Amber Archive May 2006: by subject

[Fwd: AMBER: Problem with impose in lep]
- Osmar Norberto de Souza (Wed May 10 2006 - 10:09:48 PDT)
AMBER: "atom number exceeds the MAXATOM"
- David A. Case (Wed May 17 2006 - 04:53:58 PDT)
- BAUVAIS.itodys.jussieu.fr (Tue May 16 2006 - 22:54:24 PDT)
AMBER: "The system has extended beyond" error message
- David A. Case (Thu May 18 2006 - 05:38:58 PDT)
- german (Thu May 18 2006 - 05:27:42 PDT)
- Atsutoshi Okabe (Wed May 17 2006 - 22:04:31 PDT)
AMBER: 1st 2 lines of restart files
- Steven Winfield (Thu May 25 2006 - 04:50:18 PDT)
- hayden (Thu May 25 2006 - 04:40:03 PDT)
AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil
- 3Dsig06 (Mon May 22 2006 - 15:03:45 PDT)
AMBER: A dummy atom on the center of solute molecule
- Ilyas Yildirim (Tue May 30 2006 - 16:06:54 PDT)
- Atsutoshi Okabe (Sun May 28 2006 - 22:51:49 PDT)
- Ilyas Yildirim (Sun May 28 2006 - 21:26:33 PDT)
- Ilyas Yildirim (Tue May 23 2006 - 19:49:00 PDT)
- Atsutoshi Okabe (Tue May 23 2006 - 18:46:35 PDT)
- Ilyas Yildirim (Mon May 22 2006 - 04:58:24 PDT)
- Atsutoshi Okabe (Mon May 22 2006 - 04:49:23 PDT)
AMBER: About mm_pbsa calculation setting up
- alfredoq.fcq.unc.edu.ar (Thu May 11 2006 - 19:19:03 PDT)
AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format
- wang (Mon May 08 2006 - 23:25:47 PDT)
AMBER: Again SASA
- lucas luquitas (Mon May 22 2006 - 12:51:22 PDT)
AMBER: alpha helix preference problem
- Ross Walker (Fri May 26 2006 - 08:23:27 PDT)
- harianto (Fri May 26 2006 - 07:04:30 PDT)
- Carlos Simmerling (Thu May 25 2006 - 18:35:10 PDT)
- harianto (Thu May 25 2006 - 14:16:23 PDT)
AMBER: amber .off file format question
- David A. Case (Mon May 22 2006 - 23:21:33 PDT)
- Ilyas Yildirim (Mon May 22 2006 - 22:53:19 PDT)
- Bill Ross (Mon May 22 2006 - 11:17:26 PDT)
- Wei Zhang (Mon May 22 2006 - 11:13:12 PDT)
- Ilyas Yildirim (Mon May 22 2006 - 02:16:39 PDT)
- Ilyas Yildirim (Fri May 19 2006 - 19:30:55 PDT)
AMBER: AMBER 8 - dihedral angles when clambda=1
- Ilyas Yildirim (Thu May 11 2006 - 21:57:37 PDT)
AMBER: Amber 9, sander imin = 5, -y flag
- Carlos Simmerling (Mon May 01 2006 - 06:35:56 PDT)
- z3020110.student.unsw.edu.au (Sun Apr 30 2006 - 18:08:44 PDT)
AMBER: amber compilation on Red Hat 8 with MPICH
- Ross Walker (Wed May 17 2006 - 08:35:00 PDT)
- David A. Case (Wed May 17 2006 - 04:52:55 PDT)
- kawamura_hiro.riken.jp (Tue May 16 2006 - 22:38:35 PDT)
AMBER: Amber install on RedHat Linux
- Ross Walker (Thu May 04 2006 - 08:31:56 PDT)
- David A. Case (Thu May 04 2006 - 08:17:08 PDT)
- a a (Thu May 04 2006 - 00:37:34 PDT)
- Ross Walker (Wed May 03 2006 - 19:36:45 PDT)
- a a (Wed May 03 2006 - 19:17:14 PDT)
AMBER: AMBER mdcrd file bigger than 2GB
- Thomas Cheatham (Wed May 31 2006 - 16:27:16 PDT)
- snoze pa (Wed May 31 2006 - 16:04:53 PDT)
- snoze pa (Wed May 31 2006 - 14:57:22 PDT)
AMBER: AMBER Workshops, London UK 26th - 30th June 2006
- Ross Walker (Tue May 02 2006 - 08:45:33 PDT)
AMBER: amber8 bugfix effects
- David A. Case (Wed May 24 2006 - 07:38:39 PDT)
- kawamura_hiro.riken.jp (Wed May 24 2006 - 01:17:32 PDT)
AMBER: amber8 compiled erro on opteron with 64 bit
- Andreas Svrcek-Seiler (Tue May 16 2006 - 03:53:14 PDT)
- renyanliang (Tue May 16 2006 - 02:15:24 PDT)
AMBER: AMBER9 compilation error on IBM Cluster
- Ross Walker (Mon May 15 2006 - 20:28:12 PDT)
- amit.mbu.iisc.ernet.in (Mon May 15 2006 - 04:11:50 PDT)
AMBER: AMBER9 installation error on Compaq machine.
