Amber Archive Oct 2004: by subject

AMBER:
- Jiten (Fri Oct 22 2004 - 08:17:15 PDT)
AMBER: (no subject)
- HL Eastwood (Thu Oct 14 2004 - 09:33:34 PDT)
- Rasha Radwan (Fri Oct 01 2004 - 07:30:53 PDT)
AMBER: A question on AMBER8 installation
- Robert Duke (Wed Oct 20 2004 - 05:35:00 PDT)
- David A. Case (Tue Oct 19 2004 - 22:04:36 PDT)
- Hwankyu Lee (Tue Oct 19 2004 - 21:12:20 PDT)
- David A. Case (Tue Oct 19 2004 - 16:27:08 PDT)
- Hwankyu Lee (Tue Oct 19 2004 - 13:43:48 PDT)
- David A. Case (Fri Oct 15 2004 - 07:58:29 PDT)
- Hwankyu Lee (Thu Oct 14 2004 - 20:01:05 PDT)
- M. L. Dodson (Thu Oct 14 2004 - 11:41:15 PDT)
- David A. Case (Thu Oct 14 2004 - 11:22:14 PDT)
- Hwankyu Lee (Thu Oct 14 2004 - 11:13:33 PDT)
- Hwankyu Lee (Thu Oct 14 2004 - 10:57:45 PDT)
- Ross Walker (Thu Oct 14 2004 - 09:50:25 PDT)
- David A. Case (Thu Oct 14 2004 - 09:45:30 PDT)
- Hwankyu Lee (Thu Oct 14 2004 - 09:04:18 PDT)
- Ross Walker (Wed Oct 13 2004 - 13:21:27 PDT)
- Hwankyu Lee (Wed Oct 13 2004 - 10:53:30 PDT)
- Scott Brozell (Wed Oct 13 2004 - 10:24:51 PDT)
- Bill Ross (Wed Oct 13 2004 - 10:13:48 PDT)
- David A. Case (Wed Oct 13 2004 - 07:58:58 PDT)
- Ross Walker (Tue Oct 12 2004 - 22:43:49 PDT)
- Hwankyu Lee (Tue Oct 12 2004 - 21:39:33 PDT)
AMBER: a question on ntwx and ntwr
- Carlos Simmerling (Thu Oct 28 2004 - 08:50:10 PDT)
- scopio (Thu Oct 28 2004 - 07:42:14 PDT)
AMBER: A torsion parameter in AMBER2003 force field
- Yong Duan (Fri Oct 08 2004 - 10:41:41 PDT)
- David A. Case (Fri Oct 08 2004 - 09:53:21 PDT)
- Scott E. Boesch (Fri Oct 08 2004 - 09:23:41 PDT)
AMBER: about AM1-BCC charge method
- Xiao He (Mon Oct 18 2004 - 06:59:43 PDT)
- Natasja Brooijmans (Mon Oct 18 2004 - 06:38:11 PDT)
AMBER: about antechamber
- David A. Case (Mon Oct 11 2004 - 09:13:05 PDT)
- MURAT CETINKAYA (Sat Oct 09 2004 - 18:48:52 PDT)
AMBER: About missing residues
- FyD (Mon Oct 11 2004 - 22:27:58 PDT)
AMBER: About STD in NMODE
- Xiao He (Wed Oct 20 2004 - 09:06:15 PDT)
AMBER: add charge error message: Number of electrons is odd
- David A. Case (Fri Oct 22 2004 - 14:12:00 PDT)
- berry1027 Eric (Fri Oct 22 2004 - 01:45:30 PDT)
AMBER: AddIons
- Bill Ross (Thu Oct 07 2004 - 12:36:24 PDT)
- Vincent Bisetty (Thu Oct 07 2004 - 05:15:03 PDT)
AMBER: AM1-BCC charges
- Oliver Hucke (Tue Oct 26 2004 - 18:29:02 PDT)
- Xin Hu (Tue Oct 26 2004 - 17:19:04 PDT)
AMBER: Amber 8 - OS support.
- Poh-Guan Khoo (Thu Oct 14 2004 - 22:54:27 PDT)
AMBER: AMBER 8 default is now HIS->HIE and not HIS->HID - typo?
