Amber Archive Aug 2006 by thread
- Re: AMBER: Xmgr in Windows Ilyas Yildirim (Mon Jul 31 2006 - 22:33:38 PDT)
- AMBER: How to set Bondi Radii using xleap Ilyas Yildirim (Mon Jul 31 2006 - 22:40:15 PDT)
- AMBER: regarding diffusion command output Arvind Marathe (Tue Aug 01 2006 - 03:45:21 PDT)
- Re: AMBER: Re: Confusion re AMBER SMD output Adrian Roitberg (Tue Aug 01 2006 - 04:07:03 PDT)
- Re: AMBER: Distance between two regions Guanglei Cui (Tue Aug 01 2006 - 08:35:54 PDT)
- Re: AMBER: from traj to crd Guanglei Cui (Tue Aug 01 2006 - 08:30:59 PDT)
- Re: AMBER: GB tutorials and disulphide bonds David A. Case (Tue Aug 01 2006 - 10:14:20 PDT)
- Re: AMBER: Using a trajectory and some PDB files as input for PCA David A. Case (Tue Aug 01 2006 - 10:10:29 PDT)
- AMBER: Ignoring every other frame in a .crd trajectory in Ptraj Xiaojian Deng (Tue Aug 01 2006 - 10:55:31 PDT)
- AMBER: pdb error AYTUG TUNCEL (Tue Aug 01 2006 - 12:36:39 PDT)
- AMBER: any work-around for 80 character mask string limit? Tanya Johannsen (Tue Aug 01 2006 - 13:12:22 PDT)
- AMBER: brookhaven to amber pdb format AYTUG TUNCEL (Wed Aug 02 2006 - 02:08:50 PDT)
- AMBER: mm_pbsa.pl fails to start in linux cluster pkb bioinfo (Wed Aug 02 2006 - 05:07:22 PDT)
- AMBER: neutral N-terminal amino-acid parameters for ff03 Vlad Cojocaru (Wed Aug 02 2006 - 07:21:31 PDT)
- AMBER: Bugfixes available for pmemd iwrap problem Robert Duke (Wed Aug 02 2006 - 10:05:32 PDT)
- AMBER: where can I find the force field paramete r for Silica yxiong99 (Wed Aug 02 2006 - 12:53:33 PDT)
- AMBER: Maximum system size in simulated annealing Juraj Kotulic Bunta (Wed Aug 02 2006 - 19:03:11 PDT)
- AMBER: TI-FEP for ILE--->VAL. Biswa Ranjan Meher (Wed Aug 02 2006 - 22:26:22 PDT)
- Re: AMBER: PhosphoThreonine Parms for use with ff03 Vlad Cojocaru (Thu Aug 03 2006 - 03:07:48 PDT)
- AMBER: problems with ptraj anna.schrey.gmx.de (Thu Aug 03 2006 - 07:49:39 PDT)
- 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 - 08:14:28 PDT)
- AMBER: about Silica's polarizability yxiong99 (Thu Aug 03 2006 - 08:20:19 PDT)
- AMBER: question on chargning free energy in solvent vs vacuum Lwin, ThuZar (Thu Aug 03 2006 - 10:08:07 PDT)
- AMBER: restraint=0.0000 during minimization? Evan Kelly (Thu Aug 03 2006 - 10:48:17 PDT)
- AMBER: Please DISREGARD previous message (restraint=0.0000) Evan Kelly (Thu Aug 03 2006 - 10:57:46 PDT)
- AMBER: SURFTEN in GB (mm_pbsa calculations) Shuting Wei (Thu Aug 03 2006 - 12:18:10 PDT)
- AMBER: HBOND ANALYSIS Claire Zerafa (Fri Aug 04 2006 - 07:35:50 PDT)
- AMBER: H-bonds of peptide with water sangeeta (Fri Aug 04 2006 - 06:20:13 PDT)
- AMBER: Residue connection points on prep.in Gloria T. Anderle (Fri Aug 04 2006 - 09:10:53 PDT)
- AMBER: parameter for Cd2+? JunJun Liu (Fri Aug 04 2006 - 08:50:46 PDT)
- AMBER: to do tutorial 4 using tleap Come On (Fri Aug 04 2006 - 09:50:53 PDT)
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 11:27:39 PDT)
- AMBER: how to take care of toluene system neutrality Lwin, ThuZar (Fri Aug 04 2006 - 11:31:53 PDT)
