Amber Archive Aug 2006: by subject

AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
- a a (Mon Aug 14 2006 - 22:48:49 PDT)
- Kateryna Miroshnychenko (Mon Aug 14 2006 - 06:19:46 PDT)
AMBER:
- Qingning Shu (Tue Aug 29 2006 - 09:26:34 PDT)
- David A. Case (Tue Aug 29 2006 - 08:09:23 PDT)
- Qingning Shu (Tue Aug 29 2006 - 06:01:58 PDT)
- Scott Brozell (Mon Aug 07 2006 - 17:37:19 PDT)
- Glass, Kevin A (Mon Aug 07 2006 - 13:09:02 PDT)
AMBER: (Another) Question about using antechamber with G03
- David A. Case (Tue Aug 15 2006 - 16:09:56 PDT)
- Gustavo Seabra (Tue Aug 15 2006 - 10:51:16 PDT)
AMBER: (no subject)
- Navnit Kumar Mishra (Tue Aug 15 2006 - 05:51:49 PDT)
- a a (Tue Aug 15 2006 - 03:13:49 PDT)
AMBER: 0 steps the same as 1 step?
- David A. Case (Wed Aug 23 2006 - 18:14:53 PDT)
- S. Jamal Rahi (Wed Aug 23 2006 - 14:25:44 PDT)
AMBER: 1-4 interaction in AMBER8
- Carlos Simmerling (Wed Aug 30 2006 - 14:23:26 PDT)
- Bill Ross (Wed Aug 30 2006 - 14:17:10 PDT)
- Carlos Simmerling (Wed Aug 30 2006 - 14:15:23 PDT)
- Bill Ross (Wed Aug 30 2006 - 14:05:27 PDT)
- Jianhui (Wed Aug 30 2006 - 12:48:28 PDT)
- Carlos Simmerling (Wed Aug 30 2006 - 12:22:13 PDT)
- Jianhui (Wed Aug 30 2006 - 12:08:09 PDT)
AMBER: about Silica's polarizability
- David A. Case (Thu Aug 03 2006 - 09:16:40 PDT)
- yxiong99 (Thu Aug 03 2006 - 08:20:19 PDT)
AMBER: Advice on linux cluster sought
- Feng X Zhou (Mon Aug 14 2006 - 11:34:16 PDT)
AMBER: amber 9 intel 9.1 ia64
- Fabian Boes (Tue Aug 15 2006 - 06:59:39 PDT)
- Tim Robinson (Tue Aug 15 2006 - 06:45:16 PDT)
AMBER: Amber Installation Help
- David A. Case (Tue Aug 08 2006 - 08:25:49 PDT)
- Kirk Hevener (Mon Aug 07 2006 - 05:43:25 PDT)
AMBER: Amber Installation Help; link woes
- Scott Brozell (Tue Aug 08 2006 - 12:36:32 PDT)
AMBER: amber naming conventions for structure files
- Bill Ross (Tue Aug 22 2006 - 15:00:10 PDT)
- sethl.gatech.edu (Tue Aug 22 2006 - 14:36:56 PDT)
AMBER: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number?
- a a (Mon Aug 14 2006 - 04:25:31 PDT)
AMBER: AMBER8 - RDF bug
- Petr Kulhanek (Fri Aug 11 2006 - 09:00:57 PDT)
AMBER: amber9 Test Failer
- David A. Case (Tue Aug 15 2006 - 08:05:54 PDT)
- kawamura_hiro.riken.jp (Tue Aug 15 2006 - 05:21:49 PDT)
AMBER: amidine group/ gaff parameters
- Prashanth Athri (Fri Aug 18 2006 - 12:00:17 PDT)
AMBER: antechamber bond typing questions
- David Mobley (Mon Aug 07 2006 - 13:14:42 PDT)
AMBER: antechamber charge calculation very sensitive to conformations ?
- David Mobley (Fri Aug 25 2006 - 08:08:44 PDT)
- Junmei Wang (Thu Aug 24 2006 - 19:51:07 PDT)
- Christophe Guilbert (Wed Aug 23 2006 - 18:59:08 PDT)
AMBER: antechamber error -> metals
- Junmei Wang (Wed Aug 16 2006 - 19:29:46 PDT)
- Scott Brozell (Sun Aug 13 2006 - 14:58:14 PDT)
AMBER: antechamber failure on FMN
- David A. Case (Tue Aug 15 2006 - 16:14:41 PDT)
- David Mobley (Tue Aug 15 2006 - 11:16:47 PDT)
- David Mobley (Tue Aug 15 2006 - 11:04:42 PDT)
AMBER: any work-around for 80 character mask string limit?
