Amber Archive Jun 2005: by subject

[pgannett.hsc.wvu.edu: AMBER: compiler error, SGI Octane]
- Roberto Gomperts (Wed Jun 29 2005 - 08:01:00 PDT)
AMBER :LINMIN problem
- Ross Walker (Fri Jun 17 2005 - 11:27:25 PDT)
AMBER:
- Ross Walker (Fri Jun 03 2005 - 09:51:48 PDT)
- Simon Whitehead (Thu Jun 02 2005 - 05:44:03 PDT)
AMBER: (no subject)
- Mohammed Mayeed (Wed Jun 08 2005 - 10:26:15 PDT)
AMBER: 10-12 potential and create atom type
- Fabien CAILLIEZ (Thu Jun 30 2005 - 10:19:41 PDT)
AMBER: a question about varying positions of dihedral restraints with step number
- David A. Case (Fri Jun 24 2005 - 08:09:21 PDT)
- Li Su (Wed Jun 22 2005 - 12:42:02 PDT)
AMBER: acceptor and donor in hbond calculation
- Vijay Manickam Achari (Wed Jun 29 2005 - 22:01:58 PDT)
AMBER: adenine test for LMOD in amber8
- Istvan Kolossvary (Thu Jun 16 2005 - 06:16:22 PDT)
- Giulio Rastelli (Thu Jun 16 2005 - 02:57:16 PDT)
AMBER: advice needed for minimization and dynamic protocol
- chaiann ng (Thu Jun 02 2005 - 18:33:44 PDT)
AMBER: amber 8 leap topology file dihedral term problem
- Angela Liu (Tue Jun 28 2005 - 06:59:57 PDT)
AMBER: AMBER frcmod+off input vs. prep input
- Bill Ross (Tue Jun 07 2005 - 10:58:06 PDT)
- K. Yarem (Tue Jun 07 2005 - 09:57:19 PDT)
AMBER: amber question about leap
- David A. Case (Thu Jun 02 2005 - 08:05:12 PDT)
- du yongchun (Wed Jun 01 2005 - 22:12:12 PDT)
AMBER: amber8 installation problems
- David A. Case (Thu Jun 02 2005 - 08:07:19 PDT)
- Zhang Bing (Wed Jun 01 2005 - 23:55:48 PDT)
- Zhang Bing (Wed Jun 01 2005 - 23:44:47 PDT)
AMBER: Analysing my simulation data..
- Ilyas Yildirim (Sat Jun 18 2005 - 09:47:06 PDT)
- Varsha Goyal (Sat Jun 18 2005 - 09:21:28 PDT)
- Vijay Manickam Achari (Sat Jun 18 2005 - 01:32:13 PDT)
AMBER: Announcing the LMOD website
- Istvan Kolossvary (Mon Jun 13 2005 - 11:18:52 PDT)
AMBER: antechamber error
- David A. Case (Thu Jun 30 2005 - 14:38:11 PDT)
- Peter Gannett (Thu Jun 30 2005 - 12:05:25 PDT)
AMBER: antechamber problems
- Shulin Zhuang (Mon Jun 20 2005 - 18:07:56 PDT)
- Junmei Wang (Mon Jun 20 2005 - 09:35:12 PDT)
- hj zou (Sun Jun 19 2005 - 06:50:08 PDT)
- hj zou (Fri Jun 17 2005 - 06:32:27 PDT)
AMBER: Antechamber RESP failed for large organic molecule
- junwang (Wed Jun 01 2005 - 14:18:05 PDT)
- Junmei Wang (Wed Jun 01 2005 - 09:54:42 PDT)
AMBER: Argon Box
- Biswaroop Mukherjee (Thu Jun 02 2005 - 01:44:46 PDT)
AMBER: atom type for -CH=CH-
- Guanglei Cui (Fri Jun 10 2005 - 06:56:52 PDT)
- Qizhi Cui (Thu Jun 09 2005 - 18:46:13 PDT)
AMBER: atom type question
- David A. Case (Wed Jun 15 2005 - 08:18:18 PDT)
- opitz.che.udel.edu (Mon Jun 13 2005 - 13:46:18 PDT)
- David A. Case (Mon Jun 13 2005 - 13:05:44 PDT)
- opitz.che.udel.edu (Mon Jun 13 2005 - 12:41:30 PDT)
AMBER: average structure
- Ross Walker (Sun Jun 19 2005 - 17:41:07 PDT)
- emilia wu (Sun Jun 19 2005 - 17:15:53 PDT)
AMBER: bad atom type: H
- alice (Wed Jun 15 2005 - 18:35:00 PDT)
- David A. Case (Wed Jun 15 2005 - 08:09:17 PDT)
- alice (Wed Jun 15 2005 - 03:53:50 PDT)
AMBER: Build of AMBER for YDL ?
