 - 13:15:29 PDT)
- Yu Chen (Mon Apr 21 2008 - 11:47:06 PDT)
- Yu Chen (Mon Apr 21 2008 - 07:30:10 PDT)
- David A. Case (Fri Apr 18 2008 - 14:17:32 PDT)
- David A. Case (Fri Apr 18 2008 - 13:44:36 PDT)
- Yu Chen (Fri Apr 18 2008 - 12:17:37 PDT)
AMBER: AMD Opteron: compiler recommendations?
- Sasha Buzko (Sat Apr 26 2008 - 14:15:18 PDT)
- Francesco Pietra (Sat Apr 26 2008 - 13:56:13 PDT)
- Sasha Buzko (Sat Apr 26 2008 - 13:31:23 PDT)
- Francesco Pietra (Sat Apr 26 2008 - 00:05:18 PDT)
- Francesco Pietra (Sat Apr 26 2008 - 00:01:46 PDT)
- Sasha Buzko (Fri Apr 25 2008 - 15:14:19 PDT)
- Robert Duke (Fri Apr 25 2008 - 15:04:58 PDT)
- Sasha Buzko (Fri Apr 25 2008 - 14:54:57 PDT)
AMBER: ANNOUNCE: Release of AmberTools, version 1.0
- David A. Case (Wed Apr 02 2008 - 09:49:20 PDT)
AMBER: ANNOUNCEMENT: release of Amber 10
- David A. Case (Mon Apr 14 2008 - 10:18:40 PDT)
AMBER: anything wrong with this script
- Chih-Ying Lin (Tue Apr 08 2008 - 17:27:50 PDT)
AMBER: aromatic residues lost planarity during MD simulation
- Carlos Simmerling (Mon Apr 21 2008 - 13:25:19 PDT)
- cniu.ualberta.ca (Mon Apr 21 2008 - 13:18:26 PDT)
AMBER: artifacts in ptraj avg output
- stephane acoca (Sat Apr 05 2008 - 02:52:26 PDT)
- Barbault Florent (Sat Apr 05 2008 - 02:11:37 PDT)
- stephane acoca (Sat Apr 05 2008 - 01:46:55 PDT)
AMBER: ASSERTion ' ier == 0 ' failed in nmode.f
- Qi Yan (Mon Apr 14 2008 - 14:50:27 PDT)
- David A. Case (Wed Apr 09 2008 - 22:03:14 PDT)
- Qi Yan (Wed Apr 09 2008 - 16:24:08 PDT)
AMBER: atomic posiltional fluctuation
- Thomas Cheatham III (Tue Apr 01 2008 - 09:50:43 PDT)
- Furia Gargano (Tue Apr 01 2008 - 07:11:12 PDT)
AMBER: Average structure
- Francesco Pietra (Tue Apr 22 2008 - 00:02:23 PDT)
- Ross Walker (Mon Apr 21 2008 - 19:27:08 PDT)
- David Cerutti (Mon Apr 21 2008 - 09:12:30 PDT)
- James Thomas (Mon Apr 21 2008 - 03:21:26 PDT)
AMBER: Azobenzene: dihedral angle CCNN force field parameter
- Adrian Roitberg (Sat Apr 26 2008 - 14:10:25 PDT)
- Chih-Ying Lin (Sat Apr 26 2008 - 12:09:03 PDT)
AMBER: B-factor
- Thomas Cheatham III (Wed Apr 02 2008 - 10:18:18 PDT)
- Furia Gargano (Tue Apr 01 2008 - 12:05:36 PDT)
AMBER: Build a MPI NAB
- David A. Case (Wed Apr 09 2008 - 09:27:28 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 09 2008 - 07:12:57 PDT)
- David A. Case (Tue Apr 08 2008 - 14:35:41 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Tue Apr 08 2008 - 13:19:22 PDT)
- David A. Case (Mon Apr 07 2008 - 14:28:54 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 13:45:53 PDT)
AMBER: calibration of constant pH simulations
- Adrian Roitberg (Wed Apr 30 2008 - 11:05:33 PDT)
- Lillian Chong (Wed Apr 30 2008 - 10:17:47 PDT)
AMBER: Can sander provide ESP with PBC?
- Khatcharin Siriwong (Wed Apr 23 2008 - 18:43:12 PDT)
- Thomas Steinbrecher (Wed Apr 23 2008 - 11:39:10 PDT)
- John Chodera (Mon Apr 21 2008 - 19:24:25 PDT)
- Khatcharin Siriwong (Mon Apr 21 2008 - 18:36:17 PDT)
AMBER: Charge derivation: RESP vs. antechamber
- David A. Case (Tue Apr 29 2008 - 16:40:40 PDT)
- Catein Catherine (Tue Apr 29 2008 - 03:21:55 PDT)
- Catein Catherine (Tue Apr 29 2008 - 03:21:54 PDT)
AMBER: Charge scheme for simulating protonated adenine
- prateeksha s (Wed Apr 09 2008 - 23:19:40 PDT)
- prateeksha s (Wed Apr 09 2008 - 23:11:35 PDT)
AMBER: Collect dihedral angles
- Chih-Ying Lin (Wed Apr 09 2008 - 14:35:09 PDT)
AMBER: compile Amber9 on 64bit AMD Opteron
- David A. Case (Fri Apr 18 2008 - 08:23:48 PDT)
- Jeffrey (Fri Apr 18 2008 - 00:02:24 PDT)
AMBER: Conformation search...