- Ross Walker (Thu May 18 2006 - 15:32:57 PDT)
- Soonmin Jang (Thu May 18 2006 - 00:11:46 PDT)
AMBER: AMBER9 INSTALLATION problem on O2 sgi system
- Ross Walker (Mon May 08 2006 - 08:17:55 PDT)
- Atro Tossavainen (Mon May 08 2006 - 04:48:29 PDT)
- S.Sundar Raman (Mon May 08 2006 - 04:33:58 PDT)
- David A. Case (Sun May 07 2006 - 07:27:56 PDT)
- S.Sundar Raman (Sun May 07 2006 - 00:10:15 PDT)
AMBER: amber9 serial compilation error
- David A. Case (Thu May 04 2006 - 10:36:53 PDT)
- Arvind Marathe (Thu May 04 2006 - 09:55:39 PDT)
AMBER: Amber9 test error on SGI Altix
- Robert Duke (Tue May 09 2006 - 09:06:19 PDT)
- Priti Hansia (Tue May 09 2006 - 08:18:02 PDT)
- Ray Luo (Tue May 09 2006 - 05:57:57 PDT)
- David A. Case (Mon May 08 2006 - 11:45:30 PDT)
- David A. Case (Mon May 08 2006 - 11:07:17 PDT)
- amit.mbu.iisc.ernet.in (Mon May 08 2006 - 10:14:19 PDT)
AMBER: Amber9/mpich2 performance
- Joseph Fernandez (Fri May 12 2006 - 18:09:20 PDT)
- Ross Walker (Thu May 11 2006 - 16:07:21 PDT)
- Joseph Fernandez (Thu May 11 2006 - 15:30:03 PDT)
AMBER: AMBER9: MacG5 parallel sander.MPI
- Mengjuei Hsieh (Sun May 07 2006 - 07:33:01 PDT)
- Mengjuei Hsieh (Wed May 03 2006 - 17:32:14 PDT)
AMBER: another question: is rms 2E-2 good for nmode ntrun=1?
- David A. Case (Fri May 12 2006 - 10:01:05 PDT)
- nadiav.soton.ac.uk (Fri May 12 2006 - 09:00:21 PDT)
- David A. Case (Fri May 12 2006 - 08:39:37 PDT)
- Pan, Yongmei (Fri May 12 2006 - 08:22:00 PDT)
AMBER: Antechamber : +ve charge species
- Junmei Wang (Tue May 30 2006 - 08:31:07 PDT)
- a a (Tue May 30 2006 - 03:04:05 PDT)
AMBER: antechamber help needed for FAD
- pkb bioinfo (Mon May 29 2006 - 02:38:48 PDT)
AMBER: binpos file
- Varsha Goyal (Fri May 12 2006 - 13:46:24 PDT)
AMBER: bond information in amber
- Navnit Kumar Mishra (Thu May 11 2006 - 23:28:00 PDT)
- snoze pa (Thu May 11 2006 - 12:16:56 PDT)
- snoze pa (Thu May 11 2006 - 11:41:00 PDT)
- snoze pa (Thu May 11 2006 - 11:36:18 PDT)
- Navnit Kumar Mishra (Thu May 11 2006 - 10:25:10 PDT)
- snoze pa (Thu May 11 2006 - 09:48:58 PDT)
AMBER: bug in ambpdb (AMBER8)
- David A. Case (Wed May 10 2006 - 08:10:08 PDT)
- Petr Kulhanek (Wed May 10 2006 - 03:54:55 PDT)
AMBER: carnal prob
- Bill Ross (Thu May 04 2006 - 10:31:22 PDT)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu May 04 2006 - 00:58:18 PDT)
- bala (Thu May 04 2006 - 00:44:53 PDT)
AMBER: check as error: load prepin in tleap
- jitrayut jitonnom (Fri May 26 2006 - 10:13:41 PDT)
AMBER: cluster architecture for the best amber performance
- Robert Duke (Wed May 03 2006 - 10:05:57 PDT)
- Ross Walker (Wed May 03 2006 - 08:42:19 PDT)
- Kateryna Miroshnychenko (Wed May 03 2006 - 05:54:58 PDT)
AMBER: Compiler with AMD 64 bit support
- Ross Walker (Tue May 09 2006 - 10:19:18 PDT)
- alfredoq.fcq.unc.edu.ar (Tue May 09 2006 - 10:10:30 PDT)
AMBER: Compilers and libraries for AMBER in HPC!