- Ross Walker (Wed Jun 01 2005 - 16:29:49 PDT)
- Gert Kiss (Wed Jun 01 2005 - 16:15:57 PDT)
AMBER: calculating hydrogen bonds
- Vijay Manickam Achari (Tue Jun 28 2005 - 19:50:36 PDT)
AMBER: calculating torsion angles
- Vijay Manickam Achari (Tue Jun 28 2005 - 01:59:02 PDT)
AMBER: Can constant pH be used for minimization?
- John Mongan (Tue Jun 14 2005 - 17:03:38 PDT)
- David A. Case (Sat Jun 11 2005 - 05:42:51 PDT)
- Kenley Barrett (Fri Jun 10 2005 - 14:34:41 PDT)
AMBER: center-of-mass distance restraints
- JAVIER PEREZ (Thu Jun 02 2005 - 04:14:15 PDT)
AMBER: checkoverlap
- Gustavo Pierdominici Sottile (Thu Jun 02 2005 - 10:45:19 PDT)
AMBER: Compile Problems of Parallel Amber8 on Mac G5
- Suxin Zheng (Wed Jun 08 2005 - 16:02:23 PDT)
AMBER: Compile question??
- Robert Duke (Mon Jun 06 2005 - 07:32:06 PDT)
- Robert Duke (Mon Jun 06 2005 - 07:17:48 PDT)
- Anthony Cruz (Mon Jun 06 2005 - 06:24:40 PDT)
- Robert Duke (Mon Jun 06 2005 - 05:38:02 PDT)
- Anthony Cruz (Mon Jun 06 2005 - 04:59:13 PDT)
AMBER: compiler
- David A. Case (Tue Jun 14 2005 - 11:40:16 PDT)
- David LeBard (Tue Jun 14 2005 - 10:45:27 PDT)
- Ross Walker (Tue Jun 14 2005 - 10:43:58 PDT)
- Zhang Bing (Tue Jun 14 2005 - 04:13:19 PDT)
- Zhang Bing (Tue Jun 14 2005 - 01:14:08 PDT)
AMBER: compiler error, SGI Octane
- Peter Gannett (Tue Jun 28 2005 - 05:54:35 PDT)
AMBER: Create new Unit
- David A. Case (Thu Jun 30 2005 - 18:38:42 PDT)
- Douali, Latifa (Thu Jun 30 2005 - 16:45:37 PDT)
AMBER: creating pdb file....
- Ross Walker (Tue Jun 14 2005 - 10:51:21 PDT)
- Angelo Pugliese (Tue Jun 14 2005 - 04:11:41 PDT)
- Vijay Manickam Achari (Tue Jun 14 2005 - 03:49:09 PDT)
AMBER: Cut pdb files
- Yogesh Sabnis (Thu Jun 16 2005 - 00:57:18 PDT)
AMBER: density problem
- cristian obiol (Wed Jun 08 2005 - 01:56:23 PDT)
- cristian obiol (Thu Jun 02 2005 - 01:14:21 PDT)
- Ross Walker (Wed Jun 01 2005 - 09:21:33 PDT)
- Shulin Zhuang (Tue May 31 2005 - 18:49:47 PDT)
AMBER: dielectric constant
- David LeBard (Tue Jun 28 2005 - 13:01:30 PDT)
- Germán Sciaini (Wed Jun 29 2005 - 04:02:24 PDT)
AMBER: DNA base-flipping: TI vs PMF
- Peter Varnai (Thu Jun 02 2005 - 10:21:56 PDT)
AMBER: eelnb
- Stern, Julie (Mon Jun 06 2005 - 13:16:31 PDT)
AMBER: eigenvalues in vector of ptraj
- Hwankyu Lee (Wed Jun 01 2005 - 05:53:51 PDT)
AMBER: error - compiling antechamber
- Roberto Gomperts (Wed Jun 29 2005 - 14:11:41 PDT)
- Peter Gannett (Wed Jun 29 2005 - 12:30:20 PDT)
AMBER: Error on restrained MD equilibration (AMBER 7)
- L Jin (Wed Jun 01 2005 - 08:05:12 PDT)
- Guanglei Cui (Wed Jun 01 2005 - 07:18:37 PDT)
- Petr Kulhanek (Wed Jun 01 2005 - 04:03:21 PDT)
- L Jin (Wed Jun 01 2005 - 03:24:12 PDT)
- L Jin (Wed Jun 01 2005 - 03:20:40 PDT)
- Shulin Zhuang (Tue May 31 2005 - 18:36:32 PDT)
AMBER: Error: vlimit exceeded for step
- Ross Walker (Mon Jun 06 2005 - 20:49:05 PDT)
- Bill Ross (Mon Jun 06 2005 - 17:03:38 PDT)
- Hwankyu Lee (Mon Jun 06 2005 - 16:48:56 PDT)
- Hwankyu Lee (Mon Jun 06 2005 - 16:26:16 PDT)
- Ross Walker (Mon Jun 06 2005 - 16:24:21 PDT)