- David A. Case (Tue Aug 01 2006 - 14:37:36 PDT)
- Tanya Johannsen (Tue Aug 01 2006 - 13:12:22 PDT)
AMBER: atomifluct
- Miguel Ferreira (Fri Aug 25 2006 - 04:09:03 PDT)
AMBER: Backbone & Sidechain atoms: Definition
- Zu Thur Yew (Thu Aug 24 2006 - 10:32:14 PDT)
- David A. Case (Thu Aug 24 2006 - 08:15:44 PDT)
- Zu Thur Yew (Thu Aug 24 2006 - 06:13:14 PDT)
AMBER: brookhaven to amber pdb format
- Ilyas Yildirim (Wed Aug 02 2006 - 11:55:38 PDT)
- David A. Case (Wed Aug 02 2006 - 07:48:23 PDT)
- AYTUG TUNCEL (Wed Aug 02 2006 - 02:08:50 PDT)
AMBER: Bugfixes available for pmemd iwrap problem
- Robert Duke (Wed Aug 02 2006 - 10:05:32 PDT)
AMBER: build box info for acetonitrile in the simulation with periodic boundary condition
- Eric Hu (Wed Aug 09 2006 - 14:30:04 PDT)
- David A. Case (Wed Aug 09 2006 - 13:45:42 PDT)
- Eric Hu (Wed Aug 09 2006 - 11:06:30 PDT)
AMBER: building AMBER9 with gfortran/cygwin
- David A. Case (Fri Aug 25 2006 - 09:39:40 PDT)
- David A. Case (Fri Aug 25 2006 - 08:41:49 PDT)
- Andreas Svrcek-Seiler (Fri Aug 25 2006 - 03:39:08 PDT)
- Jyh-Shyong Ho (Thu Aug 24 2006 - 19:30:02 PDT)
AMBER: Calculate interaction energy between small organic molecules
- David LeBard (Thu Aug 24 2006 - 14:01:16 PDT)
- David Mobley (Thu Aug 24 2006 - 13:07:57 PDT)
- Björn C-G. Karlsson (Wed Aug 23 2006 - 23:17:56 PDT)
- David A. Case (Mon Aug 21 2006 - 23:14:15 PDT)
- David Mobley (Mon Aug 21 2006 - 07:20:42 PDT)
- Björn C-G. Karlsson (Sun Aug 20 2006 - 23:37:24 PDT)
AMBER: Can I run RED/RESP for Platinum Complexes?
- a a (Thu Aug 24 2006 - 02:50:42 PDT)
AMBER: Carnal: Internal error: stream file name 2 out of range
- Bill Ross (Wed Aug 23 2006 - 14:16:16 PDT)
- Shuting Wei (Wed Aug 23 2006 - 13:43:31 PDT)
AMBER: checkmask
- Steve Seibold (Wed Aug 16 2006 - 11:14:29 PDT)
AMBER: compiling parallel amber 9 in linux
- Amber admin (Thu Aug 24 2006 - 17:10:57 PDT)
- David A. Case (Wed Aug 23 2006 - 13:01:35 PDT)
- Ross Walker (Wed Aug 23 2006 - 12:54:39 PDT)
- Amber admin (Wed Aug 23 2006 - 12:00:08 PDT)
AMBER: Could mm_pbsa decompose energy only for the receptor ?
- backy (Fri Aug 11 2006 - 07:10:52 PDT)
AMBER: counterions and particle-mesh-ewald
- darden (Wed Aug 30 2006 - 15:59:32 PDT)
- David A. Case (Wed Aug 30 2006 - 13:14:40 PDT)
- cristian obiol (Tue Aug 29 2006 - 01:06:20 PDT)
AMBER: cutting the box after "solvatebox"
- Ilyas Yildirim (Thu Aug 17 2006 - 12:28:55 PDT)
- Guanglei Cui (Tue Aug 08 2006 - 07:38:06 PDT)
- Vlad Cojocaru (Tue Aug 08 2006 - 05:52:39 PDT)
- Carlos Simmerling (Tue Aug 08 2006 - 05:43:47 PDT)
- Vlad Cojocaru (Tue Aug 08 2006 - 05:12:37 PDT)
AMBER: Details about Gaussian basis set for Cobalt complex
- S.Sundar Raman (Sat Aug 26 2006 - 03:51:04 PDT)
- Thomas Cheatham (Fri Aug 25 2006 - 11:21:07 PDT)
- FyD (Mon Aug 21 2006 - 05:28:49 PDT)
- S.Sundar Raman (Sun Aug 20 2006 - 07:07:57 PDT)
AMBER: DIELC?