- Pradipta Bandyopadhyay (Sun May 14 2006 - 06:25:07 PDT)
AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem
- Hall, Spencer (Tue May 23 2006 - 14:15:12 PDT)
- Hall, Spencer (Tue May 23 2006 - 14:15:08 PDT)
- Michael Crowley (Mon May 22 2006 - 11:28:58 PDT)
- Ross Walker (Thu May 18 2006 - 16:37:30 PDT)
- Hall, Spencer (Thu May 18 2006 - 15:44:14 PDT)
AMBER: concatenating .mdcrd files
- Ross Walker (Wed May 03 2006 - 09:39:11 PDT)
- Kenley Barrett (Wed May 03 2006 - 09:31:59 PDT)
AMBER: conflicting types for XawScrolledTableSetLocation
- Wei Zhang (Thu May 04 2006 - 10:17:40 PDT)
- K. Yarem (Thu May 04 2006 - 08:43:57 PDT)
AMBER: Correlation matrix used in quasih (Amber 7)
- David A. Case (Thu May 18 2006 - 05:31:00 PDT)
- Craig Gough (Thu May 18 2006 - 00:06:03 PDT)
AMBER: density
- Ross Walker (Wed May 17 2006 - 21:11:11 PDT)
- mathew k varghese (Wed May 17 2006 - 20:24:07 PDT)
- Ross Walker (Wed May 17 2006 - 08:31:20 PDT)
- mathew k varghese (Tue May 16 2006 - 21:09:17 PDT)
- Yong Duan (Mon May 15 2006 - 22:37:28 PDT)
- mathew k varghese (Mon May 15 2006 - 21:02:51 PDT)
AMBER: Difference in results for TI calculation
- David A. Case (Tue May 30 2006 - 11:01:49 PDT)
- brmeher.iitg.ernet.in (Mon May 29 2006 - 07:23:45 PDT)
- brmeher.iitg.ernet.in (Mon May 29 2006 - 06:53:41 PDT)
AMBER: Different results for TI calculation
- Biswa Ranjan Meher (Wed May 31 2006 - 00:25:13 PDT)
AMBER: different TI calculations starting from the same state
- David A. Case (Fri May 26 2006 - 08:16:19 PDT)
- Andrea Bortolato (Fri May 26 2006 - 03:12:12 PDT)
- Andrea Bortolato (Fri May 26 2006 - 06:56:47 PDT)
AMBER: distance dependent dielectric constant
- David A. Case (Wed May 17 2006 - 04:59:41 PDT)
- Mahalakshmi Sahasranaman (Wed May 17 2006 - 03:36:55 PDT)
AMBER: distance restraints
- mkseo (Mon May 01 2006 - 14:49:21 PDT)
AMBER: energy terms
- JAVIER PEREZ (Mon May 29 2006 - 08:25:31 PDT)
AMBER: error in AMBER 9.0
- David A. Case (Tue May 23 2006 - 22:19:47 PDT)
- mkseo (Tue May 23 2006 - 14:43:28 PDT)
AMBER: error propagation in MM-PBSA binding free energy calculation
- Jianyin Shao (Mon May 01 2006 - 10:17:04 PDT)
AMBER: Error while running test.serial in Amber9
- Priti Hansia (Thu May 04 2006 - 08:48:36 PDT)
- David A. Case (Wed May 03 2006 - 23:13:06 PDT)
- Priti Hansia (Wed May 03 2006 - 22:08:02 PDT)
- Ross Walker (Wed May 03 2006 - 08:21:42 PDT)
- Priti Hansia (Wed May 03 2006 - 05:02:04 PDT)
- Carlos Simmerling (Wed May 03 2006 - 04:50:37 PDT)
- Priti Hansia (Wed May 03 2006 - 04:03:27 PDT)
AMBER: ESP calculations.
- Ken Merz (Tue May 30 2006 - 04:59:38 PDT)
- Ken Merz (Tue May 30 2006 - 04:55:24 PDT)
- FyD (Tue May 30 2006 - 04:15:31 PDT)
- a a (Tue May 30 2006 - 03:10:41 PDT)
AMBER: experiences with compiling amber9 for FreeBSD
- Xuebin Qiao (Fri May 05 2006 - 23:31:06 PDT)
- M. L. Dodson (Fri May 05 2006 - 19:34:07 PDT)
- Mengjuei Hsieh (Fri May 05 2006 - 19:05:41 PDT)
- David A. Case (Fri May 05 2006 - 18:31:13 PDT)
- Mengjuei Hsieh (Fri May 05 2006 - 17:30:16 PDT)
- Mengjuei Hsieh (Fri May 05 2006 - 17:24:30 PDT)
- M. L. Dodson (Fri May 05 2006 - 15:00:10 PDT)
- Ross Walker (Fri May 05 2006 - 14:10:51 PDT)
- David A. Case (Fri May 05 2006 - 12:19:31 PDT)
- M. L. Dodson (Fri May 05 2006 - 11:59:48 PDT)
- David A. Case (Fri May 05 2006 - 11:46:29 PDT)
- M. L. Dodson (Fri May 05 2006 - 11:37:19 PDT)
AMBER: fail to execute addles
- pang zhao (Tue May 16 2006 - 07:42:36 PDT)
- Carlos Simmerling (Tue May 16 2006 - 06:47:37 PDT)
- pang zhao (Mon May 15 2006 - 23:39:28 PDT)
- pang zhao (Mon May 15 2006 - 23:17:05 PDT)
- pang zhao (Mon May 15 2006 - 23:13:21 PDT)
- Carlos Simmerling (Mon May 15 2006 - 09:59:29 PDT)
- David A. Case (Mon May 15 2006 - 09:46:28 PDT)
- pang zhao (Mon May 15 2006 - 07:31:19 PDT)
- Carlos Simmerling (Mon May 15 2006 - 05:43:31 PDT)
- pang zhao (Mon May 15 2006 - 04:59:10 PDT)
AMBER: ff02 + POL3 problem !