- Hwankyu Lee (Mon Jun 06 2005 - 15:47:29 PDT)
- Ross Walker (Mon Jun 06 2005 - 10:19:04 PDT)
- Hwankyu Lee (Mon Jun 06 2005 - 06:55:57 PDT)
AMBER: example script for hbond calculation
- Vijay Manickam Achari (Wed Jun 29 2005 - 23:27:15 PDT)
AMBER: Extended bonds-MD
- Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 05:55:41 PDT)
- Carlos Simmerling (Wed Jun 15 2005 - 04:22:29 PDT)
- Ananda Rama Krishnan Selvaraj (Wed Jun 15 2005 - 00:02:25 PDT)
- Ross Walker (Tue Jun 14 2005 - 10:28:43 PDT)
- Ananda Rama Krishnan Selvaraj (Tue Jun 14 2005 - 09:29:29 PDT)
AMBER: fail of minimization in sander
- wendy (Thu Jun 16 2005 - 19:43:11 PDT)
- David A. Case (Thu Jun 16 2005 - 07:44:21 PDT)
- Carlos Simmerling (Thu Jun 16 2005 - 04:06:42 PDT)
- wendy (Thu Jun 16 2005 - 01:19:15 PDT)
- Carlos Simmerling (Wed Jun 15 2005 - 04:24:04 PDT)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Wed Jun 15 2005 - 04:05:25 PDT)
- wendy (Wed Jun 15 2005 - 00:54:59 PDT)
- Andy Purkiss (Tue Jun 07 2005 - 05:17:24 PDT)
- Bill Ross (Mon Jun 06 2005 - 10:58:54 PDT)
- Ross Walker (Mon Jun 06 2005 - 10:25:26 PDT)
- wendy (Mon Jun 06 2005 - 09:13:10 PDT)
- Carlos Simmerling (Mon Jun 06 2005 - 09:12:38 PDT)
- wendy (Mon Jun 06 2005 - 08:57:08 PDT)
- Bill Ross (Mon Jun 06 2005 - 07:34:39 PDT)
- Carlos Simmerling (Mon Jun 06 2005 - 04:24:25 PDT)
- wendy (Mon Jun 06 2005 - 03:06:01 PDT)
- wendy (Sun Jun 05 2005 - 21:59:15 PDT)
- Bill Ross (Sun Jun 05 2005 - 20:50:48 PDT)
- wendy (Sun Jun 05 2005 - 20:01:25 PDT)
AMBER: For calculating the energy rised from deviation of equalibrium values of bond angles does amber use degree or radians
- Li Su (Thu Jun 16 2005 - 16:17:46 PDT)
- Ross Walker (Thu Jun 16 2005 - 15:00:41 PDT)
- Li Su (Thu Jun 16 2005 - 14:19:36 PDT)
AMBER: Free energy calculation for protein-protein complex using MM_PBSA
- Thomas Steinbrecher (Thu Jun 30 2005 - 00:14:01 PDT)
- Zhiguo Liu (Wed Jun 29 2005 - 18:59:01 PDT)
AMBER: Free energy calculation for protein-protein complex usingMM_PBSA
- Martin Sippel (Thu Jun 30 2005 - 03:32:11 PDT)
- Zhiguo Liu (Thu Jun 30 2005 - 02:56:42 PDT)
AMBER: Free Energy Calculation torsion missing
- mrbroad.ilstu.edu (Tue Jun 14 2005 - 11:21:54 PDT)
AMBER: gaff.dat typo
- David A. Case (Thu Jun 02 2005 - 08:01:58 PDT)
- Brent Krueger (Wed Jun 01 2005 - 18:35:58 PDT)
AMBER: GB/SA/LD parallel sander
- Carlos Simmerling (Wed Jun 08 2005 - 13:09:59 PDT)
- Lwin, ThuZar (Wed Jun 08 2005 - 12:36:41 PDT)
- Lwin, ThuZar (Mon Jun 06 2005 - 09:48:27 PDT)
AMBER: GBSA and thermodynamic ensemble
- David A. Case (Mon Jun 13 2005 - 13:13:14 PDT)
- Julien Michel (Mon Jun 13 2005 - 12:51:23 PDT)
- Osmar Norberto de Souza (Mon Jun 13 2005 - 11:29:18 PDT)
AMBER: GCC for AMBER on 64 bit machine
- Andreas Svrcek-Seiler (Thu Jun 23 2005 - 11:44:44 PDT)
- mfyang (Thu Jun 23 2005 - 10:55:01 PDT)
AMBER: Gibbs perturb DNA strands separate
- ivan.mmb.pcb.ub.es (Tue Jun 07 2005 - 04:16:41 PDT)
AMBER: Have the parameters for dUMP been calculated by somebody?