- Anthony Cruz (Thu Apr 17 2008 - 12:32:52 PDT)
AMBER: Constat area simulation
- gurpreet singh (Wed Apr 30 2008 - 04:23:35 PDT)
AMBER: converting from CNS file format
- Sally Pias (Thu Apr 10 2008 - 22:04:55 PDT)
- Sally Pias (Tue Apr 08 2008 - 22:32:11 PDT)
AMBER: cross time correlation function
- David A. Case (Wed Apr 23 2008 - 10:10:46 PDT)
- fatima.chami.durham.ac.uk (Wed Apr 23 2008 - 10:00:43 PDT)
- David A. Case (Wed Apr 23 2008 - 08:55:07 PDT)
- fatima.chami.durham.ac.uk (Wed Apr 23 2008 - 05:55:28 PDT)
AMBER: Cysteine sulphonic acid parameters
- David A. Case (Wed Apr 30 2008 - 17:06:02 PDT)
- Rima Chaudhuri (Wed Apr 30 2008 - 15:48:42 PDT)
AMBER: Distance in z dimension
- Age.Skjevik.student.uib.no (Wed Apr 16 2008 - 07:50:55 PDT)
AMBER: distance matrix command
- priya priya (Wed Apr 30 2008 - 02:01:24 PDT)
AMBER: dockmolecules in examples directory of AmberTools-1.0
- M. L. Dodson (Thu Apr 03 2008 - 08:54:50 PDT)
AMBER: Dose AMBER 10 pmemd support openmpi?
- Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 09:07:39 PDT)
- Robert Duke (Wed Apr 30 2008 - 08:40:44 PDT)
- David A. Case (Wed Apr 30 2008 - 08:22:48 PDT)
- Robert Duke (Wed Apr 30 2008 - 08:16:58 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Wed Apr 30 2008 - 06:04:28 PDT)
AMBER: double strand DNA break up (imaging)
- Thomas Cheatham III (Thu Apr 24 2008 - 12:43:36 PDT)
- Seth Lilavivat (Thu Apr 24 2008 - 11:53:44 PDT)
AMBER: Electric field on atoms in equallibrium
- Tom Darden (Tue Apr 01 2008 - 12:26:32 PDT)
- Lishan Yao (Tue Apr 01 2008 - 11:21:20 PDT)
- Tom Darden (Tue Apr 01 2008 - 10:59:17 PDT)
- Lishan Yao (Tue Apr 01 2008 - 09:55:39 PDT)
AMBER: energy decomposition vs ala scan
- Sergio Wong (Mon Apr 14 2008 - 19:05:41 PDT)
AMBER: error in compilation elsize.cc
- snoze pa (Mon Apr 14 2008 - 11:20:40 PDT)
- David A. Case (Mon Apr 14 2008 - 10:11:33 PDT)
- snoze pa (Mon Apr 14 2008 - 09:38:07 PDT)
AMBER: Error: Bond: Maximum coordination exceeded -- setting atoms pert=true overrides default limits
- David A. Case (Fri Apr 18 2008 - 15:00:23 PDT)
- Ted Fischer (Tue Apr 15 2008 - 02:09:47 PDT)
- David A. Case (Mon Apr 14 2008 - 22:26:45 PDT)
- Ted Fischer (Mon Apr 14 2008 - 05:53:42 PDT)
AMBER: ESP on atoms (2)
- Khatcharin Siriwong (Wed Apr 23 2008 - 07:29:04 PDT)
AMBER: Estimating dielectric constant
- Marcelo Puiatti (Wed Apr 09 2008 - 07:42:40 PDT)
AMBER: Extracting the electric field (and its gradient) on particular solute atoms
- John Chodera (Wed Apr 16 2008 - 15:15:19 PDT)
- Tom Darden (Wed Apr 16 2008 - 14:30:53 PDT)
- John Chodera (Tue Apr 15 2008 - 17:36:01 PDT)
AMBER: FAD and NAD parameters
- Thomas Leonard (Wed Apr 09 2008 - 23:43:47 PDT)
AMBER: Force field Parameters
- Chih-Ying Lin (Wed Apr 09 2008 - 19:17:51 PDT)
AMBER: GAFF
- Eric Germaneau (Fri Apr 04 2008 - 10:49:40 PDT)
- David A. Case (Fri Apr 04 2008 - 08:59:08 PDT)
- Eric Germaneau (Fri Apr 04 2008 - 07:10:31 PDT)
- Eric Germaneau (Fri Apr 04 2008 - 01:27:07 PDT)
- Vlad Cojocaru (Fri Apr 04 2008 - 01:22:30 PDT)
- Vlad Cojocaru (Fri Apr 04 2008 - 01:42:24 PDT)
- Eric Germaneau (Fri Apr 04 2008 - 01:18:03 PDT)
