AMBER Archive (2006) - Aug 2006 By ThreadMost recent messages
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Starting: Tue Aug 01 2006 - 00:33:38 CDT
Ending: Thu Aug 31 2006 - 23:38:02 CDT
- AMBER: How to set Bondi Radii using xleap Ilyas Yildirim (Tue Aug 01 2006 - 00:40:15 CDT)
- AMBER: regarding diffusion command output Arvind Marathe (Tue Aug 01 2006 - 05:45:21 CDT)
- AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 12:55:31 CDT)
- AMBER: pdb error AYTUG TUNCEL (Tue Aug 01 2006 - 14:36:39 CDT)
- AMBER: any work-around for 80 character mask string limit? Tanya Johannsen (Tue Aug 01 2006 - 15:12:22 CDT)
- AMBER: brookhaven to amber pdb format AYTUG TUNCEL (Wed Aug 02 2006 - 04:08:50 CDT)
- AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 07:07:22 CDT)
- AMBER: neutral N-terminal amino-acid parameters for ff03 Vlad Cojocaru (Wed Aug 02 2006 - 09:21:31 CDT)
- AMBER: Bugfixes available for pmemd iwrap problem Robert Duke (Wed Aug 02 2006 - 12:05:32 CDT)
- AMBER: where can I find the force field paramete r for Silica yxiong99 (Wed Aug 02 2006 - 14:53:33 CDT)
- AMBER: Maximum system size in simulated annealing Juraj Kotulic Bunta (Wed Aug 02 2006 - 21:03:11 CDT)
- AMBER: TI-FEP for ILE--->VAL. Biswa Ranjan Meher (Thu Aug 03 2006 - 00:26:22 CDT)
- AMBER: problems with ptraj anna.schrey_at_gmx.de (Thu Aug 03 2006 - 09:49:39 CDT)
- AMBER: Need to know meaning of numbers in parm99.dat file to be able to write frcmod file for dummy atoms Lwin, ThuZar (Thu Aug 03 2006 - 10:14:28 CDT)
- AMBER: about Silica's polarizability yxiong99 (Thu Aug 03 2006 - 10:20:19 CDT)
- AMBER: question on chargning free energy in solvent vs vacuum Lwin, ThuZar (Thu Aug 03 2006 - 12:08:07 CDT)
- AMBER: restraint=0.0000 during minimization? Evan Kelly (Thu Aug 03 2006 - 12:48:17 CDT)
- AMBER: Please DISREGARD previous message (restraint=0.0000) Evan Kelly (Thu Aug 03 2006 - 12:57:46 CDT)
- AMBER: HBOND ANALYSIS Claire Zerafa (Fri Aug 04 2006 - 09:35:50 CDT)
- AMBER: H-bonds of peptide with water sangeeta (Fri Aug 04 2006 - 08:20:13 CDT)
- AMBER: Residue connection points on prep.in Gloria T. Anderle (Fri Aug 04 2006 - 11:10:53 CDT)
- AMBER: parameter for Cd2+? JunJun Liu (Fri Aug 04 2006 - 10:50:46 CDT)
- AMBER: to do tutorial 4 using tleap Come On (Fri Aug 04 2006 - 11:50:53 CDT)
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 13:27:39 CDT)
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 13:31:53 CDT)
- RE: AMBER: question on chargning free energy in solvent vs vacuum. . Lwin, ThuZar (Fri Aug 04 2006 - 14:02:10 CDT)
- AMBER: Amber Installation Help Kirk Hevener (Mon Aug 07 2006 - 07:43:25 CDT)
- AMBER: Info regarding reduced cysteines Rafi Ahmad (Mon Aug 07 2006 - 09:06:40 CDT)
- AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 07 2006 - 11:06:50 CDT)
- AMBER: Glass, Kevin A (Mon Aug 07 2006 - 15:09:02 CDT)
- AMBER: antechamber bond typing questions David Mobley (Mon Aug 07 2006 - 15:14:42 CDT)
- AMBER: RE: antechamber bond typing questions Junmei Wang (Mon Aug 07 2006 - 20:43:05 CDT)
- AMBER: Problem with restarting MD simulation Gobind Bisht (Tue Aug 08 2006 - 00:02:56 CDT)
- AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 07:12:37 CDT)
- AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 09:17:31 CDT)
- AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Tue Aug 08 2006 - 14:53:49 CDT)
- AMBER: Format of mdcrd files Gobind Bisht (Wed Aug 09 2006 - 08:56:18 CDT)
- AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 09:46:56 CDT)
- AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 13:06:30 CDT)
- AMBER: how to reassign charges Lwin, ThuZar (Wed Aug 09 2006 - 13:16:01 CDT)