- Suxin Zheng (Fri Jun 24 2005 - 18:30:12 PDT)
AMBER: Hbond analysis
- Fabian Boes (Mon Jun 27 2005 - 06:12:34 PDT)
- xueping (Sun Jun 26 2005 - 18:27:48 PDT)
AMBER: How does Amber8 implemnet ntf=4?
- Carlos Simmerling (Thu Jun 02 2005 - 08:53:36 PDT)
- David A. Case (Thu Jun 02 2005 - 08:52:10 PDT)
- Li Su (Thu Jun 02 2005 - 08:32:30 PDT)
AMBER: how the phosphated threonine to be recognized in leap
- haixiao jin (Thu Jun 23 2005 - 02:03:26 PDT)
AMBER: How to modify force constants and equalibrium values for standard residues
- gsciaini (Fri Jun 17 2005 - 06:41:44 PDT)
- Ross Walker (Thu Jun 16 2005 - 14:05:33 PDT)
- David A. Case (Thu Jun 16 2005 - 07:41:18 PDT)
- Li Su (Thu Jun 16 2005 - 06:30:41 PDT)
AMBER: how to pull out frames
- Vijay Manickam Achari (Mon Jun 13 2005 - 21:04:42 PDT)
- Husni Fattayer (Mon Jun 13 2005 - 04:22:40 PDT)
- Vijay Manickam Achari (Sun Jun 12 2005 - 22:23:51 PDT)
AMBER: How to read unformatted restart file in PTRAJ ?
- JunJun Liu (Tue Jun 28 2005 - 23:20:57 PDT)
AMBER: How to run amber more efficiently?
- alice (Tue Jun 07 2005 - 19:59:26 PDT)
AMBER: How to set the virtual box size for a calculation run in vacuum
- Li Su (Mon Jun 20 2005 - 06:27:33 PDT)
AMBER: How to turn off pme when using periodic box
- Ross Walker (Mon Jun 20 2005 - 13:31:04 PDT)
- Li Su (Mon Jun 20 2005 - 11:31:09 PDT)
AMBER: inpcrd file
- Douali, Latifa (Fri Jun 10 2005 - 16:04:24 PDT)
AMBER: Installation problem
- Chris Harrison (Mon Jun 13 2005 - 17:33:13 PDT)
- Sukjoon Yoon (Sun Jun 12 2005 - 21:07:26 PDT)
- Sukjoon Yoon (Sun Jun 12 2005 - 19:35:37 PDT)
- Chris Harrison (Sun Jun 12 2005 - 16:04:22 PDT)
- Sukjoon Yoon (Sun Jun 12 2005 - 02:21:50 PDT)
AMBER: Installation problem - wrong address
- Andreas Svrcek-Seiler (Fri Jun 17 2005 - 10:28:43 PDT)
AMBER: Installation problem. .
- Ross Walker (Fri Jun 17 2005 - 10:39:15 PDT)
- Andreas Svrcek-Seiler (Fri Jun 17 2005 - 10:12:10 PDT)
- Ross Walker (Fri Jun 17 2005 - 09:33:42 PDT)
- Andreas Svrcek-Seiler (Thu Jun 16 2005 - 21:54:42 PDT)
- Mark Williamson (Thu Jun 16 2005 - 08:15:58 PDT)
- Mark Williamson (Thu Jun 16 2005 - 08:06:57 PDT)
- Sukjoon Yoon (Thu Jun 16 2005 - 07:49:19 PDT)
- Ross Walker (Wed Jun 15 2005 - 09:46:25 PDT)
- Andreas Svrcek-Seiler (Wed Jun 15 2005 - 05:31:46 PDT)
- Sukjoon Yoon (Tue Jun 14 2005 - 23:08:51 PDT)
- Don.Bashford.stjude.org (Mon Jun 13 2005 - 10:56:46 PDT)
AMBER: INTRA molecular hbonds
- Fabian Boes (Mon Jun 27 2005 - 07:45:13 PDT)
- Giulio Rastelli (Mon Jun 27 2005 - 07:09:23 PDT)
AMBER: Is the MD simulation normal
- Shulin Zhuang (Thu Jun 30 2005 - 08:00:11 PDT)
- Shulin Zhuang (Thu Jun 30 2005 - 07:52:03 PDT)
- Ross Walker (Wed Jun 29 2005 - 09:09:13 PDT)
- Shulin Zhuang (Wed Jun 29 2005 - 08:03:20 PDT)
- Shulin Zhuang (Wed Jun 29 2005 - 03:11:53 PDT)
- JunJun Liu (Tue May 31 2005 - 19:01:07 PDT)
AMBER: large std error in entropy estimation
- David A. Case (Thu Jun 23 2005 - 11:25:03 PDT)
- Ye Mei (Tue Jun 21 2005 - 19:51:43 PDT)
AMBER: leap issues on a powerbook
- justin litchfield (Sun Jun 12 2005 - 16:21:02 PDT)
AMBER: Make Distance restraints for non-standard residues
- gtg549i.mail.gatech.edu (Fri Jun 10 2005 - 13:45:00 PDT)
- David A. Case (Fri Jun 10 2005 - 12:59:13 PDT)
- gtg549i.mail.gatech.edu (Fri Jun 10 2005 - 08:47:41 PDT)
AMBER: MM-PBSA calculation
- Scott Pendley (Wed Jun 01 2005 - 16:44:05 PDT)
AMBER: mm/pbsa error
- Eric Hu (Wed Jun 01 2005 - 10:23:53 PDT)
AMBER: MM_PBSA !