- Yong Duan (Tue May 16 2006 - 13:06:54 PDT)
- Pradipta Bandyopadhyay (Tue May 16 2006 - 07:08:03 PDT)
- Yong Duan (Mon May 15 2006 - 09:15:02 PDT)
- Pradipta Bandyopadhyay (Mon May 15 2006 - 06:53:20 PDT)
AMBER: force field parameters
- Navnit Kumar Mishra (Fri May 19 2006 - 04:01:59 PDT)
- Douali, Latifa (Thu May 18 2006 - 11:40:53 PDT)
- Navnit Kumar Mishra (Thu May 18 2006 - 11:21:59 PDT)
- Douali, Latifa (Thu May 18 2006 - 10:33:35 PDT)
AMBER: Force units in forcedump.dat
- darden (Wed May 31 2006 - 10:53:34 PDT)
- Steven Winfield (Wed May 31 2006 - 06:41:43 PDT)
AMBER: freeze interval vibrations
- David A. Case (Wed May 24 2006 - 12:00:35 PDT)
- Eric Hu (Wed May 24 2006 - 10:52:47 PDT)
AMBER: Fwd: RESP for deprotonated tyrosine and lysine
- FyD (Thu May 25 2006 - 01:26:15 PDT)
- jitrayut jitonnom (Wed May 24 2006 - 19:57:45 PDT)
AMBER: Hexahydrated Counterions
- David A. Case (Wed May 10 2006 - 08:32:31 PDT)
- Mahalakshmi Sahasranaman (Wed May 10 2006 - 06:22:02 PDT)
AMBER: How does amber calculate HB?
- David A. Case (Mon May 01 2006 - 23:20:31 PDT)
- Li Su (Mon May 01 2006 - 18:01:05 PDT)
AMBER: How to build NH2 of amino acid in amber
- jitrayut jitonnom (Wed May 24 2006 - 20:52:25 PDT)
AMBER: How to built the deprotonated form of lysine and tyrosine
- jitrayut jitonnom (Wed May 24 2006 - 19:49:04 PDT)
AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed
- Kenley Barrett (Wed May 10 2006 - 13:04:16 PDT)
AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
- Ross Walker (Mon May 08 2006 - 11:13:11 PDT)
AMBER: Installation of Amber8 on Fedora Core 5
- DAVID P. RANGEL (Wed May 31 2006 - 15:48:11 PDT)
AMBER: installation problem
- Robert Duke (Mon May 15 2006 - 11:25:53 PDT)
- Mahalakshmi Sahasranaman (Mon May 15 2006 - 11:12:51 PDT)
AMBER: Installing / Compiling Question
- Ross Walker (Sat May 27 2006 - 22:12:46 PDT)
- David A. Case (Sat May 27 2006 - 21:50:54 PDT)
- Seth Lilavivat (Fri May 26 2006 - 20:29:06 PDT)
AMBER: Intel compiler version 9.0.033
- Priti Hansia (Mon May 08 2006 - 12:55:37 PDT)
- Ross Walker (Mon May 08 2006 - 12:40:23 PDT)
AMBER: Intel fortran compiler 7?