- David A. Case (Thu Oct 28 2004 - 09:50:34 PDT)
- Chris Moth (Tue Oct 26 2004 - 13:24:05 PDT)
AMBER: amber 8 error
- Carlos Simmerling (Tue Oct 19 2004 - 04:22:37 PDT)
- Atro Tossavainen (Tue Oct 19 2004 - 03:23:23 PDT)
- Andreas Svrcek-Seiler (Tue Oct 19 2004 - 02:00:59 PDT)
- Abd Ghani Abd Aziz (Tue Oct 19 2004 - 01:14:24 PDT)
- Ross Walker (Sat Oct 16 2004 - 22:20:34 PDT)
- Abd Ghani Abd Aziz (Sat Oct 16 2004 - 02:19:38 PDT)
- Abd Ghani Bin Abd Aziz (Sat Oct 02 2004 - 02:26:10 PDT)
- Tomas Linhart (Sat Oct 02 2004 - 01:04:43 PDT)
- Abd Ghani Bin Abd Aziz (Sat Oct 02 2004 - 00:25:30 PDT)
AMBER: AMBER 8 installation - continued
- Atro Tossavainen (Tue Oct 12 2004 - 00:37:24 PDT)
- Ross Walker (Mon Oct 11 2004 - 10:17:50 PDT)
- Atro Tossavainen (Mon Oct 11 2004 - 01:57:45 PDT)
AMBER: AMBER 8 installation trouble
- David A. Case (Fri Oct 15 2004 - 07:51:59 PDT)
- Atro Tossavainen (Fri Oct 15 2004 - 00:20:54 PDT)
- Atro Tossavainen (Tue Oct 12 2004 - 23:56:19 PDT)
- David A. Case (Tue Oct 12 2004 - 10:28:14 PDT)
- Atro Tossavainen (Tue Oct 12 2004 - 00:29:23 PDT)
- David A. Case (Mon Oct 11 2004 - 08:43:44 PDT)
- Atro Tossavainen (Mon Oct 11 2004 - 01:36:44 PDT)
AMBER: amber 8 parallel problem
- Ross Walker (Sun Oct 17 2004 - 11:05:33 PDT)
- Ross Walker (Sat Oct 16 2004 - 22:28:51 PDT)
- Abd Ghani Abd Aziz (Sat Oct 16 2004 - 03:47:44 PDT)
AMBER: amber with MPI
- Stefano.Pieraccini.unimi.it (Mon Oct 04 2004 - 07:40:16 PDT)
AMBER: amber7 test on osx
- Ross Walker (Fri Oct 29 2004 - 11:38:31 PDT)
- Michael Crowley (Fri Oct 29 2004 - 11:31:09 PDT)
- Knut Langsetmo (Fri Oct 29 2004 - 11:03:25 PDT)
AMBER: Amber8 - Energy Calculations
- David A. Case (Thu Oct 14 2004 - 10:55:38 PDT)
- Nhat-hang Duong (Thu Oct 14 2004 - 08:53:29 PDT)
AMBER: Amber8 compilation in Dec-Alpha
- Ross Walker (Mon Oct 11 2004 - 10:09:40 PDT)
- Jiten (Sun Oct 10 2004 - 09:22:01 PDT)
AMBER: amber8 compilation on AIX (regatta)
- David A. Case (Thu Oct 14 2004 - 10:36:28 PDT)
- SEKIJIMA Masakazu (Thu Oct 14 2004 - 06:41:40 PDT)
AMBER: Amber8: ifort 8.0.046 Woo hoo!
- Atro Tossavainen (Fri Oct 15 2004 - 05:38:59 PDT)
- Atro Tossavainen (Fri Oct 15 2004 - 03:55:27 PDT)
- HL Eastwood (Fri Oct 15 2004 - 03:36:57 PDT)
AMBER: Amber: what different?
- David A. Case (Sun Oct 24 2004 - 07:17:47 PDT)
AMBER: Antechamber on cluster with queue?
- David A. Case (Wed Oct 06 2004 - 09:31:53 PDT)
- opitz.che.udel.edu (Wed Oct 06 2004 - 09:06:43 PDT)
- David A. Case (Wed Oct 06 2004 - 08:24:17 PDT)
- opitz.che.udel.edu (Wed Oct 06 2004 - 08:08:25 PDT)
AMBER: antechamber, mopac RESTART
- opitz.che.udel.edu (Sun Oct 03 2004 - 11:41:24 PDT)
AMBER: atoms out of bounds
- Carlos Simmerling (Thu Oct 07 2004 - 05:17:15 PDT)
- Balvinder Singh (Thu Oct 07 2004 - 14:27:45 PDT)
AMBER: BOND energy during minimisation