- Jiten (Sun Jun 26 2005 - 17:43:13 PDT)
- Pradipta Bandyopadhyay (Sun Jun 26 2005 - 05:43:18 PDT)
AMBER: mm_pbsa script !
- Pradipta Bandyopadhyay (Sun Jun 26 2005 - 23:43:53 PDT)
AMBER: Need help in charge fitting through RESP
- junwang (Mon Jun 13 2005 - 10:51:41 PDT)
- Nadine Homeyer (Mon Jun 13 2005 - 09:20:49 PDT)
- FyD (Mon Jun 13 2005 - 09:15:42 PDT)
- Shulin Zhuang (Mon Jun 13 2005 - 07:29:02 PDT)
- S.Sundar Raman (Mon Jun 13 2005 - 06:55:29 PDT)
AMBER: New problem of parallel sander
- Ross Walker (Fri Jun 03 2005 - 09:53:55 PDT)
- David A. Case (Fri Jun 03 2005 - 08:00:30 PDT)
- Zhang Bing (Thu Jun 02 2005 - 19:46:13 PDT)
AMBER: Nmode calculations
- Martin Sippel (Fri Jun 03 2005 - 10:17:48 PDT)
AMBER: nmode with ibelly
- David A. Case (Wed Jun 08 2005 - 21:30:01 PDT)
- Martin Sippel (Wed Jun 08 2005 - 10:48:04 PDT)
- David A. Case (Tue Jun 07 2005 - 07:41:41 PDT)
- Martin Sippel (Tue Jun 07 2005 - 03:11:44 PDT)
- David A. Case (Mon Jun 06 2005 - 13:09:08 PDT)
- Martin Sippel (Mon Jun 06 2005 - 02:38:42 PDT)
AMBER: Nmode with residues excluded
- Martin Sippel (Fri Jun 03 2005 - 09:56:42 PDT)
AMBER: nmropt =1 AND ntr=1 in pmemd
- Robert Duke (Fri Jun 17 2005 - 14:58:44 PDT)
- Furse, Kristina Elisabet (Fri Jun 17 2005 - 12:16:13 PDT)
- Robert Duke (Tue Jun 14 2005 - 05:18:20 PDT)
- Christoph Brockmann (Tue Jun 14 2005 - 02:33:39 PDT)
AMBER: no corrected reaction field energy in *.out files after running mm_pbsa
- haixiao jin (Sun Jun 12 2005 - 19:04:40 PDT)
AMBER: nonbond_list question .