AMBER: Gbsa in NAB
- David A. Case (Thu Apr 10 2008 - 10:24:17 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Thu Apr 10 2008 - 10:04:14 PDT)
AMBER: H atom names in Amber
- uccabke.ucl.ac.uk (Thu Apr 17 2008 - 08:49:57 PDT)
- David A. Case (Thu Apr 17 2008 - 08:16:19 PDT)
AMBER: How to add radius of an atom
- saurabh agrawal (Sun Apr 20 2008 - 22:45:43 PDT)
AMBER: How to change default radius assigned to an atom
- Wei Zhang (Wed Apr 23 2008 - 08:29:03 PDT)
- David A. Case (Mon Apr 21 2008 - 22:36:16 PDT)
- saurabh agrawal (Mon Apr 21 2008 - 21:47:14 PDT)
AMBER: how to change the force field parameters inside the prmtop file?
- Chih-Ying Lin (Tue Apr 08 2008 - 15:39:39 PDT)
- Chih-Ying Lin (Tue Apr 08 2008 - 15:31:27 PDT)
- David A. Case (Tue Apr 08 2008 - 15:08:00 PDT)
- Chih-Ying Lin (Tue Apr 08 2008 - 14:41:38 PDT)
- David A. Case (Mon Apr 07 2008 - 21:58:53 PDT)
- Chih-Ying Lin (Mon Apr 07 2008 - 21:13:39 PDT)
- David A. Case (Mon Apr 07 2008 - 17:05:21 PDT)
- Chih-Ying Lin (Mon Apr 07 2008 - 14:24:17 PDT)
AMBER: How to print out the improper dihedral angles/wilson angles?
- Chih-Ying Lin (Thu Apr 24 2008 - 17:23:51 PDT)
AMBER: hybrid remd imaging
- Geoff Wood (Tue Apr 01 2008 - 00:47:18 PDT)
AMBER: hydrogens are flying in replica exchange simulations
- Carlos Simmerling (Tue Apr 22 2008 - 11:57:11 PDT)
- Ashish Sangwai (Mon Apr 21 2008 - 17:37:51 PDT)
- Karl Kirschner (kkirschn) (Mon Apr 21 2008 - 08:47:37 PDT)
- Carlos Simmerling (Mon Apr 21 2008 - 08:10:46 PDT)
- Carlos Simmerling (Mon Apr 21 2008 - 09:30:12 PDT)
- Adrian Roitberg (Mon Apr 21 2008 - 09:03:06 PDT)
- Adrian Roitberg (Mon Apr 21 2008 - 07:56:33 PDT)
- Ashish Sangwai (Sun Apr 20 2008 - 16:09:03 PDT)
- Carlos Simmerling (Sat Apr 19 2008 - 06:49:56 PDT)
- Ross Walker (Fri Apr 18 2008 - 22:07:54 PDT)
- Ashish Sangwai (Fri Apr 18 2008 - 17:28:02 PDT)
- Ashish Sangwai (Fri Apr 18 2008 - 17:18:32 PDT)
- Carlos Simmerling (Fri Apr 18 2008 - 17:02:39 PDT)
- Ashish Sangwai (Fri Apr 18 2008 - 16:43:01 PDT)
AMBER: Imaging before HBond analysis?
- Evan Kelly (Fri Apr 11 2008 - 16:09:32 PDT)
- Thomas Cheatham III (Fri Apr 11 2008 - 15:52:04 PDT)
- Evan Kelly (Fri Apr 11 2008 - 15:41:51 PDT)
- Thomas Cheatham III (Fri Apr 11 2008 - 15:24:29 PDT)
- Evan Kelly (Fri Apr 11 2008 - 13:34:41 PDT)
AMBER: imaging problem
- Marcin Krol (Tue Apr 15 2008 - 06:38:07 PDT)
- David Smith (Tue Apr 15 2008 - 06:30:48 PDT)
- Marcin Krol (Tue Apr 15 2008 - 06:16:01 PDT)
- Carlos Simmerling (Tue Apr 15 2008 - 05:22:18 PDT)
- Marcin Krol (Tue Apr 15 2008 - 04:54:30 PDT)
AMBER: imem keyword using mmpbsa
- David A. Case (Thu Apr 03 2008 - 21:04:11 PDT)
- Sergio Wong (Thu Apr 03 2008 - 18:18:10 PDT)
- Sergio Wong (Thu Apr 03 2008 - 13:43:01 PDT)
AMBER: Initial Equilibration
- Ross Walker (Thu Apr 10 2008 - 18:29:30 PDT)
- dpandit.brandeis.edu (Thu Apr 10 2008 - 13:45:01 PDT)
AMBER: installing pmemd with fftw
- YangMingjun (Sun Apr 13 2008 - 18:08:16 PDT)
- Robert Duke (Sun Apr 13 2008 - 06:57:36 PDT)
- YangMingjun (Sun Apr 13 2008 - 06:07:44 PDT)
AMBER: Is it possible to run PIMD simulation with QM/MM potential in Amber10?