- cailliez (Wed Oct 20 2004 - 00:16:26 PDT)
- Carlos Simmerling (Tue Oct 19 2004 - 10:33:52 PDT)
- cailliez (Tue Oct 19 2004 - 09:12:55 PDT)
- David A. Case (Tue Oct 19 2004 - 07:59:46 PDT)
- Carlos Simmerling (Tue Oct 19 2004 - 04:21:28 PDT)
- Stef (Tue Oct 19 2004 - 01:35:05 PDT)
- cailliez (Tue Oct 19 2004 - 00:53:47 PDT)
AMBER: Box information from Amber
- Carlos Simmerling (Sat Oct 09 2004 - 11:00:43 PDT)
- Priti Hansia (Sat Oct 09 2004 - 10:51:16 PDT)
- Carlos Simmerling (Sat Oct 09 2004 - 05:10:56 PDT)
- Priti Hansia (Sat Oct 09 2004 - 04:19:46 PDT)
AMBER: building a small molecule
- Oliver Hucke (Tue Oct 05 2004 - 10:15:00 PDT)
- mathew k varghese (Tue Oct 05 2004 - 02:01:09 PDT)
AMBER: Calculating H-Bond networks using ptraj
- Thomas Steinbrecher (Mon Oct 18 2004 - 07:12:05 PDT)
AMBER: Carnal & Radius of gyration
- Bill Ross (Tue Oct 12 2004 - 14:51:30 PDT)
- opitz.che.udel.edu (Tue Oct 12 2004 - 14:29:26 PDT)
AMBER: changepot
- Cai, Yufeng (Fri Oct 15 2004 - 11:33:08 PDT)
AMBER: changepot & mol2 file
- FyD (Fri Oct 15 2004 - 11:59:46 PDT)
AMBER: Comparison of simulation results on amber7 and amber 8
- Carlos Simmerling (Wed Oct 06 2004 - 10:21:54 PDT)
- Sergio E. Wong (Wed Oct 06 2004 - 09:54:44 PDT)
- Carlos Simmerling (Wed Oct 06 2004 - 06:36:03 PDT)
- anshul.imtech.res.in (Wed Oct 06 2004 - 13:28:04 PDT)
AMBER: Compiling using pgf90
- David Lomelin (Wed Oct 06 2004 - 13:30:34 PDT)
- Craig TOEPFER (Wed Oct 06 2004 - 09:52:06 PDT)
- David Lomelin (Tue Oct 05 2004 - 18:33:22 PDT)
AMBER: const-P MD at high T
- Bill Ross (Mon Oct 18 2004 - 12:16:26 PDT)
- Carlos Simmerling (Mon Oct 18 2004 - 11:29:35 PDT)
- Bill Ross (Mon Oct 18 2004 - 11:26:26 PDT)
- MURAT CETINKAYA (Mon Oct 18 2004 - 11:13:07 PDT)
- Bill Ross (Mon Oct 18 2004 - 10:47:58 PDT)
- Carlos Simmerling (Mon Oct 18 2004 - 10:22:48 PDT)
- MURAT CETINKAYA (Mon Oct 18 2004 - 09:52:11 PDT)
- Carlos Simmerling (Mon Oct 18 2004 - 09:25:52 PDT)
- MURAT CETINKAYA (Mon Oct 18 2004 - 08:27:49 PDT)
AMBER: continue for No radius for F atom in MM_PBSA
- Holger Gohlke (Sun Oct 24 2004 - 13:06:15 PDT)
- Xiao He (Sun Oct 24 2004 - 07:40:21 PDT)
AMBER: Continued:No skew or curtosis when zero variance in moment
- Elijah Gregory (Tue Oct 26 2004 - 06:48:55 PDT)
- Xiao He (Mon Oct 25 2004 - 22:02:31 PDT)
AMBER: Curves 5.3
- Mu Yuguang \(Dr\) (Thu Oct 14 2004 - 19:57:57 PDT)
AMBER: difference in GBSOL in amber7 and amber8
- David A. Case (Fri Oct 15 2004 - 08:07:04 PDT)
- Xiao He (Fri Oct 15 2004 - 04:11:11 PDT)
AMBER: distance between images
- Thomas E. Cheatham, III (Thu Oct 14 2004 - 08:51:33 PDT)
- Bill Ross (Thu Oct 14 2004 - 08:09:11 PDT)
- riccardo nifosi (Thu Oct 14 2004 - 07:56:40 PDT)
AMBER: Distance Restraints
- David A. Case (Mon Oct 11 2004 - 08:17:39 PDT)
- Nelson Fonseca (Mon Oct 11 2004 - 05:56:23 PDT)
AMBER: error in mm_pbsa