- Robert Duke (Sun Jun 19 2005 - 07:25:37 PDT)
- Petr Kulhanek (Sun Jun 19 2005 - 03:06:31 PDT)
- Robert Duke (Sat Jun 18 2005 - 20:03:07 PDT)
- Michael Crowley (Sat Jun 18 2005 - 12:51:01 PDT)
- caoch.cherry.bio.titech.ac.jp (Fri Jun 17 2005 - 18:38:27 PDT)
AMBER: normal mode mm/pbsa interupted
- Eric Hu (Thu Jun 09 2005 - 11:46:04 PDT)
AMBER: nucgen problem
- David A. Case (Tue Jun 07 2005 - 13:17:12 PDT)
- Carlos Simmerling (Tue Jun 07 2005 - 12:34:17 PDT)
- Bill Ross (Tue Jun 07 2005 - 12:27:14 PDT)
- cbala.igib.res.in (Tue Jun 07 2005 - 12:48:13 PDT)
- Bill Ross (Tue Jun 07 2005 - 09:47:42 PDT)
- David A. Case (Tue Jun 07 2005 - 07:38:15 PDT)
- cbala.igib.res.in (Tue Jun 07 2005 - 06:41:27 PDT)
AMBER: parallel error
- Zhang Bing (Mon Jun 27 2005 - 05:36:14 PDT)
AMBER: Parameters for phosphorylated amino acids
- Suxin Zheng (Thu Jun 23 2005 - 15:41:30 PDT)
- Nadine Homeyer (Thu Jun 23 2005 - 07:24:08 PDT)
- Nadine Homeyer (Thu Jun 23 2005 - 06:54:22 PDT)
AMBER: pb_pgb test fail
- David A. Case (Mon Jun 27 2005 - 11:48:32 PDT)
- acb15885.uprm.edu (Mon Jun 27 2005 - 11:17:48 PDT)
AMBER: PBSA error: PB bomb in pd_aaradi
- JunJun Liu (Wed Jun 22 2005 - 08:17:43 PDT)
- Xin Hu (Wed Jun 22 2005 - 07:34:13 PDT)
AMBER: position of protonation info from constant pH run
- Kenley Barrett (Wed Jun 15 2005 - 18:27:44 PDT)
AMBER: precision switch from 64 to 32 bit (double from single precision)
- Robert Duke (Thu Jun 09 2005 - 05:20:52 PDT)
- Cordova, Luis E. (Wed Jun 08 2005 - 22:39:59 PDT)
AMBER: pressure output
- David A. Case (Fri Jun 03 2005 - 08:05:59 PDT)
- Germán Sciaini (Thu Jun 02 2005 - 15:27:13 PDT)
AMBER: problem in minimization
- Ananda Rama Krishnan Selvaraj (Thu Jun 02 2005 - 00:39:36 PDT)
- Ross Walker (Wed Jun 01 2005 - 09:56:46 PDT)
- Ananda Rama Krishnan Selvaraj (Wed Jun 01 2005 - 01:48:46 PDT)
AMBER: Protein dynamics.
- Yong Duan (Wed Jun 08 2005 - 10:24:02 PDT)
- Laurence Lavelle (Tue Jun 07 2005 - 22:52:00 PDT)
- David A. Case (Mon Jun 06 2005 - 15:37:10 PDT)
- Laurence Lavelle (Mon Jun 06 2005 - 14:43:50 PDT)
AMBER: Protein ions?
- Anthony Cruz (Thu Jun 02 2005 - 09:45:34 PDT)
- David A. Case (Thu Jun 02 2005 - 08:25:07 PDT)
- Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Thu Jun 02 2005 - 07:57:02 PDT)
- Anthony Cruz (Thu Jun 02 2005 - 07:12:56 PDT)
AMBER: Protein-surface interaction
- Mohammed Mayeed (Wed Jun 08 2005 - 11:37:30 PDT)
AMBER: puzzling gaff parameter
- Oliver Hucke (Tue Jun 14 2005 - 18:16:35 PDT)
AMBER: quadrupole in resp
- David A. Case (Tue Jun 07 2005 - 10:30:12 PDT)
AMBER: Question about "quasih"
- David A. Case (Wed Jun 15 2005 - 14:01:33 PDT)
- Yen-Ting Lai (Wed Jun 15 2005 - 12:25:57 PDT)
- David A. Case (Wed Jun 15 2005 - 10:43:47 PDT)
- Yen-Ting Lai (Wed Jun 15 2005 - 09:46:22 PDT)
AMBER: question about Carnal
- Bill Ross (Wed Jun 22 2005 - 13:51:34 PDT)
- opitz.che.udel.edu (Wed Jun 22 2005 - 13:03:45 PDT)
AMBER: Question about GAFF atom types
- Ilyas Yildirim (Mon Jun 20 2005 - 12:51:59 PDT)
- Herbert Georg (Mon Jun 20 2005 - 09:47:38 PDT)
- Ilyas Yildirim (Fri Jun 17 2005 - 18:29:24 PDT)
- Herbert Georg (Fri Jun 17 2005 - 15:31:52 PDT)
- Ilyas Yildirim (Fri Jun 17 2005 - 13:42:18 PDT)
- Herbert Georg (Fri Jun 17 2005 - 12:49:53 PDT)
- Herbert Georg (Thu Jun 16 2005 - 12:18:50 PDT)
AMBER: Question about tutorial-9
- Varsha Goyal (Tue Jun 07 2005 - 09:27:57 PDT)
AMBER: question whem using leap
- Carlos Simmerling (Thu Jun 02 2005 - 04:45:53 PDT)
- du yongchun (Thu Jun 02 2005 - 00:25:16 PDT)
AMBER: questions about RNA
- xinhuang.indiana.edu (Mon Jun 27 2005 - 20:19:58 PDT)
AMBER: radius parameter for Mg2+ in mm_pbsa calculation
- Thomas Steinbrecher (Mon Jun 06 2005 - 00:23:16 PDT)
- Guanglei Cui (Sat Jun 04 2005 - 08:17:11 PDT)
- Ye Mei (Sat Jun 04 2005 - 07:37:04 PDT)
AMBER: RED question
- FyD (Wed Jun 29 2005 - 09:34:16 PDT)
- Kara Di Giorgio (Sun Jun 26 2005 - 22:13:13 PDT)
- FyD (Sun Jun 26 2005 - 20:37:59 PDT)
- Kara Di Giorgio (Sat Jun 25 2005 - 15:44:23 PDT)
AMBER: Request for calculating free energy using AMBER6
- S.Sundar Raman (Mon Jun 27 2005 - 04:59:00 PDT)
AMBER: Request for g98 (IOP...)