- David A. Case (Tue Apr 15 2008 - 14:01:15 PDT)
- Ross Walker (Tue Apr 15 2008 - 08:47:53 PDT)
- cgji (Tue Apr 15 2008 - 08:27:08 PDT)
AMBER: JavaGenes
- Shultz, Jack (Mon Apr 14 2008 - 12:26:25 PDT)
AMBER: leap - using default radius 1.500000 for HO3
- Nina Fischer (Wed Apr 16 2008 - 02:08:59 PDT)
AMBER: LEap error message for parmBSC0 force field
- Bill Ross (Thu Apr 03 2008 - 13:16:27 PDT)
- Bill Ross (Thu Apr 03 2008 - 13:12:12 PDT)
- Cenk Andac (Thu Apr 03 2008 - 11:08:58 PDT)
- Bill Ross (Thu Apr 03 2008 - 10:28:51 PDT)
- Alberto Perez (Thu Apr 03 2008 - 07:00:09 PDT)
- Cenk Andac (Thu Apr 03 2008 - 05:52:37 PDT)
- Thomas Cheatham III (Tue Apr 01 2008 - 16:55:38 PDT)
- Cenk Andac (Tue Apr 01 2008 - 16:31:17 PDT)
AMBER: ligand slips out of pocket
- Hannes Wallnoefer (Fri Apr 04 2008 - 00:58:29 PDT)
AMBER: LJ parameters
- aneesh cna (Thu Apr 03 2008 - 04:30:39 PDT)
- Thomas Steinbrecher (Wed Apr 02 2008 - 10:31:57 PDT)
- aneesh cna (Wed Apr 02 2008 - 04:46:22 PDT)
AMBER: loading pdb in leap to create parameter files
- Steve Spronk (Mon Apr 21 2008 - 10:04:34 PDT)
- Cristina Sisu (Tue Apr 15 2008 - 07:50:12 PDT)
- Da-Wei Li (Tue Apr 15 2008 - 06:53:06 PDT)
- Cristina Sisu (Tue Apr 15 2008 - 06:43:57 PDT)
AMBER: loadPdb returns extra atoms
- Thomas Cheatham III (Mon Apr 14 2008 - 12:19:03 PDT)
- Seth Lilavivat (Mon Apr 14 2008 - 11:50:32 PDT)
AMBER: matrxi dist command
- priya priya (Tue Apr 22 2008 - 04:37:50 PDT)
AMBER: meet problems in adding ions and waterbox
- David A. Case (Wed Apr 02 2008 - 09:37:05 PDT)
- Qiang Li (Tue Apr 01 2008 - 23:12:13 PDT)
- David A. Case (Tue Apr 01 2008 - 22:22:52 PDT)
- Qiang Li (Tue Apr 01 2008 - 22:12:31 PDT)
AMBER: memory usage
- David A. Case (Mon Apr 28 2008 - 10:26:22 PDT)
- Ye Mei (Mon Apr 28 2008 - 07:06:20 PDT)
- Ross Walker (Sun Apr 27 2008 - 09:45:16 PDT)
- Ye Mei (Sun Apr 27 2008 - 07:52:42 PDT)
- Ross Walker (Sat Apr 26 2008 - 23:07:04 PDT)
- Ye Mei (Sat Apr 26 2008 - 06:57:44 PDT)
AMBER: Minimisation: cis-azobenzene parameters
- David A. Case (Sat Apr 05 2008 - 14:11:17 PDT)
- Chih-Ying Lin (Sat Apr 05 2008 - 06:45:34 PDT)
AMBER: minimization
- san_amber roy (Tue Apr 22 2008 - 07:01:52 PDT)
AMBER: mm-pbsa multiple trajectory approach?