- Xiao He (Sat Oct 16 2004 - 08:40:17 PDT)
- Holger Gohlke (Sat Oct 16 2004 - 06:53:36 PDT)
- Wu Yingliang (Sat Oct 16 2004 - 02:52:47 PDT)
- Xiao He (Sat Oct 16 2004 - 02:12:41 PDT)
AMBER: error in using AM1-BCC charge by antechamber
- Xiao He (Mon Oct 18 2004 - 21:22:04 PDT)
AMBER: errors in SGI
- Ross Walker (Thu Oct 14 2004 - 09:34:46 PDT)
- David A. Case (Thu Oct 14 2004 - 09:33:32 PDT)
- Xiao He (Thu Oct 14 2004 - 09:09:40 PDT)
- David A. Case (Thu Oct 14 2004 - 08:04:24 PDT)
- Xiao He (Thu Oct 14 2004 - 00:08:42 PDT)
AMBER: exclusion list
- Guanglei Cui (Mon Oct 11 2004 - 08:26:20 PDT)
- Guanglei Cui (Sun Oct 10 2004 - 09:34:38 PDT)
AMBER: file corruption with ptraj
- cailliez (Mon Oct 18 2004 - 08:32:32 PDT)
- Thomas E. Cheatham, III (Mon Oct 18 2004 - 08:42:02 PDT)
- Steve Seibold (Mon Oct 18 2004 - 08:10:51 PDT)
AMBER: frcmod_dmso
- Ross Walker (Tue Oct 05 2004 - 13:10:41 PDT)
- Ross Walker (Fri Oct 01 2004 - 15:05:05 PDT)
- Vincent Bisetty (Fri Oct 01 2004 - 14:21:42 PDT)
AMBER: from gaussian to antechamber
- Robyn Ayscue (Fri Oct 15 2004 - 11:41:56 PDT)
- Cai, Yufeng (Fri Oct 15 2004 - 11:14:48 PDT)
AMBER: generalized Born parameters
- David A. Case (Fri Oct 08 2004 - 09:08:02 PDT)
- Peter Varnai (Fri Oct 08 2004 - 07:16:08 PDT)
AMBER: getting new box info
- Melinda Layten (Thu Oct 28 2004 - 08:46:57 PDT)
- David A. Case (Thu Oct 28 2004 - 07:39:07 PDT)
- Vincent Bisetty (Thu Oct 28 2004 - 07:25:51 PDT)
AMBER: GIbbs : failure to start
- sachin patil (Wed Oct 06 2004 - 11:01:23 PDT)
AMBER: H bond calculation of CHARMM trajactory using PTRAJ
- Thomas E. Cheatham, III (Wed Oct 20 2004 - 07:16:50 PDT)
- anshul.imtech.res.in (Fri Oct 15 2004 - 21:59:33 PDT)
AMBER: Hot solvent/cold solute reference
- Stef (Mon Oct 11 2004 - 09:41:10 PDT)
- Andreas Svrcek-Seiler (Mon Oct 11 2004 - 06:16:18 PDT)
- Stef (Mon Oct 11 2004 - 03:56:30 PDT)
AMBER: how to neutralize the peptide
- Chris Moth (Wed Oct 27 2004 - 09:57:23 PDT)
- Joseph Nachman (Wed Oct 27 2004 - 10:04:50 PDT)
- Ye Mei (Tue Oct 26 2004 - 19:10:23 PDT)
AMBER: how to set up more than 3 groups constrain
- 卢强 (Mon Oct 11 2004 - 11:33:51 PDT)
AMBER: hydrogen bonds
- Tim Meyer (Tue Oct 05 2004 - 04:11:09 PDT)
- Jessica Koplin (Fri Oct 01 2004 - 09:24:29 PDT)
AMBER: icc 8.0 built antechamber
- Scott Brozell (Thu Oct 28 2004 - 10:24:02 PDT)
AMBER: Is AME equal to NME?
- myang.vitamin.uni.cc (Mon Oct 04 2004 - 13:07:12 PDT)
- myang.vitamin.uni.cc (Mon Oct 04 2004 - 12:15:46 PDT)
AMBER: klambdas and Weights for Gaussian Quadrature
- David A. Case (Tue Oct 12 2004 - 16:37:11 PDT)
- Nelson Fonseca (Tue Oct 12 2004 - 10:01:33 PDT)
AMBER: long minimization in sander
- Ross Walker (Mon Oct 25 2004 - 17:03:19 PDT)
- Bill Ross (Mon Oct 25 2004 - 13:30:32 PDT)
- MURAT CETINKAYA (Mon Oct 25 2004 - 08:32:10 PDT)