- Robert Duke (Fri May 19 2006 - 04:59:43 PDT)
- Simon Whitehead (Fri May 19 2006 - 02:47:55 PDT)
AMBER: internal coordinates
- Ioana Cozmuta (Tue May 02 2006 - 11:01:45 PDT)
- David A. Case (Mon May 01 2006 - 13:50:10 PDT)
AMBER: lipid bi-layer system
- Lwin, ThuZar (Thu May 04 2006 - 10:41:11 PDT)
AMBER: Macromodel Amber* vs. Amber7
- opitz.che.udel.edu (Mon May 22 2006 - 05:56:54 PDT)
AMBER: md error : sander
- Carlos Simmerling (Sun May 28 2006 - 13:06:21 PDT)
- jitrayut jitonnom (Sun May 28 2006 - 11:11:45 PDT)
AMBER: molsurf.c error
- David A. Case (Fri May 05 2006 - 10:34:32 PDT)
- Miguel Ferreira (Fri May 05 2006 - 04:46:24 PDT)
- David A. Case (Thu May 04 2006 - 13:21:28 PDT)
- Miguel Ferreira (Thu May 04 2006 - 12:43:41 PDT)
- Ross Walker (Thu May 04 2006 - 09:28:49 PDT)
- Miguel Ferreira (Thu May 04 2006 - 09:00:31 PDT)
AMBER: More Amber 9 Benchmarks available
- Robert Duke (Mon May 22 2006 - 07:23:15 PDT)
AMBER: MPI parallel problem in AMBER 8.0
- Ross Walker (Tue May 02 2006 - 15:40:37 PDT)
- mkseo (Tue May 02 2006 - 15:14:16 PDT)
- Ross Walker (Tue May 02 2006 - 14:42:33 PDT)
- mkseo (Tue May 02 2006 - 14:21:50 PDT)
AMBER: Namelists in input files
- Steven Winfield (Wed May 31 2006 - 09:42:05 PDT)
AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua)
- David A. Case (Thu May 25 2006 - 13:33:33 PDT)
- Ray Luo (Wed May 24 2006 - 16:14:33 PDT)
- Soonmin Jang (Thu May 25 2006 - 03:51:02 PDT)
AMBER: Opteron vs. Xeon performance
- Yong Duan (Sun May 14 2006 - 17:53:55 PDT)
- Robert Duke (Fri May 12 2006 - 08:24:43 PDT)
- Ross Walker (Fri May 12 2006 - 08:13:48 PDT)
- Ye Mei (Fri May 12 2006 - 06:23:00 PDT)
- Robert Duke (Fri May 12 2006 - 05:46:08 PDT)
- Robert Duke (Fri May 12 2006 - 05:29:14 PDT)
- Ye Mei (Fri May 12 2006 - 01:04:45 PDT)
- ian gould (Fri May 12 2006 - 00:35:12 PDT)
- Robert Duke (Thu May 11 2006 - 19:02:10 PDT)
- Ross Walker (Thu May 11 2006 - 16:17:12 PDT)
- Jim Paugh (Thu May 11 2006 - 11:47:42 PDT)
AMBER: OT: software to support AMBER?
- Steve Gwaltney (Thu May 18 2006 - 11:37:06 PDT)
AMBER: output of first stage RESP calculation
- FyD (Thu May 25 2006 - 01:12:12 PDT)
- JunJun Liu (Wed May 24 2006 - 15:23:55 PDT)
AMBER: PBS script for lemieux
- Stern, Julie (Sun May 14 2006 - 16:09:30 PDT)
AMBER: Please reply
- David A. Case (Fri May 26 2006 - 12:39:02 PDT)
- Ananda Rama Krishnan Selvaraj (Fri May 26 2006 - 12:36:26 PDT)
- Shafinaz (Fri May 26 2006 - 12:19:42 PDT)
AMBER: PMEMD compilation error
- Robert Duke (Mon May 08 2006 - 13:18:05 PDT)
- Joseph Fernandez (Mon May 08 2006 - 12:37:03 PDT)
AMBER: problem loading forcefield leaprc.ff86
- David A. Case (Fri May 19 2006 - 08:45:33 PDT)
- Mahalakshmi Sahasranaman (Fri May 19 2006 - 07:27:38 PDT)
AMBER: Problem with "impose" in leap
- Osmar Norberto de Souza (Mon May 15 2006 - 04:27:13 PDT)
AMBER: Problem with impose in lep
- Osmar Norberto de Souza (Mon May 08 2006 - 10:31:16 PDT)
AMBER: problem with installation, or bug?
- Kenley Barrett (Thu May 18 2006 - 03:09:10 PDT)
AMBER: problem with prep file
- Junmei Wang (Mon May 15 2006 - 14:10:53 PDT)
- David A. Case (Wed May 10 2006 - 09:12:59 PDT)
- Simon Whitehead (Wed May 10 2006 - 03:52:32 PDT)
AMBER: problem with prepfile
- Junmei Wang (Thu May 25 2006 - 09:24:51 PDT)
- David A. Case (Wed May 24 2006 - 13:56:08 PDT)
- Shafinaz (Wed May 24 2006 - 12:50:21 PDT)
AMBER: Problem with running xleap remotely
- heaton.chem.utah.edu (Sat May 20 2006 - 13:43:53 PDT)
- Ross Walker (Sat May 20 2006 - 12:37:35 PDT)
- heaton.chem.utah.edu (Sat May 20 2006 - 12:20:27 PDT)
AMBER: Problem with shared libraries: libimf.so
- Ross Walker (Sun May 07 2006 - 09:10:54 PDT)
- Priti Hansia (Sat May 06 2006 - 22:40:49 PDT)
- David A. Case (Sat May 06 2006 - 14:17:51 PDT)
- Priti Hansia (Sat May 06 2006 - 00:01:51 PDT)
- Ross Walker (Fri May 05 2006 - 14:08:31 PDT)
- Priti Hansia (Fri May 05 2006 - 11:39:50 PDT)
- Ross Walker (Fri May 05 2006 - 11:04:10 PDT)
- Priti Hansia (Fri May 05 2006 - 10:55:39 PDT)
AMBER: Problems compiling amber9
- Don Harden (Tue May 23 2006 - 12:45:02 PDT)
- Andreas Svrcek-Seiler (Mon May 22 2006 - 12:01:09 PDT)
- David A. Case (Mon May 22 2006 - 11:46:09 PDT)
- Don Harden (Mon May 22 2006 - 10:10:15 PDT)
AMBER: problems with antechamber
- Junmei Wang (Tue May 30 2006 - 08:20:33 PDT)
- linfu (Tue May 30 2006 - 05:01:59 PDT)
- JAVIER PEREZ (Mon May 29 2006 - 08:04:52 PDT)
AMBER: process_mdout.perl error
- Ross Walker (Fri May 19 2006 - 07:43:25 PDT)
- a a (Fri May 19 2006 - 02:35:20 PDT)
AMBER: proper restart procedure?