- AMBER: Heme parameters Marcelo Puiatti (Wed Aug 09 2006 - 17:58:35 CDT)
- AMBER: Re: Simulated annealing Carlos Simmerling (Thu Aug 10 2006 - 06:40:24 CDT)
- AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Thu Aug 10 2006 - 14:23:55 CDT)
- AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Jing Huang (Fri Aug 11 2006 - 08:35:12 CDT)
- AMBER: ptraj quasiharmonic analysis question Shawn yy (Fri Aug 11 2006 - 09:45:21 CDT)
- AMBER: how to do a molecular dynamic study on a trimer Abhilash (Fri Aug 11 2006 - 10:05:44 CDT)
- AMBER: AMBER8 - RDF bug Petr Kulhanek (Fri Aug 11 2006 - 11:00:57 CDT)
- AMBER: Nature of QM scanning protocol for parameter development Isherwood, James (Fri Aug 11 2006 - 11:17:01 CDT)
- AMBER: Middlebury College Cluster and Amber 8 Lubans, Peter S (Fri Aug 11 2006 - 11:55:19 CDT)
- AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file Jianhui (Fri Aug 11 2006 - 13:50:54 CDT)
- AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Cheng Luo, Ph.D. (Fri Aug 11 2006 - 15:41:32 CDT)
- AMBER: impose command in leap problem Piotr Cieplak (Fri Aug 11 2006 - 19:56:40 CDT)
- AMBER: DIELC? backy (Sat Aug 12 2006 - 07:16:47 CDT)
- AMBER: parallel pmemd with intel 9 fc bala (Sat Aug 12 2006 - 10:56:15 CDT)
- Re: AMBER: antechamber error -> metals Scott Brozell (Sun Aug 13 2006 - 16:58:14 CDT)
- AMBER: Problem with sander in Linux Wimal (Mon Aug 14 2006 - 03:14:00 CDT)
- AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? Kateryna Miroshnychenko (Mon Aug 14 2006 - 08:19:46 CDT)
- AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 11:27:24 CDT)
- AMBER: source code Yannick Bomble (Mon Aug 14 2006 - 13:09:31 CDT)
- AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 13:25:19 CDT)
- AMBER: Advice on linux cluster sought Feng X Zhou (Mon Aug 14 2006 - 13:34:16 CDT)
- AMBER: amber9 Test Failer kawamura_hiro_at_riken.jp (Tue Aug 15 2006 - 07:21:49 CDT)
- AMBER: amber 9 intel 9.1 ia64 Tim Robinson (Tue Aug 15 2006 - 08:45:16 CDT)
- AMBER: Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 10:58:40 CDT)
- AMBER: (Another) Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 12:51:16 CDT)
- AMBER: DOTA-Lanthanide complexes in Amber opitz_at_che.udel.edu (Tue Aug 15 2006 - 12:48:23 CDT)
- AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 13:04:42 CDT)
- AMBER: TI tutorial Mingfeng Yang (Tue Aug 15 2006 - 17:22:10 CDT)
- AMBER: input conversion error mm_pbsa AYTUG TUNCEL (Tue Aug 15 2006 - 17:23:28 CDT)
- AMBER: MM_PBSA : Question about Stability? Guillaume Bollot (Wed Aug 16 2006 - 02:00:15 CDT)
- AMBER: MMPBSA: positive energies during nmode Zu Thur Yew (Wed Aug 16 2006 - 09:15:11 CDT)
- AMBER: reading ff file into XLeap Petr Jerabek (Wed Aug 16 2006 - 11:21:00 CDT)
- AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 12:05:16 CDT)
- AMBER: checkmask Steve Seibold (Wed Aug 16 2006 - 13:14:29 CDT)
- AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Wed Aug 16 2006 - 13:23:44 CDT)
- AMBER: pmf input files Lauren O'Neil (Wed Aug 16 2006 - 12:20:45 CDT)
- AMBER: generate "template" frcmod from standard residues? mernst_at_tricity.wsu.edu (Wed Aug 16 2006 - 13:41:02 CDT)
- AMBER: help with leap sethl_at_gatech.edu (Wed Aug 16 2006 - 18:24:42 CDT)
- Re: AMBER: help with leap Bill Ross (Wed Aug 16 2006 - 19:51:56 CDT)
- RE: AMBER: antechamber error -> metals Junmei Wang (Wed Aug 16 2006 - 21:29:46 CDT)
- AMBER: RE: antechamber failure on FMN Junmei Wang (Thu Aug 17 2006 - 18:14:47 CDT)
- AMBER: Execution time discrepancies Glass, Kevin A (Thu Aug 17 2006 - 19:18:20 CDT)
- Re: AMBER: Execution time discrepancies Bill Ross (Thu Aug 17 2006 - 20:24:13 CDT)