- backy (Sat Aug 19 2006 - 01:04:14 PDT)
- David A. Case (Sun Aug 13 2006 - 09:43:58 PDT)
- backy (Sat Aug 12 2006 - 05:16:47 PDT)
AMBER: Distance between two regions
- Guanglei Cui (Tue Aug 01 2006 - 08:35:54 PDT)
AMBER: DOTA-Lanthanide complexes in Amber
- Brent Krueger (Wed Aug 16 2006 - 13:08:57 PDT)
- opitz.che.udel.edu (Wed Aug 16 2006 - 10:27:23 PDT)
- David A. Case (Wed Aug 16 2006 - 09:59:22 PDT)
- opitz.che.udel.edu (Tue Aug 15 2006 - 10:48:23 PDT)
AMBER: Energy differecnes as using igb=1 and igb=0
- Carlos Simmerling (Thu Aug 10 2006 - 03:09:23 PDT)
- backy (Wed Aug 09 2006 - 23:47:37 PDT)
- Carlos Simmerling (Wed Aug 09 2006 - 08:01:27 PDT)
- backy (Wed Aug 09 2006 - 07:46:56 PDT)
AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine
- David A. Case (Sun Aug 27 2006 - 09:03:54 PDT)
- Gobind Bisht (Sat Aug 26 2006 - 22:24:12 PDT)
AMBER: Execution time discrepancies
- Ross Walker (Thu Aug 17 2006 - 20:00:29 PDT)
- Bill Ross (Thu Aug 17 2006 - 18:24:13 PDT)
- Glass, Kevin A (Thu Aug 17 2006 - 17:18:20 PDT)
AMBER: ff03 and ff99SB force fields
- Yong Duan (Fri Aug 04 2006 - 04:58:51 PDT)
- Vlad Cojocaru (Fri Aug 04 2006 - 01:17:59 PDT)
- Ray Luo (Thu Aug 03 2006 - 05:21:03 PDT)
- Yong Duan (Thu Aug 03 2006 - 12:29:51 PDT)
- Carlos Simmerling (Thu Aug 03 2006 - 03:59:11 PDT)
AMBER: Format of mdcrd files
- Mark Williamson (Wed Aug 09 2006 - 07:32:06 PDT)
- Carlos Simmerling (Wed Aug 09 2006 - 07:24:35 PDT)
- Gobind Bisht (Wed Aug 09 2006 - 06:56:18 PDT)
AMBER: from traj to crd
- Fabián Alejandro Rodríguez (Tue Aug 01 2006 - 08:41:22 PDT)
- Guanglei Cui (Tue Aug 01 2006 - 08:30:59 PDT)
AMBER: GAFF parameters: DPPC Bilayer
- Akshay Patny (Wed Aug 09 2006 - 14:08:00 PDT)
- Yong Duan (Tue Aug 08 2006 - 13:42:50 PDT)
- Nitin Bhardwaj (Tue Aug 08 2006 - 12:58:59 PDT)
- Akshay Patny (Tue Aug 08 2006 - 12:53:49 PDT)
AMBER: GB tutorials and disulphide bonds
- David A. Case (Tue Aug 01 2006 - 10:14:20 PDT)
AMBER: GBSA EGB = NaN
- David A. Case (Mon Aug 21 2006 - 11:21:10 PDT)
- William Wei (Mon Aug 21 2006 - 11:00:21 PDT)
- David A. Case (Mon Aug 21 2006 - 10:10:24 PDT)
- William Wei (Mon Aug 21 2006 - 09:37:47 PDT)
- Ilyas Yildirim (Mon Aug 21 2006 - 09:14:54 PDT)
- William Wei (Mon Aug 21 2006 - 09:04:26 PDT)
- William Wei (Mon Aug 21 2006 - 09:04:36 PDT)
- Ross Walker (Fri Aug 18 2006 - 15:11:52 PDT)
- William Wei (Fri Aug 18 2006 - 08:12:10 PDT)
- Ross Walker (Thu Aug 17 2006 - 19:57:29 PDT)
- William Lianhu Wei (Thu Aug 17 2006 - 19:30:50 PDT)
AMBER: generate "template" frcmod from standard residues?