- RE: AMBER: question on chargning free energy in solvent vs vacuum. . Lwin, ThuZar (Fri Aug 04 2006 - 12:02:10 PDT)
- AMBER: Amber Installation Help Kirk Hevener (Mon Aug 07 2006 - 05:43:25 PDT)
- AMBER: Info regarding reduced cysteines Rafi Ahmad (Mon Aug 07 2006 - 07:06:40 PDT)
- AMBER: transition state John Chuang莊曜遠老師 (Mon Aug 07 2006 - 09:06:50 PDT)
- AMBER: Glass, Kevin A (Mon Aug 07 2006 - 13:09:02 PDT)
- AMBER: antechamber bond typing questions David Mobley (Mon Aug 07 2006 - 13:14:42 PDT)
- AMBER: RE: antechamber bond typing questions Junmei Wang (Mon Aug 07 2006 - 18:43:05 PDT)
- AMBER: Problem with restarting MD simulation Gobind Bisht (Mon Aug 07 2006 - 22:02:56 PDT)
- AMBER: cutting the box after "solvatebox" Vlad Cojocaru (Tue Aug 08 2006 - 05:12:37 PDT)
- AMBER: PCA: can't complete projection Zu Thur Yew (Tue Aug 08 2006 - 07:17:31 PDT)
- AMBER: GAFF parameters: DPPC Bilayer Akshay Patny (Tue Aug 08 2006 - 12:53:49 PDT)
- AMBER: Format of mdcrd files Gobind Bisht (Wed Aug 09 2006 - 06:56:18 PDT)
- AMBER: Energy differecnes as using igb=1 and igb=0 backy (Wed Aug 09 2006 - 07:46:56 PDT)
- AMBER: build box info for acetonitrile in the simulation with periodic boundary condition Eric Hu (Wed Aug 09 2006 - 11:06:30 PDT)
- AMBER: how to reassign charges Lwin, ThuZar (Wed Aug 09 2006 - 11:16:01 PDT)
- AMBER: Heme parameters Marcelo Puiatti (Wed Aug 09 2006 - 15:58:35 PDT)
- AMBER: Re: Simulated annealing Carlos Simmerling (Thu Aug 10 2006 - 04:40:24 PDT)
- AMBER: Leap adds hydrogens but cannot resolve their type. Paul R Brenner (Thu Aug 10 2006 - 12:23:55 PDT)
- AMBER: zero entry in LENNARD_JONES_ACOEF of prmtop files Jing Huang (Fri Aug 11 2006 - 06:35:12 PDT)
- AMBER: ptraj quasiharmonic analysis question Shawn yy (Fri Aug 11 2006 - 07:45:21 PDT)
- AMBER: how to do a molecular dynamic study on a trimer Abhilash (Fri Aug 11 2006 - 08:05:44 PDT)
- AMBER: AMBER8 - RDF bug Petr Kulhanek (Fri Aug 11 2006 - 09:00:57 PDT)
- AMBER: Nature of QM scanning protocol for parameter development Isherwood, James (Fri Aug 11 2006 - 09:17:01 PDT)
- AMBER: Middlebury College Cluster and Amber 8 Lubans, Peter S (Fri Aug 11 2006 - 09:55:19 PDT)
- AMBER: Problem: Flag "SOLVENT_POINTERS" not found in PARM file Jianhui (Fri Aug 11 2006 - 11:50:54 PDT)
- AMBER: Where can I find the SMD parameter file (or simple turtorial) in AMBER9 Cheng Luo, Ph.D. (Fri Aug 11 2006 - 13:41:32 PDT)
- AMBER: impose command in leap problem Piotr Cieplak (Fri Aug 11 2006 - 17:56:40 PDT)
- AMBER: DIELC? backy (Sat Aug 12 2006 - 05:16:47 PDT)
- AMBER: parallel pmemd with intel 9 fc bala (Sat Aug 12 2006 - 08:56:15 PDT)
- Re: AMBER: antechamber error -> metals Scott Brozell (Sun Aug 13 2006 - 14:58:14 PDT)
- AMBER: Problem with sander in Linux Wimal (Mon Aug 14 2006 - 01:14:00 PDT)
- AMBER: RE: AMBER Tutorial 2 section 6, rmsd calculation: rmsd for residues number? Kateryna Miroshnychenko (Mon Aug 14 2006 - 06:19:46 PDT)