- Ross Walker (Mon Oct 25 2004 - 08:11:29 PDT)
- Bill Ross (Mon Oct 25 2004 - 08:09:49 PDT)
- MURAT CETINKAYA (Mon Oct 25 2004 - 07:53:14 PDT)
AMBER: MAXATOM failure in ANTECHAMBER
- david.evans.ulsop.ac.uk (Fri Oct 08 2004 - 03:09:18 PDT)
- Cenk Andac (Fri Oct 08 2004 - 02:31:18 PDT)
AMBER: MAXMASK problem
- Qiang Lu (Tue Oct 19 2004 - 15:25:03 PDT)
- David A. Case (Tue Oct 19 2004 - 14:10:29 PDT)
- Qiang Lu (Tue Oct 19 2004 - 10:19:54 PDT)
AMBER: MD after partially solvated
- Carlos Simmerling (Sat Oct 30 2004 - 20:11:27 PDT)
- Xiao He (Sat Oct 30 2004 - 19:52:51 PDT)
AMBER: MD problem (very long parhabs endless runtime)
- Daniel Wetzler (Sun Oct 24 2004 - 02:40:09 PDT)
- Ross Walker (Sat Oct 23 2004 - 11:53:22 PDT)
- myang.vitamin.uni.cc (Sat Oct 23 2004 - 11:35:59 PDT)
- Daniel Wetzler (Sat Oct 23 2004 - 11:16:12 PDT)
- Ross Walker (Sat Oct 23 2004 - 09:57:39 PDT)
- Daniel Wetzler (Sat Oct 23 2004 - 06:05:49 PDT)
AMBER: mdinfo on amber6
- Carlos Simmerling (Mon Oct 04 2004 - 04:40:03 PDT)
- Tomas Linhart (Mon Oct 04 2004 - 00:49:29 PDT)
- Abd Ghani Bin Abd Aziz (Sun Oct 03 2004 - 22:26:41 PDT)
AMBER: mm-pbsa problem
- Dawei Zhang (Thu Oct 14 2004 - 07:36:03 PDT)
AMBER: MM_PBSA reproduction of literature values and accuracy
- Carlos Simmerling (Tue Oct 26 2004 - 15:51:16 PDT)
- Karl N. Kirschner (Tue Oct 26 2004 - 15:35:19 PDT)
- Thomas Steinbrecher (Tue Oct 26 2004 - 00:05:51 PDT)
- Carlos Simmerling (Mon Oct 25 2004 - 10:53:50 PDT)
- Karl N. Kirschner (Mon Oct 25 2004 - 10:41:34 PDT)
AMBER: MMPBSA PB parameters - PARSE implementation in Amber
- Marc Baaden (Wed Oct 13 2004 - 10:42:34 PDT)
AMBER: modes analysis in ptraj
- David A. Case (Fri Oct 15 2004 - 08:18:50 PDT)
- Vlad Cojocaru (Thu Oct 14 2004 - 05:13:14 PDT)
AMBER: More AMBER 8 compilation problems on OSF1 4.0F
- David A. Case (Tue Oct 19 2004 - 07:48:52 PDT)
- Atro Tossavainen (Tue Oct 19 2004 - 05:39:21 PDT)
- M. L. Dodson (Tue Oct 19 2004 - 05:22:32 PDT)
- Atro Tossavainen (Mon Oct 18 2004 - 23:21:57 PDT)
- David A. Case (Mon Oct 18 2004 - 08:59:58 PDT)
- Atro Tossavainen (Mon Oct 18 2004 - 01:08:30 PDT)
AMBER: More installation problems on Solaris 8
- Atro Tossavainen (Tue Oct 12 2004 - 00:44:01 PDT)
AMBER: neutral Arg, charged Tyr ??
- Peter Trodler (Mon Oct 04 2004 - 00:25:49 PDT)
AMBER: nmode error
- David A. Case (Mon Oct 11 2004 - 08:09:18 PDT)
- Xiao He (Mon Oct 11 2004 - 00:10:22 PDT)
AMBER: No radius for F atom in MM_PBSA
- Xiao He (Sun Oct 24 2004 - 06:30:48 PDT)
AMBER: No skew or curtosis when zero variance in moment
- Xiao He (Mon Oct 25 2004 - 21:55:08 PDT)
AMBER: normal mode analysis after energy minimizaiton using sander
- David A. Case (Thu Oct 14 2004 - 16:35:01 PDT)
- xiaowei li (Thu Oct 14 2004 - 14:57:30 PDT)
AMBER: Note to all concerning filtering of messages posted to the amber list.