- Oliver Hucke (Tue Jun 14 2005 - 09:20:51 PDT)
- FyD (Tue Jun 14 2005 - 08:55:27 PDT)
- Paramasivam Manikandan (Tue Jun 14 2005 - 08:04:30 PDT)
AMBER: RESP charges of RNA nucleotides with 3' and 5' ends
- Ilyas Yildirim (Wed Jun 22 2005 - 15:13:19 PDT)
- FyD (Wed Jun 22 2005 - 14:56:30 PDT)
- Ilyas Yildirim (Mon Jun 20 2005 - 18:51:11 PDT)
AMBER: Restrained-MD
- David A. Case (Mon Jun 13 2005 - 16:10:00 PDT)
- Ananda Rama Krishnan Selvaraj (Mon Jun 13 2005 - 16:04:14 PDT)
AMBER: runtime error in sander?
- Dave S Walker (Mon Jun 20 2005 - 11:02:16 PDT)
AMBER: Sander is changing directories
- Andreas Kerzmann (Wed Jun 08 2005 - 02:37:58 PDT)
- Andreas Kerzmann (Wed Jun 08 2005 - 02:39:23 PDT)
AMBER: Saturated DNA bases
- L.C. Heady (Wed Jun 01 2005 - 01:55:54 PDT)
AMBER: script for calculating hydrogen bond
- Ross Walker (Mon Jun 27 2005 - 20:04:43 PDT)
- Vijay Manickam Achari (Mon Jun 27 2005 - 19:57:30 PDT)
AMBER: Searching for NAD parameter files / Problems with parameter file creation
- Ross Walker (Thu Jun 23 2005 - 09:26:56 PDT)
- Rhoad, Jonathan S. (Thu Jun 23 2005 - 08:08:01 PDT)
- Daniel Wetzler (Thu Jun 23 2005 - 07:43:29 PDT)
AMBER: segmentation fault in sander
- Bill Ross (Tue Jun 07 2005 - 09:35:27 PDT)
- Kenley Barrett (Tue Jun 07 2005 - 08:36:44 PDT)
- Bill Ross (Mon Jun 06 2005 - 15:18:45 PDT)
- Kenley Barrett (Mon Jun 06 2005 - 15:07:59 PDT)
AMBER: setting up restraint with ntr option
- Viktor Hornak (Thu Jun 09 2005 - 16:53:05 PDT)
- Lwin, ThuZar (Thu Jun 09 2005 - 14:49:04 PDT)
AMBER: SHAKE in md with partial solvation
- Ye Mei (Tue Jun 07 2005 - 06:46:49 PDT)
- Ross Walker (Mon Jun 06 2005 - 10:12:20 PDT)
- Ye Mei (Mon Jun 06 2005 - 03:49:44 PDT)
- Germán Sciaini (Mon Jun 06 2005 - 03:34:09 PDT)
- Ye Mei (Sun Jun 05 2005 - 04:19:45 PDT)
- Ye Mei (Sun Jun 05 2005 - 00:30:00 PDT)
AMBER: software for real polymer MD simulation
- xhu1.memphis.edu (Wed Jun 22 2005 - 14:31:51 PDT)
AMBER: solutions of amber installation problems
- Ross Walker (Tue Jun 14 2005 - 21:55:20 PDT)
- Zhang Bing (Tue Jun 14 2005 - 19:42:13 PDT)
AMBER: Solvate question?
- Anthony Cruz (Tue Jun 07 2005 - 05:31:30 PDT)
- Carlos Simmerling (Mon Jun 06 2005 - 09:13:37 PDT)
- Anthony Cruz (Mon Jun 06 2005 - 08:59:06 PDT)
- Carlos Simmerling (Mon Jun 06 2005 - 04:26:53 PDT)
- Anthony Cruz (Mon Jun 06 2005 - 03:30:44 PDT)
AMBER: Solvents
- Anthony Cruz (Mon Jun 06 2005 - 09:00:07 PDT)
AMBER: SOURCE3 in gaff.dat
- Stern, Julie (Fri Jun 10 2005 - 02:40:20 PDT)
AMBER: sp2 carbon atom parametrization
- Gustavo Pierdominici Sottile (Tue Jun 14 2005 - 09:30:16 PDT)
AMBER: stripwater
- Lukasz Bielecki (Wed Jun 01 2005 - 07:16:05 PDT)
AMBER: substitute missing residues?