- Chris Moth (Wed Apr 02 2008 - 14:18:06 PDT)
AMBER: mm_pbsa error
- Scott Pendley (Fri Apr 04 2008 - 09:29:16 PDT)
- stephane acoca (Thu Apr 03 2008 - 13:21:29 PDT)
- rams rams (Thu Apr 03 2008 - 09:28:56 PDT)
AMBER: mmpbsa with gromacs trajectory
- jacopo.sgrignani.unifi.it (Tue Apr 15 2008 - 07:10:21 PDT)
AMBER: MPI run problem
- Qi Yan (Thu Apr 03 2008 - 14:59:27 PDT)
- Robert Duke (Thu Apr 03 2008 - 13:57:33 PDT)
- David A. Case (Thu Apr 03 2008 - 13:38:38 PDT)
- Qi Yan (Thu Apr 03 2008 - 09:33:19 PDT)
AMBER: multiple dihedral restraints using group
- David A. Case (Wed Apr 02 2008 - 13:44:20 PDT)
AMBER: NAB examples
- David A. Case (Mon Apr 07 2008 - 10:42:34 PDT)
- Andreas Svrcek-Seiler (Mon Apr 07 2008 - 09:46:34 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 09:43:06 PDT)
- David A. Case (Mon Apr 07 2008 - 09:26:58 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 09:09:44 PDT)
- David A. Case (Mon Apr 07 2008 - 08:33:26 PDT)
- Hu, Shaowen (JSC-SK)[USRA] (Mon Apr 07 2008 - 07:32:07 PDT)
AMBER: NAD parameters
- Ross Walker (Thu Apr 03 2008 - 07:56:45 PDT)
- David A. Case (Thu Apr 03 2008 - 08:01:46 PDT)
- Urszula Uciechowska (Thu Apr 03 2008 - 07:30:05 PDT)
AMBER: nmode
- David A. Case (Mon Apr 21 2008 - 14:05:20 PDT)
- jacopo.sgrignani.unifi.it (Mon Apr 21 2008 - 10:38:44 PDT)
AMBER: nmode output
- Lachele Foley (Lists) (Fri Apr 25 2008 - 07:09:37 PDT)
- jacopo.sgrignani.unifi.it (Fri Apr 25 2008 - 01:36:35 PDT)
AMBER: nmode problem
- Hannes Wallnoefer (Fri Apr 18 2008 - 02:44:38 PDT)
- Hannes Wallnoefer (Fri Apr 18 2008 - 02:01:27 PDT)
AMBER: Nmode segmentation fault
- David A. Case (Wed Apr 02 2008 - 10:50:09 PDT)
AMBER: NMR restraints
- David A. Case (Mon Apr 28 2008 - 08:20:53 PDT)
- Ilyas Yildirim (Sun Apr 27 2008 - 23:53:51 PDT)
AMBER: parallel error : undefined reference to `MAIN_'
- Arturas Ziemys (Fri Apr 25 2008 - 14:14:59 PDT)
AMBER: Parrallel computing
- Ross Walker (Mon Apr 28 2008 - 23:09:44 PDT)
- Chih-Ying Lin (Mon Apr 28 2008 - 17:14:10 PDT)
AMBER: Performance issues on Ethernet clusters
- Sasha Buzko (Thu Apr 17 2008 - 14:18:44 PDT)
- Robert Duke (Thu Apr 17 2008 - 13:14:32 PDT)
- David A. Case (Thu Apr 17 2008 - 12:02:45 PDT)
- Sasha Buzko (Thu Apr 17 2008 - 11:20:52 PDT)
AMBER: pmemd: "undefined reference to `mpi_(name-varies)'"
- Robert Duke (Thu Apr 24 2008 - 12:45:31 PDT)
- Lachele Foley (Lists) (Thu Apr 24 2008 - 12:16:50 PDT)
- Gustavo Seabra (Thu Apr 24 2008 - 10:51:10 PDT)
- Robert Duke (Thu Apr 24 2008 - 08:04:31 PDT)
- Lachele Foley (Lists) (Thu Apr 24 2008 - 07:22:42 PDT)
AMBER: PMF calculation for binding constant or rate constant?
- David A. Case (Wed Apr 16 2008 - 14:26:13 PDT)
- Catein Catherine (Tue Apr 15 2008 - 19:26:46 PDT)
AMBER: PMF calculation for rate constant or binding constant?