- David A. Case (Wed May 03 2006 - 08:18:43 PDT)
- Carlos Simmerling (Wed May 03 2006 - 04:48:25 PDT)
- John J. Love (Tue May 02 2006 - 20:33:57 PDT)
AMBER: Pt containing complex: antechamber
- David A. Case (Tue May 30 2006 - 10:39:20 PDT)
- a a (Sun May 28 2006 - 20:42:31 PDT)
AMBER: Pt containing complex: xleap
- Ilyas Yildirim (Sun May 28 2006 - 21:00:08 PDT)
- a a (Sun May 28 2006 - 20:30:48 PDT)
AMBER: ptraj: calculating distances between atoms in charges residues
- Thomas Cheatham (Fri May 26 2006 - 09:12:40 PDT)
- Magne Olufsen (Fri May 26 2006 - 00:13:48 PDT)
AMBER: Qestion about input for RESP program
- FyD (Thu May 25 2006 - 08:53:28 PDT)
- JunJun Liu (Thu May 25 2006 - 07:01:41 PDT)
- FyD (Thu May 25 2006 - 01:22:13 PDT)
- Ilyas Yildirim (Wed May 24 2006 - 21:49:11 PDT)
- JunJun Liu (Wed May 24 2006 - 19:44:41 PDT)
AMBER: Question about .off file
- Ilyas Yildirim (Fri May 26 2006 - 01:58:19 PDT)
- Sergey Krishtal (Fri May 26 2006 - 01:15:06 PDT)
AMBER: question about group format
- Holly Freedman (Thu May 04 2006 - 16:16:22 PDT)
- Viktor Hornak (Thu May 04 2006 - 11:49:20 PDT)
- Holly Freedman (Wed May 03 2006 - 12:18:36 PDT)
AMBER: question about QM/MM in amber9
- Ross Walker (Thu May 25 2006 - 08:33:17 PDT)
- Adrian Roitberg (Thu May 25 2006 - 03:57:25 PDT)
- aixiaoli (Thu May 25 2006 - 01:37:10 PDT)
AMBER: question about REDII
- Raffaella D'Auria (Fri May 12 2006 - 12:12:41 PDT)
- FyD (Thu May 11 2006 - 23:34:48 PDT)
- Raffaella D'Auria (Thu May 11 2006 - 19:04:51 PDT)
AMBER: Question bonds and angles in frcmod and lib files
- Jennie Thomas (Wed May 03 2006 - 10:26:55 PDT)
- Bill Ross (Wed May 03 2006 - 09:28:08 PDT)
- Jennie Thomas (Wed May 03 2006 - 08:54:43 PDT)
- David A. Case (Wed May 03 2006 - 08:23:12 PDT)
- Jennie Thomas (Wed May 03 2006 - 01:02:55 PDT)
AMBER: Question bonds and angles in frcmod and lib files]
- Jennie Thomas (Thu May 04 2006 - 15:45:21 PDT)
- Bill Ross (Wed May 03 2006 - 15:00:58 PDT)
- Jennie Thomas (Wed May 03 2006 - 14:49:19 PDT)
AMBER: question on distance calculation
- bala (Mon May 08 2006 - 03:09:23 PDT)
AMBER: Replica exchage: about exchange interval
- Carlos Simmerling (Wed May 31 2006 - 06:02:32 PDT)
- Atsutoshi Okabe (Wed May 31 2006 - 05:36:27 PDT)
AMBER: restraintmask
- Viktor Hornak (Thu May 04 2006 - 11:41:37 PDT)
- Joseph Fernandez (Thu May 04 2006 - 11:22:21 PDT)
AMBER: RMSD calculation between ligands
- Stefan Henrich (Fri May 12 2006 - 05:09:15 PDT)
AMBER: RMSd calculations
- Claire Zerafa (Thu May 18 2006 - 12:25:57 PDT)
AMBER: RMSd error
- Claire Zerafa (Sun May 28 2006 - 09:26:14 PDT)
- Thomas Cheatham (Fri May 26 2006 - 08:59:34 PDT)
- Claire Zerafa (Fri May 26 2006 - 06:30:57 PDT)
- Carlos Simmerling (Fri May 26 2006 - 05:58:42 PDT)
- Claire Zerafa (Fri May 26 2006 - 05:26:06 PDT)