- David Mobley (Fri Aug 18 2006 - 09:13:08 PDT)
- David A. Case (Thu Aug 17 2006 - 11:01:45 PDT)
- mernst.tricity.wsu.edu (Thu Aug 17 2006 - 10:06:07 PDT)
- David A. Case (Thu Aug 17 2006 - 09:04:22 PDT)
- David Mobley (Wed Aug 16 2006 - 14:51:47 PDT)
- mernst.tricity.wsu.edu (Wed Aug 16 2006 - 11:41:02 PDT)
AMBER: H-bonds of peptide with water
- Scott Pendley (Mon Aug 07 2006 - 12:56:04 PDT)
- sangeeta (Fri Aug 04 2006 - 06:20:13 PDT)
AMBER: HBOND ANALYSIS
- Thomas Cheatham (Thu Aug 10 2006 - 16:57:34 PDT)
- Claire Zerafa (Sat Aug 05 2006 - 12:45:10 PDT)
- Claire Zerafa (Fri Aug 04 2006 - 07:35:50 PDT)
AMBER: help with leap
- Franck_Vendeix.ncsu.edu (Thu Aug 17 2006 - 07:46:07 PDT)
- Bill Ross (Wed Aug 16 2006 - 17:51:56 PDT)
- sethl.gatech.edu (Wed Aug 16 2006 - 16:24:42 PDT)
AMBER: Heme parameters
- Weihua Li (Wed Aug 09 2006 - 19:44:15 PDT)
- Marcelo Puiatti (Wed Aug 09 2006 - 15:58:35 PDT)
AMBER: holding a pair of residues fixed during minimization
- Bill Ross (Wed Aug 23 2006 - 13:45:13 PDT)
- David A. Case (Wed Aug 23 2006 - 13:05:25 PDT)
- Seth Lilavivat (Tue Aug 22 2006 - 20:22:06 PDT)
AMBER: How to create a modified NA in leap
- Bill Ross (Sat Aug 26 2006 - 17:21:41 PDT)
- sethl.gatech.edu (Sat Aug 26 2006 - 13:13:10 PDT)
- Bill Ross (Fri Aug 25 2006 - 14:52:40 PDT)
- sethl.gatech.edu (Fri Aug 25 2006 - 13:20:35 PDT)
AMBER: how to do a molecular dynamic study on a trimer
- David A. Case (Sun Aug 13 2006 - 09:37:03 PDT)
- Gobind Bisht (Sat Aug 12 2006 - 10:05:29 PDT)
- David A. Case (Fri Aug 11 2006 - 09:05:12 PDT)
- Abhilash (Fri Aug 11 2006 - 08:05:44 PDT)
AMBER: how to limit the simulation space
- Bill Ross (Mon Aug 28 2006 - 18:04:39 PDT)
- Eric Hu (Mon Aug 28 2006 - 17:55:11 PDT)
AMBER: how to reassign charges
- Yong Duan (Wed Aug 09 2006 - 14:26:10 PDT)
- David A. Case (Wed Aug 09 2006 - 13:43:07 PDT)
- David Mobley (Wed Aug 09 2006 - 13:03:10 PDT)
- Lwin, ThuZar (Wed Aug 09 2006 - 11:16:01 PDT)
AMBER: How to set Bondi Radii using xleap
- Carlos Simmerling (Tue Aug 01 2006 - 10:43:04 PDT)
- David A. Case (Tue Aug 01 2006 - 10:17:38 PDT)
- Ilyas Yildirim (Mon Jul 31 2006 - 22:40:15 PDT)
AMBER: How to set Bondi Radii using xleap. .
- Don.Bashford.stjude.org (Tue Aug 01 2006 - 10:23:51 PDT)
AMBER: how to take care of toluene system neutrality
- Lwin, ThuZar (Fri Aug 04 2006 - 11:31:53 PDT)
- Lwin, ThuZar (Fri Aug 04 2006 - 11:27:39 PDT)
AMBER: how to use AddPdbAtomMap
- David A. Case (Thu Aug 24 2006 - 15:47:50 PDT)
- Ilyas Yildirim (Thu Aug 24 2006 - 13:27:41 PDT)
- sethl.gatech.edu (Thu Aug 24 2006 - 13:03:59 PDT)
AMBER: identical high energies
- Thomas Cheatham (Thu Aug 17 2006 - 19:57:23 PDT)
- Ross Walker (Thu Aug 17 2006 - 19:52:38 PDT)
- Tanya Johannsen (Thu Aug 17 2006 - 19:22:40 PDT)
AMBER: Ignoring every other frame in a .crd trajectory in Ptraj
- Carlos Simmerling (Tue Aug 01 2006 - 11:13:07 PDT)
- Xiaojian Deng (Tue Aug 01 2006 - 11:02:22 PDT)
- Xiaojian Deng (Tue Aug 01 2006 - 10:55:31 PDT)
AMBER: impose command in leap problem
- Piotr Cieplak (Mon Aug 14 2006 - 13:44:02 PDT)
- Scott Brozell (Fri Aug 11 2006 - 18:57:21 PDT)
- Piotr Cieplak (Fri Aug 11 2006 - 17:56:40 PDT)
AMBER: increase force constants
- Amber admin (Thu Aug 24 2006 - 17:15:24 PDT)
- David A. Case (Thu Aug 24 2006 - 15:56:33 PDT)
- Mahalakshmi Sahasranaman (Thu Aug 24 2006 - 06:45:28 PDT)
AMBER: Info regarding reduced cysteines
- David A. Case (Mon Aug 07 2006 - 08:02:57 PDT)
- Rafi Ahmad (Mon Aug 07 2006 - 07:06:40 PDT)
AMBER: input conversion error mm_pbsa
- David A. Case (Tue Aug 15 2006 - 15:47:19 PDT)
- AYTUG TUNCEL (Tue Aug 15 2006 - 15:23:28 PDT)
AMBER: Installation amber 9 on IBM SP4
- Myunggi Yi (Fri Aug 25 2006 - 19:41:46 PDT)
- Jyh-Shyong Ho (Fri Aug 25 2006 - 19:11:21 PDT)
- Myunggi Yi (Fri Aug 25 2006 - 18:20:47 PDT)
- Ross Walker (Fri Aug 25 2006 - 09:16:13 PDT)
- David A. Case (Fri Aug 25 2006 - 08:03:10 PDT)
- Scott Brozell (Thu Aug 24 2006 - 23:45:09 PDT)
- Scott Brozell (Thu Aug 24 2006 - 23:28:35 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 20:20:12 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 20:09:29 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 19:59:09 PDT)
- Scott Brozell (Thu Aug 24 2006 - 19:58:20 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 19:48:07 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 19:39:43 PDT)
- Scott Brozell (Thu Aug 24 2006 - 18:50:31 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 18:29:58 PDT)
- Ross Walker (Thu Aug 24 2006 - 15:08:03 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 12:00:04 PDT)
- Ross Walker (Thu Aug 24 2006 - 10:23:02 PDT)
- Myunggi Yi (Thu Aug 24 2006 - 09:05:50 PDT)
AMBER: Installation amber 9 on IBM SP4; bugfix 12
- Scott Brozell (Thu Aug 24 2006 - 19:57:03 PDT)
AMBER: klambda
- Ilyas Yildirim (Mon Aug 14 2006 - 10:31:24 PDT)
- David A. Case (Mon Aug 14 2006 - 09:48:30 PDT)
- Vitor Manuel Sousa F?x (Mon Aug 14 2006 - 03:45:10 PDT)
AMBER: Leap adds hydrogens but cannot resolve their type.