- Stef (Wed Oct 06 2004 - 01:33:17 PDT)
- Ross Walker (Tue Oct 05 2004 - 12:51:34 PDT)
AMBER: order parameter
- Carlos Simmerling (Sun Oct 17 2004 - 06:14:43 PDT)
- Jessica Koplin (Sun Oct 17 2004 - 03:30:44 PDT)
AMBER: parallel of sander_classic
- Michael Crowley (Tue Oct 26 2004 - 13:03:36 PDT)
- Ross Walker (Mon Oct 25 2004 - 06:15:58 PDT)
- David A. Case (Mon Oct 25 2004 - 06:17:44 PDT)
- Xioling Chuang (Sun Oct 24 2004 - 22:57:16 PDT)
AMBER: parameter error for a ligand
- Sivanesan Dakshanamurthy (Tue Oct 05 2004 - 14:45:51 PDT)
- David A. Case (Tue Oct 05 2004 - 13:23:01 PDT)
- Sivanesan Dakshanamurthy (Tue Oct 05 2004 - 09:59:54 PDT)
AMBER: Parameter for chlorophyll
- Fajar Rakhman Wibowo (Tue Oct 12 2004 - 03:46:27 PDT)
AMBER: Parameters for phosphorylated aminoacids
- Nadine Homeyer (Wed Oct 06 2004 - 03:57:14 PDT)
- Carlos Simmerling (Tue Oct 05 2004 - 08:58:07 PDT)
- Nadine Homeyer (Tue Oct 05 2004 - 08:21:31 PDT)
AMBER: PBSA parameter question (Radii and Charges)
- Ray Luo (Wed Oct 13 2004 - 09:38:38 PDT)
- Marc Baaden (Tue Oct 12 2004 - 17:01:19 PDT)
AMBER: Phosphoserine
- Venkata S Koppuravuri (Mon Oct 04 2004 - 12:26:28 PDT)
AMBER: Plot B-factor extracted from PDB file
- Xin Hu (Wed Oct 13 2004 - 07:41:29 PDT)
AMBER: pmemd and ifort 8.1
- Robert Duke (Fri Oct 15 2004 - 10:10:08 PDT)
- Niko Jukarainen (Fri Oct 15 2004 - 06:14:03 PDT)
AMBER: PMF
- Carlos Simmerling (Mon Oct 25 2004 - 05:14:19 PDT)
- tang kwa (Mon Oct 25 2004 - 04:59:22 PDT)
AMBER: Problem with AMBER/ANAL
- David A. Case (Fri Oct 08 2004 - 09:15:12 PDT)
- Daniel Wetzler (Fri Oct 08 2004 - 01:31:29 PDT)
AMBER: problem with antechamber
- David A. Case (Mon Oct 18 2004 - 13:14:29 PDT)
- Cai, Yufeng (Sun Oct 17 2004 - 19:04:28 PDT)
AMBER: Problem with EDIT (AMBER 5)
- Daniel Wetzler (Thu Oct 14 2004 - 05:23:32 PDT)
- Daniel Wetzler (Thu Oct 14 2004 - 04:53:45 PDT)
AMBER: Problem with installing Amber8: Where are the MK libraries?
- Atro Tossavainen (Fri Oct 15 2004 - 02:59:29 PDT)
- Ross Walker (Fri Oct 15 2004 - 00:29:47 PDT)
- Ross Walker (Fri Oct 15 2004 - 00:26:32 PDT)
- Atro Tossavainen (Fri Oct 15 2004 - 00:13:55 PDT)
- Atro Tossavainen (Thu Oct 14 2004 - 23:24:13 PDT)
- Ross Walker (Thu Oct 14 2004 - 11:06:52 PDT)
- HL Eastwood (Thu Oct 14 2004 - 10:42:54 PDT)
- Andreas Svrcek-Seiler (Thu Oct 14 2004 - 10:42:35 PDT)
- Ross Walker (Thu Oct 14 2004 - 10:00:02 PDT)
- HL Eastwood (Thu Oct 14 2004 - 09:34:54 PDT)
AMBER: problem with protonate
- David A. Case (Tue Oct 05 2004 - 14:31:12 PDT)
- myang.vitamin.uni.cc (Tue Oct 05 2004 - 13:36:36 PDT)
- Richard Stefl (Tue Oct 05 2004 - 10:44:05 PDT)
AMBER: problems with dihedrals
- Carlos Simmerling (Fri Oct 08 2004 - 06:27:44 PDT)
- Petr Kulhanek (Fri Oct 08 2004 - 05:53:03 PDT)
AMBER: problems with dihedrals - extended information
- Bill Ross (Mon Oct 18 2004 - 11:04:33 PDT)
- David A. Case (Mon Oct 18 2004 - 10:42:50 PDT)
- Petr Kulhanek (Sun Oct 17 2004 - 08:39:31 PDT)
AMBER: process_mdout.perl
- Tomas Linhart (Tue Oct 12 2004 - 00:43:28 PDT)
- Donald Thomas (Mon Oct 11 2004 - 23:23:13 PDT)
- bybaker.itsa.ucsf.edu (Mon Oct 11 2004 - 23:08:06 PDT)
AMBER: process_mdout.perl: work now
- bybaker.itsa.ucsf.edu (Tue Oct 12 2004 - 18:32:49 PDT)
AMBER: ptraj analyze modes question
- Vlad Cojocaru (Thu Oct 07 2004 - 06:17:02 PDT)
AMBER: ptraj and clustering
- Fabian Boes (Fri Oct 15 2004 - 01:15:51 PDT)
AMBER: ptraj and PCA
- J Pang (Wed Oct 06 2004 - 03:54:17 PDT)
AMBER: ptraj questions
- Viktor Hornak (Sun Oct 31 2004 - 11:39:48 PST)
- Carlos Simmerling (Sun Oct 31 2004 - 09:06:54 PST)
- Carlos Simmerling (Sun Oct 31 2004 - 07:45:21 PST)
- Amber admin (Sun Oct 31 2004 - 06:59:51 PST)
AMBER: pure aromatic?