- Carlos Simmerling (Fri May 26 2006 - 04:27:18 PDT)
- Claire Zerafa (Thu May 25 2006 - 21:37:54 PDT)
- Carlos Simmerling (Mon May 22 2006 - 05:02:02 PDT)
- Claire Zerafa (Mon May 22 2006 - 01:52:34 PDT)
AMBER: San Fransisco Amber users
- homeira amirkhani (Tue May 09 2006 - 04:38:06 PDT)
AMBER: SAVEPDB in Xleap could not save 4 character atom names
- Andy Purkiss (Tue May 30 2006 - 11:18:58 PDT)
- David A. Case (Tue May 30 2006 - 10:36:37 PDT)
- Bill Ross (Mon May 29 2006 - 13:26:56 PDT)
- Jiayun Pang (Mon May 29 2006 - 09:38:22 PDT)
AMBER: Saving RMSD values in VMD
- Carlos Simmerling (Fri May 26 2006 - 08:45:17 PDT)
- Ross Walker (Fri May 26 2006 - 08:27:08 PDT)
- nag raj (Fri May 26 2006 - 07:33:00 PDT)
AMBER: sequential execution of number of parallel jobs
- Petr Kulhanek (Tue May 02 2006 - 01:20:51 PDT)
- In Hee Park (Mon May 01 2006 - 13:13:23 PDT)
AMBER: SHAKE, TIP3P and 2fs Timesteps
- Andreas Svrcek-Seiler (Wed May 31 2006 - 11:38:29 PDT)
- Ross Walker (Wed May 31 2006 - 10:56:31 PDT)
- Mark Williamson (Wed May 31 2006 - 10:32:56 PDT)
AMBER: Shared libraries error
- Viktor Hornak (Thu May 04 2006 - 11:54:26 PDT)
- Ross Walker (Wed May 03 2006 - 08:13:32 PDT)
- Andrew Box (Tue May 02 2006 - 20:14:38 PDT)
AMBER: simulate proteins with non-standard residues
- Hui Lei (Wed May 24 2006 - 10:10:08 PDT)
AMBER: Simulation of crystal - problem with excluded atom list
- Jennie Thomas (Tue May 02 2006 - 10:07:20 PDT)
AMBER: some new tutorials
- David A. Case (Mon May 01 2006 - 16:55:19 PDT)
AMBER: strange mm_pbsa output
- alfredoq.fcq.unc.edu.ar (Sun May 14 2006 - 07:22:14 PDT)
- David A. Case (Sat May 13 2006 - 15:44:14 PDT)
- alfredoq.fcq.unc.edu.ar (Sat May 13 2006 - 13:43:53 PDT)
- Ray Luo (Fri May 12 2006 - 17:22:57 PDT)
- alfredoq.fcq.unc.edu.ar (Sat May 13 2006 - 08:44:58 PDT)
AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs
- Zhihong Yu (Mon May 15 2006 - 02:00:03 PDT)
- Ross Walker (Sun May 14 2006 - 22:13:01 PDT)
- Zhihong Yu (Sun May 14 2006 - 20:55:51 PDT)
AMBER: Thermodynamic integration using the amber 9
- Ilyas Yildirim (Mon May 29 2006 - 07:25:21 PDT)
- Vitor Manuel Sousa F?x (Mon May 29 2006 - 06:41:14 PDT)
AMBER: trajin and rms
- a a (Wed May 24 2006 - 03:49:05 PDT)
- Carlos Simmerling (Mon May 22 2006 - 04:58:04 PDT)
- a a (Mon May 22 2006 - 01:55:03 PDT)
- Ross Walker (Sun May 21 2006 - 21:43:09 PDT)
- a a (Sun May 21 2006 - 21:18:37 PDT)
AMBER: trouble stripping waters with ptraj
- Asim Okur (Tue May 16 2006 - 13:17:32 PDT)
- Adam Pelzer (Tue May 16 2006 - 13:09:30 PDT)
AMBER: Trouble with ptraj closestwater in Amber8
- Kerry P Donny-Clark (Thu May 04 2006 - 10:29:23 PDT)
AMBER: Tutorial one : libsvml.so error
- Mark Williamson (Wed May 17 2006 - 00:27:05 PDT)
- a a (Tue May 16 2006 - 23:01:26 PDT)
AMBER: Tutorial one : xaLeap command not found.