- Paul R Brenner (Tue Aug 15 2006 - 08:39:08 PDT)
- David A. Case (Thu Aug 10 2006 - 13:15:16 PDT)
- Paul R Brenner (Thu Aug 10 2006 - 12:23:55 PDT)
AMBER: Maximum system size in simulated annealing
- Carlos Simmerling (Thu Aug 03 2006 - 03:26:58 PDT)
- Andreas Svrcek-Seiler (Thu Aug 03 2006 - 02:23:13 PDT)
- Juraj Kotulic Bunta (Wed Aug 02 2006 - 19:03:11 PDT)
AMBER: Middlebury College Cluster and Amber 8
- David A. Case (Fri Aug 11 2006 - 11:30:46 PDT)
- Robert Duke (Fri Aug 11 2006 - 10:33:13 PDT)
- Lubans, Peter S (Fri Aug 11 2006 - 09:55:19 PDT)
AMBER: minimization with my own charges
- Thomas Cheatham (Thu Aug 31 2006 - 21:07:40 PDT)
- Ilyas Yildirim (Thu Aug 31 2006 - 20:37:18 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 18:16:49 PDT)
- Ilyas Yildirim (Thu Aug 31 2006 - 16:47:54 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 16:13:29 PDT)
- Ilyas Yildirim (Thu Aug 31 2006 - 15:50:26 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 15:22:08 PDT)
- Ilyas Yildirim (Thu Aug 31 2006 - 15:12:24 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 15:01:24 PDT)
AMBER: Missing LES reference in Amber 9 manual
- David A. Case (Wed Aug 30 2006 - 09:03:34 PDT)
- Chris Moth (Tue Aug 29 2006 - 11:43:12 PDT)
AMBER: missing values in md.out
- Carlos Simmerling (Fri Aug 25 2006 - 05:53:26 PDT)
- Jardas sucuriba (Fri Aug 25 2006 - 05:36:45 PDT)
- Carlos Simmerling (Thu Aug 24 2006 - 09:24:28 PDT)
- Jardas sucuriba (Thu Aug 24 2006 - 09:15:40 PDT)
AMBER: MM_PBSA : Question about Stability?
- David A. Case (Wed Aug 16 2006 - 09:24:48 PDT)
- Guillaume Bollot (Wed Aug 16 2006 - 00:00:15 PDT)
AMBER: mm_pbsa calculation allocation error
- Ray Luo (Mon Aug 21 2006 - 09:37:14 PDT)
- AYTUG TUNCEL (Mon Aug 21 2006 - 06:15:31 PDT)
AMBER: mm_pbsa.pl fails to start in linux cluster
- pkb bioinfo (Wed Aug 02 2006 - 06:58:48 PDT)
- pkb bioinfo (Wed Aug 02 2006 - 05:07:22 PDT)
AMBER: mm_pbsa_statistical.pl
- William Wei (Wed Aug 30 2006 - 14:11:51 PDT)
- Jianyin Shao (Wed Aug 30 2006 - 10:52:56 PDT)
- William Wei (Tue Aug 29 2006 - 14:02:32 PDT)
AMBER: MMPBSA: positive energies during nmode
- David A. Case (Wed Aug 16 2006 - 09:10:29 PDT)
- Zu Thur Yew (Wed Aug 16 2006 - 07:15:11 PDT)
AMBER: Modify charges to increase/decrease hydrogen bond interaction
- Mingfeng Yang (Mon Aug 14 2006 - 12:06:56 PDT)
- Thomas Cheatham (Mon Aug 14 2006 - 11:42:52 PDT)
- Mingfeng Yang (Mon Aug 14 2006 - 11:25:19 PDT)
AMBER: Nature of QM scanning protocol for parameter development
- Isherwood, James (Fri Aug 11 2006 - 09:17:01 PDT)
AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms
- Carlos Simmerling (Thu Aug 03 2006 - 08:33:34 PDT)
- Lwin, ThuZar (Thu Aug 03 2006 - 08:14:28 PDT)
AMBER: neutral N-terminal amino-acid parameters for ff03
- FyD (Sat Aug 05 2006 - 01:16:23 PDT)
- Vlad Cojocaru (Wed Aug 02 2006 - 07:21:31 PDT)
AMBER: nmode memory problem
- Atro Tossavainen (Fri Aug 25 2006 - 03:10:50 PDT)
- William Wei (Thu Aug 24 2006 - 14:05:55 PDT)
- Ross Walker (Thu Aug 24 2006 - 10:57:12 PDT)
- William Wei (Thu Aug 24 2006 - 10:04:59 PDT)
- Knut Langsestmo (Thu Aug 24 2006 - 09:17:04 PDT)
- William Wei (Thu Aug 24 2006 - 08:29:13 PDT)
AMBER: nmode: number of atoms limitation
- Cenk Andac (Wed Aug 30 2006 - 06:01:58 PDT)
- Changge Ji (Mon Aug 28 2006 - 23:33:27 PDT)
- David A. Case (Mon Aug 28 2006 - 22:55:53 PDT)
- AYTUG TUNCEL (Mon Aug 28 2006 - 16:15:04 PDT)
AMBER: parallel pmemd with intel 9 fc
- Robert Duke (Sat Aug 12 2006 - 11:58:59 PDT)
- bala (Sat Aug 12 2006 - 08:56:15 PDT)
AMBER: parameter for Cd2+?
- JunJun Liu (Fri Aug 04 2006 - 08:50:46 PDT)
AMBER: PCA: can't complete projection
- Zu Thur Yew (Tue Aug 08 2006 - 09:42:04 PDT)
- Vlad Cojocaru (Tue Aug 08 2006 - 07:56:49 PDT)
- Zu Thur Yew (Tue Aug 08 2006 - 07:17:31 PDT)
AMBER: pdb error
- Ilyas Yildirim (Tue Aug 01 2006 - 12:23:30 PDT)
- AYTUG TUNCEL (Tue Aug 01 2006 - 12:36:39 PDT)
AMBER: Periodic boundary condition (PBC)
- David A. Case (Mon Aug 28 2006 - 17:17:42 PDT)
- Bill Ross (Mon Aug 28 2006 - 16:21:57 PDT)
- Carlos Simmerling (Mon Aug 28 2006 - 13:40:05 PDT)
- Rahaman, Asif (Mon Aug 28 2006 - 13:24:19 PDT)
AMBER: Periodic boundary condition (PBC) > Problem now with ptraj
- Thomas Cheatham (Thu Aug 31 2006 - 21:38:02 PDT)
- Rahaman, Asif (Thu Aug 31 2006 - 15:29:25 PDT)
- Thomas Cheatham (Thu Aug 31 2006 - 14:50:33 PDT)
- Rahaman, Asif (Thu Aug 31 2006 - 14:34:50 PDT)
- Thomas Cheatham (Thu Aug 31 2006 - 13:49:42 PDT)
- Rahaman, Asif (Thu Aug 31 2006 - 13:24:43 PDT)
AMBER: Phosphated Tyrosine, not a type (xleap)?
- a a (Thu Aug 10 2006 - 19:38:47 PDT)
- David A. Case (Thu Aug 10 2006 - 09:07:09 PDT)
- a a (Thu Aug 10 2006 - 02:22:27 PDT)
AMBER: PhosphoThreonine Parms for use with ff03
- Vlad Cojocaru (Thu Aug 03 2006 - 03:07:48 PDT)
AMBER: Please DISREGARD previous message (restraint=0.0000)
- Evan Kelly (Thu Aug 03 2006 - 10:57:46 PDT)
AMBER: pmf input files
- Lauren O'Neil (Wed Aug 16 2006 - 10:20:45 PDT)
AMBER: PO2 in a DNA fragement, not a type in xleap? What can I do next?
- FyD (Sat Aug 12 2006 - 12:09:29 PDT)
- a a (Thu Aug 10 2006 - 19:39:54 PDT)
- Thomas Cheatham (Thu Aug 10 2006 - 15:18:00 PDT)
- a a (Thu Aug 10 2006 - 02:26:01 PDT)
AMBER: PO2 in a DNA fragement, not a type in xleap? What canI do next?