- AMBER: problem imposing arbitrary peptide bonds through leap Amarda Shehu (Mon Aug 14 2006 - 09:27:24 PDT)
- AMBER: source code Yannick Bomble (Mon Aug 14 2006 - 11:09:31 PDT)
- AMBER: Modify charges to increase/decrease hydrogen bond interaction Mingfeng Yang (Mon Aug 14 2006 - 11:25:19 PDT)
- AMBER: Advice on linux cluster sought Feng X Zhou (Mon Aug 14 2006 - 11:34:16 PDT)
- AMBER: amber9 Test Failer kawamura_hiro.riken.jp (Tue Aug 15 2006 - 05:21:49 PDT)
- AMBER: amber 9 intel 9.1 ia64 Tim Robinson (Tue Aug 15 2006 - 06:45:16 PDT)
- AMBER: Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 08:58:40 PDT)
- AMBER: DOTA-Lanthanide complexes in Amber opitz.che.udel.edu (Tue Aug 15 2006 - 10:48:23 PDT)
- AMBER: (Another) Question about using antechamber with G03 Gustavo Seabra (Tue Aug 15 2006 - 10:51:16 PDT)
- AMBER: antechamber failure on FMN David Mobley (Tue Aug 15 2006 - 11:04:42 PDT)
- AMBER: input conversion error mm_pbsa AYTUG TUNCEL (Tue Aug 15 2006 - 15:23:28 PDT)
- AMBER: TI tutorial Mingfeng Yang (Tue Aug 15 2006 - 15:22:10 PDT)
- AMBER: MM_PBSA : Question about Stability? Guillaume Bollot (Wed Aug 16 2006 - 00:00:15 PDT)
- AMBER: MMPBSA: positive energies during nmode Zu Thur Yew (Wed Aug 16 2006 - 07:15:11 PDT)
- AMBER: reading ff file into XLeap Petr Jerabek (Wed Aug 16 2006 - 09:21:00 PDT)
- AMBER: Ptraj selecting specific atoms in specific residues Steve Seibold (Wed Aug 16 2006 - 10:05:16 PDT)
- AMBER: checkmask Steve Seibold (Wed Aug 16 2006 - 11:14:29 PDT)
- AMBER: The PB GB energy from mm_pbsa will be positive on high charged system Suxin Zheng (Wed Aug 16 2006 - 11:23:44 PDT)
- AMBER: pmf input files Lauren O'Neil (Wed Aug 16 2006 - 10:20:45 PDT)
- AMBER: generate "template" frcmod from standard residues? mernst.tricity.wsu.edu (Wed Aug 16 2006 - 11:41:02 PDT)
- AMBER: help with leap sethl.gatech.edu (Wed Aug 16 2006 - 16:24:42 PDT)
- Re: AMBER: help with leap Bill Ross (Wed Aug 16 2006 - 17:51:56 PDT)
- RE: AMBER: antechamber error -> metals Junmei Wang (Wed Aug 16 2006 - 19:29:46 PDT)
- AMBER: RE: antechamber failure on FMN Junmei Wang (Thu Aug 17 2006 - 16:14:47 PDT)
- AMBER: Execution time discrepancies Glass, Kevin A (Thu Aug 17 2006 - 17:18:20 PDT)
- Re: AMBER: Execution time discrepancies Bill Ross (Thu Aug 17 2006 - 18:24:13 PDT)
- AMBER: identical high energies Tanya Johannsen (Thu Aug 17 2006 - 19:22:40 PDT)
- AMBER: GBSA EGB = NaN William Lianhu Wei (Thu Aug 17 2006 - 19:30:50 PDT)
- AMBER: amidine group/ gaff parameters Prashanth Athri (Fri Aug 18 2006 - 12:00:17 PDT)
- AMBER: ptraj script Jardas sucuriba (Fri Aug 18 2006 - 13:08:31 PDT)
- AMBER: Details about Gaussian basis set for Cobalt complex S.Sundar Raman (Sun Aug 20 2006 - 07:07:57 PDT)
- AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson (Sun Aug 20 2006 - 23:37:24 PDT)
- AMBER: problem relating all atom structure prediction and folding simulations on AMBER8 priya priya (Mon Aug 21 2006 - 00:46:29 PDT)