- AMBER: identical high energies Tanya Johannsen (Thu Aug 17 2006 - 21:22:40 CDT)
- AMBER: GBSA EGB = NaN William Lianhu Wei (Thu Aug 17 2006 - 21:30:50 CDT)
- AMBER: amidine group/ gaff parameters Prashanth Athri (Fri Aug 18 2006 - 14:00:17 CDT)
- AMBER: ptraj script Jardas sucuriba (Fri Aug 18 2006 - 15:08:31 CDT)
- AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sun Aug 20 2006 - 09:07:57 CDT)
- AMBER: Calculate interaction energy between small organic molecules Bj顤n C-G. Karlsson (Mon Aug 21 2006 - 01:37:24 CDT)
- AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Mon Aug 21 2006 - 02:46:29 CDT)
- AMBER: mm_pbsa calculation allocation error AYTUG TUNCEL (Mon Aug 21 2006 - 08:15:31 CDT)
- AMBER: amber naming conventions for structure files sethl_at_gatech.edu (Tue Aug 22 2006 - 16:36:56 CDT)
- Re: AMBER: amber naming conventions for structure files Bill Ross (Tue Aug 22 2006 - 17:00:10 CDT)
- AMBER: holding a pair of residues fixed during minimization Seth Lilavivat (Tue Aug 22 2006 - 22:22:06 CDT)
- AMBER: compiling parallel amber 9 in linux Amber admin (Wed Aug 23 2006 - 14:00:08 CDT)
- AMBER: 0 steps the same as 1 step? S. Jamal Rahi (Wed Aug 23 2006 - 16:25:44 CDT)
- Re: AMBER: Carnal: Internal error: stream file name 2 out of range Bill Ross (Wed Aug 23 2006 - 16:16:16 CDT)
- AMBER: antechamber charge calculation very sensitive to conformations ? Christophe Guilbert (Wed Aug 23 2006 - 20:59:08 CDT)
- AMBER: Calculate interaction energy between small organic molecules Bj顤n C-G. Karlsson (Thu Aug 24 2006 - 01:17:56 CDT)
- AMBER: ptraj dumpq feature/bug Markus Kaukonen (Thu Aug 24 2006 - 03:31:51 CDT)
- AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 08:13:14 CDT)
- AMBER: TI vlimit exceeded Andrea Bortolato (Thu Aug 24 2006 - 08:42:21 CDT)
- AMBER: increase force constants Mahalakshmi Sahasranaman (Thu Aug 24 2006 - 08:45:28 CDT)
- AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 11:05:50 CDT)
- AMBER: how to use AddPdbAtomMap sethl_at_gatech.edu (Thu Aug 24 2006 - 15:03:59 CDT)
- AMBER: atomifluct Miguel Ferreira (Fri Aug 25 2006 - 06:09:03 CDT)
- AMBER: How to create a modified NA in leap sethl_at_gatech.edu (Fri Aug 25 2006 - 15:20:35 CDT)
- Re: AMBER: How to create a modified NA in leap Bill Ross (Fri Aug 25 2006 - 16:52:40 CDT)
- AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine Gobind Bisht (Sun Aug 27 2006 - 00:24:12 CDT)
- AMBER: Temperature fluctuation with Langevin Temperature control Gobind Singh Bisht (Sun Aug 27 2006 - 14:06:49 CDT)
- AMBER: TI, mutation eric.henon_at_univ-reims.fr (Mon Aug 28 2006 - 07:39:48 CDT)
- AMBER: preparing ligand/rna structure for MD sethl_at_gatech.edu (Mon Aug 28 2006 - 13:45:17 CDT)
- AMBER: Periodic boundary condition (PBC) Rahaman, Asif (Mon Aug 28 2006 - 15:24:19 CDT)
- AMBER: nmode: number of atoms limitation AYTUG TUNCEL (Mon Aug 28 2006 - 18:15:04 CDT)
- AMBER: how to limit the simulation space Eric Hu (Mon Aug 28 2006 - 19:55:11 CDT)
- Re: AMBER: how to limit the simulation space Bill Ross (Mon Aug 28 2006 - 20:04:39 CDT)
- AMBER: counterions and particle-mesh-ewald cristian obiol (Tue Aug 29 2006 - 03:06:20 CDT)
- AMBER: Qingning Shu (Tue Aug 29 2006 - 08:01:58 CDT)
- AMBER: REMD: Hybrid topology file Austin B. Yongye (Wed Aug 30 2006 - 09:30:34 CDT)
- AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 14:08:09 CDT)
- AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 10:59:51 CDT)
- AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 17:01:24 CDT)
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
389 messages sorted by:
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