- Catein Catherine (Tue Apr 15 2008 - 19:28:43 PDT)
AMBER: pressure varies in constant pressure membrane simulation
- Vijay Manickam Achari (Tue Apr 22 2008 - 21:10:54 PDT)
- David A. Case (Tue Apr 22 2008 - 11:31:53 PDT)
- Vijay Manickam Achari (Mon Apr 21 2008 - 22:58:29 PDT)
AMBER: prmtop spec trivia
- Lachele Foley (Lists) (Tue Apr 29 2008 - 12:21:43 PDT)
- David A. Case (Tue Apr 29 2008 - 11:58:30 PDT)
- Lachele Foley (Lists) (Tue Apr 29 2008 - 11:25:53 PDT)
- Ross Walker (Tue Apr 29 2008 - 10:55:02 PDT)
- Lachele Foley (Lists) (Tue Apr 29 2008 - 09:13:41 PDT)
- Ross Walker (Tue Apr 29 2008 - 08:34:04 PDT)
- Lachele Foley (Lists) (Tue Apr 29 2008 - 08:07:29 PDT)
AMBER: problem with Mg2+ during MD
- Zhenwei Lu (Thu Apr 03 2008 - 09:48:13 PDT)
AMBER: Problems compiling Amber with MKL
- Sasha Buzko (Mon Apr 14 2008 - 16:24:05 PDT)
- Sasha Buzko (Mon Apr 14 2008 - 15:25:43 PDT)
- Ross Walker (Mon Apr 14 2008 - 14:32:49 PDT)
- Sasha Buzko (Mon Apr 14 2008 - 12:13:23 PDT)
AMBER: Protein rotating out of box
- David A. Case (Tue Apr 08 2008 - 18:54:29 PDT)
- Lars Skjærven (Wed Apr 02 2008 - 14:01:54 PDT)
- Lars Skjærven (Wed Apr 02 2008 - 12:17:23 PDT)
- Qiang Li (Wed Apr 02 2008 - 10:35:04 PDT)
- Thomas Cheatham III (Wed Apr 02 2008 - 09:54:46 PDT)
- Steve Spronk (Wed Apr 02 2008 - 06:13:12 PDT)
- Lars Skjærven (Wed Apr 02 2008 - 05:36:20 PDT)
- Steve Spronk (Tue Apr 01 2008 - 07:55:20 PDT)
AMBER: protein-ligand complex problem
- David A. Case (Thu Apr 10 2008 - 16:51:55 PDT)
- Ross Walker (Thu Apr 10 2008 - 16:50:19 PDT)
- Lynn (Thu Apr 10 2008 - 15:51:32 PDT)
AMBER: Protonation states in Constant pH Simulations
- Neil Bruce (Wed Apr 16 2008 - 05:54:44 PDT)
AMBER: ptraj / covariance / quasiharmonic approximation / entropy
- Chris Moth (Wed Apr 02 2008 - 14:09:14 PDT)
- Seth Lilavivat (Wed Apr 02 2008 - 12:18:55 PDT)
AMBER: query about Generalized Born simulation
- rpaduri.chem.wayne.edu (Fri Apr 11 2008 - 07:31:21 PDT)
- Carlos Simmerling (Fri Apr 11 2008 - 07:15:53 PDT)
- gurvisha.leadinvent.com (Fri Apr 11 2008 - 06:42:23 PDT)
AMBER: query regarding energy minimization
- Ross Walker (Mon Apr 28 2008 - 23:16:11 PDT)
- D.Usharani (Mon Apr 28 2008 - 22:20:29 PDT)
- Deepangi Pandit (Mon Apr 28 2008 - 07:39:39 PDT)
- rpaduri.chem.wayne.edu (Mon Apr 28 2008 - 07:26:25 PDT)
- Anamika Awasthi (Mon Apr 28 2008 - 06:22:24 PDT)
AMBER: query regarding loadpadb
- Reena ..... (Fri Apr 25 2008 - 04:07:21 PDT)
- Anamika Awasthi (Fri Apr 25 2008 - 01:33:19 PDT)
AMBER: questions about run MD at different pH
- Taufik Al-Sarraj (Tue Apr 15 2008 - 15:47:10 PDT)
- David A. Case (Tue Apr 15 2008 - 13:59:27 PDT)
- Taufik Al-Sarraj (Tue Apr 15 2008 - 13:06:39 PDT)
- David A. Case (Tue Apr 15 2008 - 10:19:11 PDT)
- Taufik Al-Sarraj (Tue Apr 15 2008 - 09:15:28 PDT)
AMBER: Read trajectories generated by CHARMM
- Jeffrey (Mon Apr 28 2008 - 17:58:36 PDT)
- David A. Case (Mon Apr 28 2008 - 08:25:13 PDT)
- Jeffrey (Mon Apr 28 2008 - 06:06:17 PDT)
AMBER: refine cyana structures!