- Wai Keat Yam (Fri Jun 10 2005 - 01:20:29 PDT)
AMBER: Thanks
- Zhang Bing (Tue Jun 14 2005 - 19:26:23 PDT)
AMBER: TI calculation using sander
- David A. Case (Tue Jun 07 2005 - 18:32:34 PDT)
- Latifa Douali (Tue Jun 07 2005 - 17:10:54 PDT)
AMBER: TI in Amber8
- David A. Case (Fri Jun 03 2005 - 08:04:45 PDT)
- 建平胡 (Fri Jun 03 2005 - 02:49:02 PDT)
AMBER: TI tutorial in Amber 8
- David A. Case (Wed Jun 08 2005 - 21:27:42 PDT)
- huhu (Wed Jun 08 2005 - 02:52:24 PDT)
AMBER: TI-FEP for ALA --> GLY
- Ilyas Yildirim (Mon Jun 27 2005 - 22:46:17 PDT)
- Jiten (Mon Jun 27 2005 - 19:24:56 PDT)
- Ilyas Yildirim (Fri Jun 24 2005 - 23:48:36 PDT)
- Jiten (Fri Jun 24 2005 - 22:07:03 PDT)
AMBER: TI-FEP for VAL --> ALA
- Ilyas Yildirim (Mon Jun 27 2005 - 16:43:16 PDT)
- Jiten (Sun Jun 26 2005 - 19:11:03 PDT)
- Ilyas Yildirim (Sat Jun 25 2005 - 16:39:11 PDT)
- Jiten (Sat Jun 25 2005 - 09:13:44 PDT)
AMBER: time and lifetime in hbond analysis (ptraj)
- Angelo Pugliese (Tue Jun 14 2005 - 07:57:56 PDT)
- Giulio Rastelli (Tue Jun 14 2005 - 07:23:50 PDT)
AMBER: total energy leaps
- Carlos Simmerling (Wed Jun 08 2005 - 04:22:06 PDT)
- cristian obiol (Wed Jun 08 2005 - 03:44:18 PDT)
AMBER: transfer data from Linux to windows
- Fajar Rakhman Wibowo (Thu Jun 09 2005 - 16:11:33 PDT)
- Thomas Patko (Thu Jun 09 2005 - 15:49:02 PDT)
- Carlos Simmerling (Thu Jun 09 2005 - 15:41:26 PDT)
- Lihua Wang (Thu Jun 09 2005 - 15:32:14 PDT)
- gtg549i.mail.gatech.edu (Thu Jun 09 2005 - 15:24:05 PDT)
AMBER: using xmgrace....
- Vijay Manickam Achari (Thu Jun 23 2005 - 19:51:37 PDT)
AMBER: vdw for terminal phosphate
- Bill Ross (Mon Jun 13 2005 - 13:22:47 PDT)
- Rhoad, Jonathan S. (Mon Jun 13 2005 - 09:21:49 PDT)
- Bill Ross (Fri Jun 10 2005 - 11:10:32 PDT)
- Rhoad, Jonathan S. (Fri Jun 10 2005 - 09:16:47 PDT)
AMBER: Vibrational spectrum?
- milion.c-box.cz (Fri Jun 10 2005 - 09:53:01 PDT)
AMBER: Vibrational spectrum? [SOLUTION]
- Mark Williamson (Fri Jun 10 2005 - 03:33:51 PDT)
AMBER: why the dipeptide always moving out the virtual box
- David A. Case (Tue Jun 14 2005 - 15:50:03 PDT)
- Li Su (Tue Jun 14 2005 - 14:11:41 PDT)
- David A. Case (Mon Jun 13 2005 - 15:55:19 PDT)
- Li Su (Mon Jun 13 2005 - 14:40:47 PDT)
TI tutorial
- Jiten (Wed Jun 29 2005 - 10:24:19 PDT)
- David A. Case (Wed Jun 29 2005 - 10:01:23 PDT)
- Jiten (Wed Jun 29 2005 - 09:22:04 PDT)
- David A. Case (Wed Jun 29 2005 - 07:30:31 PDT)
- Jiten (Tue Jun 28 2005 - 20:46:17 PDT)
- David A. Case (Tue Jun 28 2005 - 18:09:44 PDT)
- Jiten (Tue Jun 28 2005 - 09:36:59 PDT)
- David A. Case (Tue Jun 28 2005 - 08:49:53 PDT)
- Jiten (Tue Jun 28 2005 - 07:17:39 PDT)
TI tutorial --> ALA --> GLY TI calculation
- Jiten (Tue Jun 28 2005 - 08:02:42 PDT)
tutorial 8
- Ross Walker (Wed Jun 22 2005 - 14:15:33 PDT)

Amber Archive Jun 2005 by subject