- Cai, Yufeng (Mon Oct 25 2004 - 14:16:06 PDT)
AMBER: Question about Amino acid mutations
- sachin patil (Wed Oct 13 2004 - 16:03:22 PDT)
AMBER: question about mm_pbsa and nmode
- Xiao He (Mon Oct 11 2004 - 00:43:53 PDT)
AMBER: question about molsurf
- David A. Case (Fri Oct 15 2004 - 08:28:10 PDT)
- Xiao He (Fri Oct 15 2004 - 01:13:05 PDT)
AMBER: question about nmode
- David A. Case (Tue Oct 05 2004 - 12:03:52 PDT)
- xiaowei li (Tue Oct 05 2004 - 11:09:15 PDT)
AMBER: question about ptraj's Mask
- Kun Song (Thu Oct 28 2004 - 14:10:34 PDT)
- Viktor Hornak (Thu Oct 28 2004 - 14:03:45 PDT)
- Kun Song (Thu Oct 28 2004 - 13:52:08 PDT)
AMBER: Question about restart MD
- Ross Walker (Mon Oct 11 2004 - 12:06:09 PDT)
- myang.vitamin.uni.cc (Mon Oct 11 2004 - 12:05:04 PDT)
- Carlos Simmerling (Mon Oct 11 2004 - 11:55:39 PDT)
- Xin Hu (Mon Oct 11 2004 - 11:38:38 PDT)
AMBER: Question about Xleap
- Ross Walker (Fri Oct 22 2004 - 06:31:58 PDT)
- David LeBard (Wed Oct 20 2004 - 15:28:28 PDT)
AMBER: question on NAB
- David A. Case (Tue Oct 19 2004 - 08:06:50 PDT)
- ioana.pegasus.arc.nasa.gov (Mon Oct 18 2004 - 14:18:19 PDT)
AMBER: question on NMR restrain
- David A. Case (Mon Oct 18 2004 - 18:30:30 PDT)
- 卢强 (Mon Oct 18 2004 - 15:55:54 PDT)
AMBER: Questions about MD sampling
- Ross Walker (Tue Oct 12 2004 - 10:31:12 PDT)
- Ross Walker (Tue Oct 12 2004 - 10:25:30 PDT)
- Thomas E. Cheatham, III (Tue Oct 12 2004 - 09:12:18 PDT)
- Xin Hu (Tue Oct 12 2004 - 08:03:06 PDT)
AMBER: questions regarding JTREE
- Bill Ross (Wed Oct 27 2004 - 10:53:39 PDT)
- Annette Höglund (Wed Oct 27 2004 - 08:37:06 PDT)
AMBER: recovering total force array
- Dave S Walker (Tue Oct 19 2004 - 16:59:00 PDT)
- David A. Case (Tue Oct 19 2004 - 14:26:31 PDT)
- Dave S Walker (Tue Oct 19 2004 - 12:04:16 PDT)
AMBER: restrain one tosion angle
- Carlos Simmerling (Fri Oct 08 2004 - 13:50:34 PDT)
- Yaroslava Yingling (Fri Oct 08 2004 - 12:20:09 PDT)
- Carlos Simmerling (Fri Oct 08 2004 - 12:10:16 PDT)
- Yaroslava Yingling (Fri Oct 08 2004 - 12:02:01 PDT)
AMBER: rms fluct and displacement in modes analysis
- David A. Case (Tue Oct 12 2004 - 09:19:48 PDT)
- Vlad Cojocaru (Tue Oct 12 2004 - 03:47:34 PDT)
AMBER: rms fluctuation units from ptraj
- Vlad Cojocaru (Thu Oct 07 2004 - 06:36:03 PDT)
AMBER: RSM & ptraj
- Elijah Gregory (Sat Oct 30 2004 - 23:29:23 PDT)
- Carlos Simmerling (Sat Oct 30 2004 - 23:25:14 PDT)
- bybaker.itsa.ucsf.edu (Sat Oct 30 2004 - 23:13:10 PDT)
AMBER: RSM fluctuation & residues
- bybaker.itsa.ucsf.edu (Fri Oct 29 2004 - 13:21:42 PDT)
AMBER: RSM fluctuation by residues
- bybaker.itsa.ucsf.edu (Sat Oct 30 2004 - 23:22:53 PDT)
AMBER: Running on MPI
- Bill Ross (Wed Oct 13 2004 - 10:02:42 PDT)
- Ross Walker (Wed Oct 13 2004 - 09:51:23 PDT)
- David A. Case (Wed Oct 13 2004 - 08:57:24 PDT)
- Wu Yingliang (Wed Oct 13 2004 - 06:49:48 PDT)
- Carlos Simmerling (Wed Oct 13 2004 - 06:59:38 PDT)
- Carlos Simmerling (Wed Oct 06 2004 - 07:33:19 PDT)