- Hongyan Li (Tue Apr 22 2008 - 18:33:08 PDT)
AMBER: regarding segfault during energy minimization
- Ross Walker (Tue Apr 29 2008 - 22:40:21 PDT)
- Anamika Awasthi (Tue Apr 29 2008 - 22:13:21 PDT)
AMBER: Regarding SHAKE
- David A. Case (Wed Apr 02 2008 - 10:54:59 PDT)
AMBER: REMD simulation error
- Guillaume Renvez (Wed Apr 02 2008 - 05:47:20 PDT)
AMBER: reproducing http://amber.scripps.edu/tutorials/advanced/tutorial6/index.htm with explicit water
- David A. Case (Mon Apr 07 2008 - 13:40:27 PDT)
AMBER: residual dipolar couplings - alignment tensor energy
- David A. Case (Wed Apr 02 2008 - 10:53:38 PDT)
- Douglas Kojetin (Tue Apr 01 2008 - 08:53:55 PDT)
- Douglas Kojetin (Tue Apr 01 2008 - 08:23:59 PDT)
AMBER: RESP charges
- Jena M (Tue Apr 22 2008 - 05:31:54 PDT)
AMBER: restraint box dimension
- Carlos Simmerling (Fri Apr 11 2008 - 03:22:38 PDT)
- aneesh cna (Fri Apr 11 2008 - 02:56:17 PDT)
- David A. Case (Tue Apr 08 2008 - 17:34:05 PDT)
- aneesh cna (Tue Apr 08 2008 - 03:45:20 PDT)
AMBER: Restraintmask and Restraint_WT : Question
- Thomas Steinbrecher (Fri Apr 04 2008 - 09:18:17 PDT)
- dpandit.brandeis.edu (Fri Apr 04 2008 - 08:24:32 PDT)
AMBER: running minimisation on cis-azobenzene
- Chih-Ying Lin (Tue Apr 08 2008 - 15:27:52 PDT)
- Junmei Wang (Tue Apr 08 2008 - 15:11:35 PDT)
- Chih-Ying Lin (Tue Apr 08 2008 - 15:00:20 PDT)
- Chih-Ying Lin (Tue Apr 08 2008 - 14:51:51 PDT)
- Junmei Wang (Tue Apr 08 2008 - 14:37:54 PDT)
- Thomas Steinbrecher (Tue Apr 08 2008 - 13:37:39 PDT)
- Chih-Ying Lin (Mon Apr 07 2008 - 21:40:20 PDT)
- Chih-Ying Lin (Mon Apr 07 2008 - 11:03:18 PDT)
- Thomas Steinbrecher (Mon Apr 07 2008 - 10:39:18 PDT)
- Chih-Ying Lin (Mon Apr 07 2008 - 10:31:51 PDT)
- Chih-Ying Lin (Mon Apr 07 2008 - 10:10:43 PDT)
- David A. Case (Mon Apr 07 2008 - 08:39:24 PDT)
- Chih-Ying Lin (Sun Apr 06 2008 - 17:33:11 PDT)
- Chih-Ying Lin (Sat Apr 05 2008 - 06:33:46 PDT)
AMBER: running minimisation on cis-azobenzene----an electron-withdrew atom
- Chih-Ying Lin (Tue Apr 08 2008 - 14:45:51 PDT)
AMBER: sander & imin=5
- David A. Case (Fri Apr 25 2008 - 11:38:25 PDT)
- Xioling Chuang (Thu Apr 24 2008 - 00:03:09 PDT)
AMBER: sander.MPI setup with SGE
- Sasha Buzko (Mon Apr 07 2008 - 13:51:20 PDT)
- Ross Walker (Sat Apr 05 2008 - 09:18:45 PDT)
- Sasha Buzko (Fri Apr 04 2008 - 09:59:34 PDT)
AMBER: saveamberparm
- David A. Case (Thu Apr 24 2008 - 07:58:20 PDT)
- taufik.alsarraj.utoronto.ca (Wed Apr 23 2008 - 17:38:16 PDT)
- taufik.alsarraj.utoronto.ca (Wed Apr 23 2008 - 17:34:02 PDT)
AMBER: Scale LJ parameters
- David A. Case (Thu Apr 17 2008 - 17:54:43 PDT)
- fatima.chami.durham.ac.uk (Thu Apr 17 2008 - 04:20:40 PDT)
AMBER: segmentation fault in SANDER
- Ross Walker (Tue Apr 29 2008 - 07:15:08 PDT)
- Anamika Awasthi (Tue Apr 29 2008 - 04:44:29 PDT)
AMBER: Short trajectory segments / frequent restarts causes explosion
- Robert Duke (Thu Apr 17 2008 - 14:52:55 PDT)
- David Cerutti (Thu Apr 17 2008 - 14:04:14 PDT)
AMBER: Should the two phenyl rings of the trans-azobenzene on the same plane after minimisation?