- a a (Sun Aug 13 2006 - 21:29:59 PDT)
AMBER: preparing ligand/rna structure for MD
- David A. Case (Mon Aug 28 2006 - 17:11:34 PDT)
- sethl.gatech.edu (Mon Aug 28 2006 - 11:45:17 PDT)
AMBER: problem imposing arbitrary peptide bonds through leap
- Amarda Shehu (Mon Aug 14 2006 - 09:56:31 PDT)
- David A. Case (Mon Aug 14 2006 - 09:45:48 PDT)
- Amarda Shehu (Mon Aug 14 2006 - 09:27:24 PDT)
AMBER: problem relating all atom structure prediction and folding simulations on AMBER8
- Carlos Simmerling (Wed Aug 23 2006 - 05:18:03 PDT)
- priya priya (Tue Aug 22 2006 - 21:16:42 PDT)
- Ross Walker (Mon Aug 21 2006 - 08:48:00 PDT)
- Carlos Simmerling (Mon Aug 21 2006 - 07:19:10 PDT)
- priya priya (Mon Aug 21 2006 - 00:46:29 PDT)
AMBER: Problem with restarting MD simulation
- Carlos Simmerling (Tue Aug 08 2006 - 04:08:27 PDT)
- Gobind Bisht (Mon Aug 07 2006 - 22:02:56 PDT)
AMBER: Problem with sander in Linux
- David A. Case (Mon Aug 14 2006 - 09:49:53 PDT)
- Wimal (Mon Aug 14 2006 - 01:14:00 PDT)
AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file
- David A. Case (Sun Aug 13 2006 - 09:49:27 PDT)
- Jianhui (Fri Aug 11 2006 - 11:50:54 PDT)
AMBER: problems with ptraj
- Thomas Cheatham (Thu Aug 10 2006 - 12:25:18 PDT)
- David A. Case (Thu Aug 03 2006 - 09:46:19 PDT)
- anna.schrey.gmx.de (Thu Aug 03 2006 - 07:49:39 PDT)
AMBER: ptraj dumpq feature/bug
- Thomas Cheatham (Thu Aug 24 2006 - 13:16:23 PDT)
- Markus Kaukonen (Thu Aug 24 2006 - 01:31:51 PDT)
AMBER: ptraj quasiharmonic analysis question
- Shawn yy (Fri Aug 11 2006 - 07:45:21 PDT)
AMBER: ptraj script
- Jardas sucuriba (Fri Aug 18 2006 - 13:08:31 PDT)
AMBER: Ptraj selecting specific atoms in specific residues
- Steve Seibold (Wed Aug 16 2006 - 10:50:16 PDT)
- Thomas Cheatham (Wed Aug 16 2006 - 10:32:24 PDT)
- Scott Pendley (Wed Aug 16 2006 - 10:19:31 PDT)
- Steve Seibold (Wed Aug 16 2006 - 10:05:16 PDT)
AMBER: ptraj: nofit option for rmsd
- Joseph Nachman (Tue Aug 08 2006 - 08:27:41 PDT)
AMBER: Question about free energy with mm_pbsa
- David A. Case (Thu Aug 31 2006 - 22:32:54 PDT)
- William Wei (Thu Aug 31 2006 - 11:50:11 PDT)
AMBER: Question about using antechamber with G03
- Gustavo Seabra (Wed Aug 16 2006 - 06:49:42 PDT)
- David A. Case (Tue Aug 15 2006 - 14:15:26 PDT)
- Gustavo Seabra (Tue Aug 15 2006 - 08:58:40 PDT)
AMBER: question on chargning free energy in solvent vs vacuum
- David A. Case (Fri Aug 04 2006 - 09:18:53 PDT)
- Lwin, ThuZar (Thu Aug 03 2006 - 10:08:07 PDT)
AMBER: question on chargning free energy in solvent vs vacuum. .
- Lwin, ThuZar (Fri Aug 04 2006 - 12:02:10 PDT)
AMBER: RDF output
- Thomas Cheatham (Wed Aug 30 2006 - 15:18:29 PDT)
- Jardas sucuriba (Wed Aug 30 2006 - 14:31:08 PDT)
- Jardas sucuriba (Tue Aug 29 2006 - 07:48:29 PDT)
AMBER: reading ff file into XLeap
- David A. Case (Wed Aug 16 2006 - 10:21:47 PDT)
- Petr Jerabek (Wed Aug 16 2006 - 09:21:00 PDT)
AMBER: reference of ff99
- David A. Case (Thu Aug 31 2006 - 09:43:50 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 09:26:09 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 09:21:59 PDT)
- Carlos Simmerling (Thu Aug 31 2006 - 09:18:09 PDT)
- Myunggi Yi (Thu Aug 31 2006 - 08:59:51 PDT)
AMBER: regarding diffusion command output
- Arvind Marathe (Tue Aug 01 2006 - 03:45:21 PDT)
AMBER: REMD: Hybrid topology file
- Carlos Simmerling (Wed Aug 30 2006 - 07:48:20 PDT)
- Austin B. Yongye (Wed Aug 30 2006 - 07:30:34 PDT)
AMBER: Residue connection points on prep.in
- Gloria T. Anderle (Fri Aug 04 2006 - 09:10:53 PDT)
AMBER: restraint=0.0000 during minimization?