- wish_71 (Tue Oct 05 2004 - 19:43:16 PDT)
- Carlos Simmerling (Tue Oct 05 2004 - 05:16:59 PDT)
- wish_71 (Tue Oct 05 2004 - 03:17:55 PDT)
- Carlos Simmerling (Mon Oct 04 2004 - 04:37:18 PDT)
- Jiten (Sun Oct 03 2004 - 20:08:54 PDT)
- wish_71 (Sun Oct 03 2004 - 18:59:58 PDT)
AMBER: sander error
- Xiao He (Sat Oct 30 2004 - 01:19:15 PDT)
- Jiten (Sat Oct 30 2004 - 00:58:33 PDT)
- Xiao He (Fri Oct 29 2004 - 23:49:17 PDT)
AMBER: sander gets stuck
- MURAT CETINKAYA (Fri Oct 29 2004 - 08:11:15 PDT)
- Ross Walker (Fri Oct 29 2004 - 07:52:43 PDT)
- MURAT CETINKAYA (Fri Oct 29 2004 - 07:32:22 PDT)
AMBER: Sander-7 for Win32
- David A. Case (Wed Oct 20 2004 - 16:03:49 PDT)
- Vlad (Tue Oct 19 2004 - 16:11:38 PDT)
AMBER: sander8
- Carlos Simmerling (Sat Oct 09 2004 - 10:39:34 PDT)
- Vincent Bisetty (Sat Oct 09 2004 - 09:13:55 PDT)
- Carlos Simmerling (Fri Oct 08 2004 - 08:07:23 PDT)
- Vincent Bisetty (Fri Oct 08 2004 - 07:59:01 PDT)
AMBER: Settings about frozen atoms in sander
- Bill Ross (Fri Oct 29 2004 - 11:44:41 PDT)
- Jiten (Fri Oct 29 2004 - 09:05:36 PDT)
- Oliver Hucke (Fri Oct 29 2004 - 09:54:10 PDT)
- Xiao He (Fri Oct 29 2004 - 08:17:07 PDT)
AMBER: small molecule simulation
- Carlos Simmerling (Sun Oct 03 2004 - 05:54:40 PDT)
- hj zou (Sat Oct 02 2004 - 22:59:55 PDT)
AMBER: solute leaving PBC box
- Carlos Simmerling (Fri Oct 08 2004 - 07:02:42 PDT)
- opitz.che.udel.edu (Fri Oct 08 2004 - 06:43:06 PDT)
- Carlos Simmerling (Thu Oct 07 2004 - 15:43:49 PDT)
- opitz.che.udel.edu (Thu Oct 07 2004 - 15:01:19 PDT)
- myang.vitamin.uni.cc (Thu Oct 07 2004 - 15:00:09 PDT)
- Carlos Simmerling (Thu Oct 07 2004 - 14:48:12 PDT)
- opitz.che.udel.edu (Thu Oct 07 2004 - 14:24:47 PDT)
AMBER: solvation free energies using mmpbsa
- Ray Luo (Wed Oct 27 2004 - 21:06:07 PDT)
- FyD (Thu Oct 28 2004 - 10:33:34 PDT)
- Karl N. Kirschner (Thu Oct 28 2004 - 10:15:38 PDT)
AMBER: Trajectory corruption
- Bill Ross (Fri Oct 15 2004 - 11:00:59 PDT)
- Adrian E. Roitberg (Fri Oct 15 2004 - 10:06:23 PDT)
- Carlos Simmerling (Fri Oct 15 2004 - 07:54:14 PDT)
- Steve Seibold (Fri Oct 15 2004 - 06:48:50 PDT)
AMBER: trajectory file question?
- Melinda Layten (Thu Oct 28 2004 - 12:35:17 PDT)
- opitz.che.udel.edu (Thu Oct 28 2004 - 11:15:12 PDT)
AMBER: Use of intel compilers v8.1 for Amber 8.
- Ross Walker (Thu Oct 14 2004 - 11:13:15 PDT)
AMBER: Wich CPU?
- Robert Duke (Thu Oct 21 2004 - 06:23:48 PDT)
- Joachim Reichelt (Thu Oct 21 2004 - 02:34:26 PDT)
HIERARCHY OF INTERACTIONS"
- Vlad Cojocaru (Wed Oct 20 2004 - 09:10:43 PDT)
process_mdout.perl
- bybaker.itsa.ucsf.edu (Tue Oct 12 2004 - 18:36:45 PDT)
rms fluct and displacement in modes analysis
- Vlad Cojocaru (Tue Oct 12 2004 - 10:39:33 PDT)
RSM & ptraj
- bybaker.itsa.ucsf.edu (Sun Oct 31 2004 - 10:43:41 PST)
sander8
- Carlos Simmerling (Tue Oct 12 2004 - 04:21:02 PDT)
- Vincent Bisetty (Tue Oct 12 2004 - 00:19:35 PDT)

Amber Archive Oct 2004 by subject