- Chih-Ying Lin (Tue Apr 08 2008 - 18:09:24 PDT)
- Chih-Ying Lin (Tue Apr 08 2008 - 18:03:53 PDT)
AMBER: Si parameters for MD (AMBER9)
- Taufik Al-Sarraj (Fri Apr 25 2008 - 15:08:44 PDT)
AMBER: SiCortex as an alternative to Ethernet and infiniband clusters
- Sasha Buzko (Thu Apr 17 2008 - 15:39:46 PDT)
- Kevin Abbey (Thu Apr 17 2008 - 14:37:23 PDT)
AMBER: Simple Minimization - Error
- Daniel Smith (Thu Apr 03 2008 - 13:10:28 PDT)
- David A. Case (Thu Apr 03 2008 - 13:11:13 PDT)
- dpandit.brandeis.edu (Thu Apr 03 2008 - 12:55:08 PDT)
AMBER: Simulating DNA Backbone in NAB
- David A. Case (Wed Apr 02 2008 - 13:24:25 PDT)
- Adelene Sim (Tue Apr 01 2008 - 12:23:16 PDT)
AMBER: solvateOct produces strange residues compared to solvateCap
- David A. Case (Thu Apr 10 2008 - 12:29:52 PDT)
- Markus Kaukonen (Fri Apr 04 2008 - 01:08:53 PDT)
AMBER: tempi in Replica Exchange
- Carlos Simmerling (Thu Apr 10 2008 - 08:37:46 PDT)
- rebeca.mmb.pcb.ub.es (Thu Apr 10 2008 - 02:23:00 PDT)
AMBER: TIP5P water simulation with AMBER7
- Biman Jana (Tue Apr 01 2008 - 00:14:54 PDT)
AMBER: topology file
- David A. Case (Wed Apr 16 2008 - 10:45:52 PDT)
- Giuseppe De Marco (Mon Apr 14 2008 - 02:38:37 PDT)
AMBER: Topology file format for Amber9
- David A. Case (Wed Apr 23 2008 - 09:01:13 PDT)
- Xioling Chuang (Tue Apr 22 2008 - 22:41:32 PDT)
AMBER: Trans-azobenzene and cis-azobenzene
- Chih-Ying Lin (Mon Apr 07 2008 - 11:13:01 PDT)
AMBER: trans-azobenzene under minimisation
- Chih-Ying Lin (Thu Apr 10 2008 - 17:29:37 PDT)
AMBER: Tutorial B3- Section6
- Carlos Simmerling (Fri Apr 11 2008 - 03:26:28 PDT)
- Chih-Ying Lin (Thu Apr 10 2008 - 16:50:14 PDT)
- Chih-Ying Lin (Wed Apr 09 2008 - 19:13:32 PDT)
- David A. Case (Wed Apr 09 2008 - 18:46:16 PDT)
- Chih-Ying Lin (Wed Apr 09 2008 - 18:30:27 PDT)
AMBER: Tutorial B5
- Chih-Ying Lin (Wed Apr 23 2008 - 20:08:19 PDT)
- Ross Walker (Wed Apr 23 2008 - 19:06:42 PDT)
- Chih-Ying Lin (Wed Apr 23 2008 - 18:09:23 PDT)
- Alessandro Nascimento (Wed Apr 23 2008 - 17:25:12 PDT)
- Chih-Ying Lin (Wed Apr 23 2008 - 15:13:56 PDT)
AMBER: Using mdcrd files to look at minor charge changes
- David A. Case (Thu Apr 03 2008 - 12:46:46 PDT)
- Cooper, Matthew (Thu Apr 03 2008 - 11:45:12 PDT)
AMBER: vlimit-problems after image and restart
- Ross Walker (Tue Apr 22 2008 - 21:45:29 PDT)
- Anselm Horn (Tue Apr 22 2008 - 02:04:46 PDT)
AMBER: WARNING in readAmberTrajectory(): Set #7918 is corrupted (-)
- zachary hartman (Wed Apr 09 2008 - 07:00:45 PDT)
AMBER: water in the binding site MMPBSA
- jacopo.sgrignani.unifi.it (Thu Apr 24 2008 - 06:51:43 PDT)
AMBER: WHAM: how frequently do I need data on the system coordinates?
- John Chodera (Thu Apr 10 2008 - 10:47:57 PDT)
- David Cerutti (Thu Apr 10 2008 - 09:14:23 PDT)
AMBER: Whole System Equilibration & Pressure
- dpandit.brandeis.edu (Tue Apr 15 2008 - 07:16:35 PDT)
- Ross Walker (Mon Apr 14 2008 - 14:37:51 PDT)
- dpandit.brandeis.edu (Mon Apr 14 2008 - 13:57:54 PDT)
AMBER: working with unformatted restart files in AMBER9
- Thomas Cheatham III (Wed Apr 02 2008 - 10:26:00 PDT)
- Vlad Cojocaru (Tue Apr 01 2008 - 06:35:57 PDT)
AMBER: xleap segmentation fault on SaveAmberParm
- David A. Case (Tue Apr 15 2008 - 14:00:47 PDT)
- Wei Zhang (Tue Apr 15 2008 - 12:32:32 PDT)
- Brendan Duggan (Tue Apr 15 2008 - 12:15:46 PDT)
AMBER: xLeap unit editor "seg fault"
- David A. Case (Thu Apr 17 2008 - 17:53:29 PDT)
- inonshar.post.tau.ac.il (Wed Apr 16 2008 - 22:49:01 PDT)

Amber Archive Apr 2008 by subject