- AMBER: mm_pbsa calculation allocation error AYTUG TUNCEL (Mon Aug 21 2006 - 06:15:31 PDT)
- AMBER: amber naming conventions for structure files sethl.gatech.edu (Tue Aug 22 2006 - 14:36:56 PDT)
- Re: AMBER: amber naming conventions for structure files Bill Ross (Tue Aug 22 2006 - 15:00:10 PDT)
- AMBER: holding a pair of residues fixed during minimization Seth Lilavivat (Tue Aug 22 2006 - 20:22:06 PDT)
- AMBER: compiling parallel amber 9 in linux Amber admin (Wed Aug 23 2006 - 12:00:08 PDT)
- Re: AMBER: Carnal: Internal error: stream file name 2 out of range Bill Ross (Wed Aug 23 2006 - 14:16:16 PDT)
- AMBER: 0 steps the same as 1 step? S. Jamal Rahi (Wed Aug 23 2006 - 14:25:44 PDT)
- AMBER: antechamber charge calculation very sensitive to conformations ? Christophe Guilbert (Wed Aug 23 2006 - 18:59:08 PDT)
- AMBER: Calculate interaction energy between small organic molecules Björn C-G. Karlsson (Wed Aug 23 2006 - 23:17:56 PDT)
- AMBER: ptraj dumpq feature/bug Markus Kaukonen (Thu Aug 24 2006 - 01:31:51 PDT)
- AMBER: Backbone & Sidechain atoms: Definition Zu Thur Yew (Thu Aug 24 2006 - 06:13:14 PDT)
- AMBER: TI vlimit exceeded Andrea Bortolato (Thu Aug 24 2006 - 06:42:21 PDT)
- AMBER: increase force constants Mahalakshmi Sahasranaman (Thu Aug 24 2006 - 06:45:28 PDT)
- AMBER: Installation amber 9 on IBM SP4 Myunggi Yi (Thu Aug 24 2006 - 09:05:50 PDT)
- AMBER: how to use AddPdbAtomMap sethl.gatech.edu (Thu Aug 24 2006 - 13:03:59 PDT)
- AMBER: atomifluct Miguel Ferreira (Fri Aug 25 2006 - 04:09:03 PDT)
- AMBER: How to create a modified NA in leap sethl.gatech.edu (Fri Aug 25 2006 - 13:20:35 PDT)
- Re: AMBER: How to create a modified NA in leap Bill Ross (Fri Aug 25 2006 - 14:52:40 PDT)
- AMBER: Error in compliling AMBER 9 on Fedora 5 linux machine Gobind Bisht (Sat Aug 26 2006 - 22:24:12 PDT)
- AMBER: Temperature fluctuation with Langevin Temperature control Gobind Singh Bisht (Sun Aug 27 2006 - 12:06:49 PDT)
- AMBER: TI, mutation eric.henon.univ-reims.fr (Mon Aug 28 2006 - 05:39:48 PDT)
- AMBER: preparing ligand/rna structure for MD sethl.gatech.edu (Mon Aug 28 2006 - 11:45:17 PDT)
- AMBER: Periodic boundary condition (PBC) Rahaman, Asif (Mon Aug 28 2006 - 13:24:19 PDT)
- AMBER: nmode: number of atoms limitation AYTUG TUNCEL (Mon Aug 28 2006 - 16:15:04 PDT)
- AMBER: how to limit the simulation space Eric Hu (Mon Aug 28 2006 - 17:55:11 PDT)
- Re: AMBER: how to limit the simulation space Bill Ross (Mon Aug 28 2006 - 18:04:39 PDT)
- AMBER: counterions and particle-mesh-ewald cristian obiol (Tue Aug 29 2006 - 01:06:20 PDT)
- AMBER: Qingning Shu (Tue Aug 29 2006 - 06:01:58 PDT)
- AMBER: REMD: Hybrid topology file Austin B. Yongye (Wed Aug 30 2006 - 07:30:34 PDT)
- AMBER: 1-4 interaction in AMBER8 Jianhui (Wed Aug 30 2006 - 12:08:09 PDT)
- AMBER: reference of ff99 Myunggi Yi (Thu Aug 31 2006 - 08:59:51 PDT)
- AMBER: minimization with my own charges Myunggi Yi (Thu Aug 31 2006 - 15:01:24 PDT)
- Last message date: Sun Sep 03 2006 - 06:07:18 PDT
- Archived on: Wed Dec 25 2024 - 05:53:33 PST