- Ross Walker (Wed May 17 2006 - 08:40:12 PDT)
- a a (Wed May 17 2006 - 03:12:53 PDT)
AMBER: use_pme=0 problem
- Bill Ross (Fri May 26 2006 - 13:32:35 PDT)
- luckyang.gmail.com (Fri May 26 2006 - 13:19:11 PDT)
- David A. Case (Fri May 26 2006 - 12:30:01 PDT)
- luckyang.gmail.com (Fri May 26 2006 - 12:10:19 PDT)
- David A. Case (Fri May 26 2006 - 10:34:39 PDT)
- luckyang.gmail.com (Thu May 25 2006 - 18:56:30 PDT)
- David A. Case (Thu May 25 2006 - 10:56:56 PDT)
- luckyang.gmail.com (Thu May 25 2006 - 10:09:59 PDT)
- luckyang.gmail.com (Wed May 24 2006 - 17:51:10 PDT)
- David A. Case (Wed May 24 2006 - 17:33:53 PDT)
- luckyang.gmail.com (Wed May 24 2006 - 17:20:35 PDT)
- David A. Case (Wed May 24 2006 - 16:50:56 PDT)
- luckyang.gmail.com (Wed May 24 2006 - 16:18:47 PDT)
AMBER: vlimit exceeded
- David A. Case (Thu May 18 2006 - 05:24:49 PDT)
- aixiaoli (Thu May 18 2006 - 01:14:29 PDT)
AMBER: Water density output
- Navnit Kumar Mishra (Mon May 22 2006 - 04:02:48 PDT)
AMBER: which patch for ioutfm = 1 in Amber8?
- Hannes Loeffler (Wed May 10 2006 - 22:21:25 PDT)
AMBER: which time should I use to calculate the number of "ps/Day"
- Zhihong Yu (Mon May 29 2006 - 17:42:01 PDT)
- Robert Duke (Mon May 29 2006 - 06:10:04 PDT)
- Carlos Simmerling (Mon May 29 2006 - 02:50:31 PDT)
- Zhihong Yu (Mon May 29 2006 - 02:32:26 PDT)
AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1?
- David A. Case (Thu May 11 2006 - 07:43:28 PDT)
- Pan, Yongmei (Thu May 11 2006 - 07:13:02 PDT)
AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7
- David Mobley (Fri May 12 2006 - 10:22:41 PDT)
- Pan, Yongmei (Thu May 11 2006 - 11:50:36 PDT)
AMBER: Xleap compilation problem
- Sergio Dall'Angelo (Fri May 12 2006 - 08:21:02 PDT)
- Sergio Dall'Angelo (Fri May 12 2006 - 03:19:48 PDT)
- Sergio Dall'Angelo (Fri May 12 2006 - 02:49:16 PDT)
AMBER: xleap not recognizing residue
- David A. Case (Tue May 09 2006 - 15:42:14 PDT)
- Kenley Barrett (Mon May 08 2006 - 10:04:37 PDT)
- David A. Case (Sun May 07 2006 - 18:50:06 PDT)
- Kenley Barrett (Sun May 07 2006 - 17:13:13 PDT)
AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why
- David A. Case (Wed May 10 2006 - 13:12:52 PDT)
- Kenley Barrett (Wed May 10 2006 - 12:54:46 PDT)
AMBER: xleap on iMac G5
- Mengjuei Hsieh (Fri May 05 2006 - 22:44:00 PDT)
- Evan Kelly (Fri May 05 2006 - 21:01:53 PDT)
AMBER: xleap problem and answer
- Thomas Pochapsky (Wed May 31 2006 - 11:32:32 PDT)
AMBER: xmgr error
- Douali, Latifa (Fri May 19 2006 - 10:07:01 PDT)
- mathew k varghese (Fri May 19 2006 - 03:54:00 PDT)
- a a (Fri May 19 2006 - 02:50:25 PDT)
IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031
- amit.mbu.iisc.ernet.in (Wed May 10 2006 - 00:06:46 PDT)
- David A. Case (Tue May 09 2006 - 13:16:30 PDT)
- Ross Walker (Tue May 09 2006 - 12:12:09 PDT)
- amit.mbu.iisc.ernet.in (Tue May 09 2006 - 11:32:52 PDT)
Intel Compiler.
- Priti Hansia (Wed May 10 2006 - 08:39:04 PDT)
- Ross Walker (Tue May 09 2006 - 10:21:43 PDT)
- Priti Hansia (Tue May 09 2006 - 10:12:18 PDT)
- Ross Walker (Tue May 09 2006 - 09:05:28 PDT)
PMEMD compilation problems
- Robert Duke (Fri May 19 2006 - 09:20:52 PDT)
- Simon Whitehead (Fri May 19 2006 - 08:37:46 PDT)
RMSd calculations
- Carlos Simmerling (Fri May 19 2006 - 06:00:50 PDT)
- Claire Zerafa (Fri May 19 2006 - 05:07:30 PDT)
trouble stripping waters with ptraj
- Thomas Cheatham (Tue May 30 2006 - 10:17:31 PDT)
- Adam Pelzer (Mon May 29 2006 - 15:20:23 PDT)
- Thomas Cheatham (Fri May 26 2006 - 09:04:22 PDT)
- Carlos Simmerling (Fri May 26 2006 - 04:28:35 PDT)
- Adam Pelzer (Thu May 25 2006 - 21:50:53 PDT)
- Asim Okur (Mon May 22 2006 - 09:49:46 PDT)
- Carlos Simmerling (Sat May 20 2006 - 10:10:24 PDT)
- Adam Pelzer (Sat May 20 2006 - 09:00:12 PDT)

Amber Archive May 2006 by subject