- Evan Kelly (Thu Aug 03 2006 - 10:48:17 PDT)
AMBER: source code
- Thomas Cheatham (Mon Aug 14 2006 - 11:31:08 PDT)
- Yannick Bomble (Mon Aug 14 2006 - 11:09:31 PDT)
AMBER: SURFTEN in GB (mm_pbsa calculations)
- Carlos Simmerling (Thu Aug 03 2006 - 12:38:59 PDT)
- Shuting Wei (Thu Aug 03 2006 - 12:18:10 PDT)
AMBER: Temperature fluctuation with Langevin Temperature control
- David A. Case (Mon Aug 28 2006 - 10:32:08 PDT)
- Adrian Roitberg (Sun Aug 27 2006 - 14:07:07 PDT)
- Gobind Singh Bisht (Sun Aug 27 2006 - 12:06:49 PDT)
AMBER: The PB GB energy from mm_pbsa will be positive on high charged system
- David A. Case (Fri Aug 18 2006 - 11:35:04 PDT)
- Suxin Zheng (Fri Aug 18 2006 - 11:23:17 PDT)
- David A. Case (Fri Aug 18 2006 - 10:50:32 PDT)
- Suxin Zheng (Wed Aug 16 2006 - 11:23:44 PDT)
AMBER: TI tutorial
- David A. Case (Tue Aug 15 2006 - 16:34:58 PDT)
- Mingfeng Yang (Tue Aug 15 2006 - 15:22:10 PDT)
AMBER: TI vlimit exceeded
- David A. Case (Sat Aug 26 2006 - 10:38:58 PDT)
- Andrea Bortolato (Thu Aug 24 2006 - 06:42:21 PDT)
AMBER: TI, mutation
- eric.henon.univ-reims.fr (Tue Aug 29 2006 - 01:43:04 PDT)
- Pradipta Bandyopadhyay (Mon Aug 28 2006 - 05:46:43 PDT)
- Carlos Simmerling (Mon Aug 28 2006 - 05:18:56 PDT)
- eric.henon.univ-reims.fr (Mon Aug 28 2006 - 05:39:48 PDT)
AMBER: TI-FEP for ILE--->VAL.
- David A. Case (Thu Aug 03 2006 - 09:43:44 PDT)
- Ilyas Yildirim (Wed Aug 02 2006 - 23:15:10 PDT)
- Biswa Ranjan Meher (Wed Aug 02 2006 - 22:26:22 PDT)
AMBER: to do tutorial 4 using tleap
- Come On (Fri Aug 04 2006 - 09:50:53 PDT)
AMBER: transition state
- Eric Hu (Mon Aug 21 2006 - 17:06:22 PDT)
- John Chuang莊曜遠老師 (Mon Aug 14 2006 - 15:20:20 PDT)
- Eric Hu (Wed Aug 09 2006 - 12:05:14 PDT)
- John Chuang莊曜遠老師 (Mon Aug 07 2006 - 09:06:50 PDT)
AMBER: Tutorial 2 - Section 4: Summary.density and summary.temp
- Ross Walker (Wed Aug 30 2006 - 19:04:36 PDT)
- a a (Tue Aug 29 2006 - 03:15:07 PDT)
AMBER: Using a trajectory and some PDB files as input for PCA
- David A. Case (Tue Aug 01 2006 - 10:10:29 PDT)
AMBER: waters closest to specific residues
- Jardas sucuriba (Sat Aug 26 2006 - 08:39:35 PDT)
AMBER: where can I find the force field paramete r for Silica
- yxiong99 (Wed Aug 02 2006 - 12:53:33 PDT)
AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9
- Adrian Roitberg (Fri Aug 11 2006 - 13:23:10 PDT)
- Cheng Luo, Ph.D. (Fri Aug 11 2006 - 13:41:32 PDT)
AMBER: Xmgr in Windows
- Florian Haberl (Tue Aug 01 2006 - 05:11:44 PDT)
- Fabián Alejandro Rodríguez (Tue Aug 01 2006 - 04:39:19 PDT)
- Ilyas Yildirim (Mon Jul 31 2006 - 22:33:38 PDT)
AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files
- Guanglei Cui (Fri Aug 11 2006 - 06:57:46 PDT)
- Jing Huang (Fri Aug 11 2006 - 06:35:12 PDT)
AMBER: 答复: AMBER: pmf input files
- Chunhu Tan (Thu Aug 17 2006 - 09:36:30 PDT)
antechamber bond typing questions
- Junmei Wang (Mon Aug 07 2006 - 18:43:05 PDT)
antechamber failure on FMN
- David Mobley (Fri Aug 18 2006 - 11:46:58 PDT)
- Junmei Wang (Thu Aug 17 2006 - 16:14:47 PDT)
Confusion re AMBER SMD output
- Adrian Roitberg (Tue Aug 01 2006 - 04:07:03 PDT)
Simulated annealing
- Carlos Simmerling (Thu Aug 10 2006 - 04:40:24 PDT)

Amber Archive Aug 2006 by subject