AMBER Archive (2005) - Jul 2005 By ThreadMost recent messages
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Starting: Fri Jul 01 2005 - 00:52:15 CDT
Ending: Sun Jul 31 2005 - 23:55:46 CDT
- AMBER: question about leaprc.gaff and xxx.top Vijay Manickam Achari (Fri Jul 01 2005 - 00:52:15 CDT)
- AMBER: how to make cluster files? Ananda Rama Krishnan Selvaraj (Fri Jul 01 2005 - 02:10:05 CDT)
- AMBER: molecular dynamics simulation of protein containing Mg2+ cation Ye Mei (Fri Jul 01 2005 - 04:33:31 CDT)
- AMBER: cavity volume Anthony Cruz (Fri Jul 01 2005 - 07:46:24 CDT)
- AMBER: Replica exchange Anthony Cruz (Fri Jul 01 2005 - 09:33:46 CDT)
- AMBER: Temperature varible in MMPBSA script JunJun Liu (Fri Jul 01 2005 - 08:59:05 CDT)
- AMBER: please help us on partial charge calculation of PT complex using RESP peng79_at_email.unc.edu (Fri Jul 01 2005 - 10:10:31 CDT)
- AMBER: questions about topology file Fabien CAILLIEZ (Fri Jul 01 2005 - 10:49:20 CDT)
- AMBER: (no subject) Varsha Goyal (Fri Jul 01 2005 - 16:46:55 CDT)
- AMBER: loading DNA-RNA hybrid in xleap cbala_at_igib.res.in (Sat Jul 02 2005 - 10:36:59 CDT)
- AMBER: Question about Lennard-Jones Parameters in Topology file Linda Prengaman (Sat Jul 02 2005 - 13:15:51 CDT)
- AMBER: MM-PBSA-big energies John (Sun Jul 03 2005 - 16:31:56 CDT)
- AMBER: estimation of interface size Ye Mei (Sun Jul 03 2005 - 21:19:55 CDT)
- AMBER: Loading a macmodel file complex Yogesh Sabnis (Mon Jul 04 2005 - 10:02:49 CDT)
- AMBER: pmemd - bug report Petr Kulhanek (Mon Jul 04 2005 - 11:33:05 CDT)
- AMBER: nucgen and nukit dthomas_at_chem.uwa.edu.au (Tue Jul 05 2005 - 09:55:44 CDT)
- Re: AMBER: nucgen and nukit Bill Ross (Tue Jul 05 2005 - 11:33:04 CDT)
- AMBER: restart file Harianto Tjong (Tue Jul 05 2005 - 13:49:20 CDT)
- AMBER: DNA strands separate ivan_at_mmb.pcb.ub.es (Wed Jul 06 2005 - 05:39:24 CDT)
- AMBER: how to average the structure along md trajectory Ye Mei (Wed Jul 06 2005 - 08:51:56 CDT)
- AMBER: AMBER on Mac OS X Varsha Goyal (Wed Jul 06 2005 - 09:55:12 CDT)
- AMBER: box size in explicit water Lwin, ThuZar (Wed Jul 06 2005 - 11:39:47 CDT)
- AMBER: sander problem Anthony Cruz (Wed Jul 06 2005 - 18:05:44 CDT)
- AMBER: problem with addIons Lwin, ThuZar (Wed Jul 06 2005 - 16:41:25 CDT)
- AMBER: question about sander minimization error drugdesign (Thu Jul 07 2005 - 03:37:51 CDT)
- Re: AMBER: Replica Exchange Carlos Simmerling (Thu Jul 07 2005 - 08:43:17 CDT)
- AMBER: tyrosyl charges Ozlem Demir (Thu Jul 07 2005 - 12:07:24 CDT)
- AMBER: Release of R.E.D-II FyD (Thu Jul 07 2005 - 12:58:54 CDT)
- AMBER: problems with bonds in sander Fabien CAILLIEZ (Thu Jul 07 2005 - 13:18:19 CDT)
- AMBER: how is truncated octahedron box calculated Lwin, ThuZar (Thu Jul 07 2005 - 15:38:05 CDT)
- AMBER: building nucleic acids mathew k varghese (Thu Jul 07 2005 - 23:07:03 CDT)
- Re: AMBER: building nucleic acids Bill Ross (Fri Jul 08 2005 - 14:05:15 CDT)
- AMBER: LCPO SASA parameters for other elements when using gbsa=1 option David.Maxwell_at_di.mdacc.tmc.edu (Fri Jul 08 2005 - 15:10:00 CDT)
- AMBER: infinite DNA Stern, Julie (Fri Jul 08 2005 - 16:44:25 CDT)
- AMBER: glc0358_at_vip.sina.com (Sat Jul 09 2005 - 01:22:45 CDT)
- AMBER: simulation with Mg2+ ions and counter ions Ye Mei (Sat Jul 09 2005 - 01:54:16 CDT)
- AMBER: glc0358_at_vip.sina.com (Sat Jul 09 2005 - 02:03:23 CDT)
- AMBER: how to see the box lines Ananda Rama Krishnan Selvaraj (Sat Jul 09 2005 - 13:10:50 CDT)
- AMBER: molecular dynamics Vijay Manickam Achari (Sat Jul 09 2005 - 21:55:55 CDT)
- AMBER: Leap compilation issues justin litchfield (Sun Jul 10 2005 - 20:41:50 CDT)
- Re: AMBER: Leap compilation issues Bill Ross (Sun Jul 10 2005 - 21:11:43 CDT)
- AMBER: Critical PMEMD 8 Bugfix Robert Duke (Mon Jul 11 2005 - 07:38:59 CDT)
- AMBER: MM_PBSA help, please opitz_at_che.udel.edu (Mon Jul 11 2005 - 10:55:47 CDT)
- AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Mon Jul 11 2005 - 19:26:09 CDT)
- AMBER: MD simulation on a protein solvated by a combination of some water models ? B $BIp;V (Mon Jul 11 2005 - 23:10:12 CDT)
- AMBER: doubt on the value of Pressure on MD run Ananda Rama Krishnan Selvaraj (Tue Jul 12 2005 - 03:21:07 CDT)
- AMBER: Anal - problems with energy analysis Yogesh Sabnis (Tue Jul 12 2005 - 03:33:30 CDT)
- AMBER: TI - frcmod file Oliver Hucke (Tue Jul 12 2005 - 14:21:44 CDT)
- AMBER: question replica exchange acceptance ratio Zhuang (Tue Jul 12 2005 - 16:01:19 CDT)
- AMBER: Comparison of AMBER against DL-POLY Devashish Kumar (Tue Jul 12 2005 - 17:32:03 CDT)
- AMBER: Amber 8: create topology for solvent - PBC box size problem Angela Liu (Wed Jul 13 2005 - 13:41:04 CDT)
- AMBER: Amber 8: heterogeneous multiple copy LES method Angela Liu (Wed Jul 13 2005 - 13:47:08 CDT)
- AMBER: lib file for nonstandard residue Eric Hu (Wed Jul 13 2005 - 18:52:19 CDT)
- AMBER: units of mwcovar matrix befor conversion Kateryna Miroshnychenko (Thu Jul 14 2005 - 03:18:28 CDT)
- Re:AMBER: MD simulation on a protein solvated by a combination of some water mod B $BIp;V (Thu Jul 14 2005 - 04:56:39 CDT)
- AMBER: Modeling of a radical L Jin (Thu Jul 14 2005 - 05:46:20 CDT)
- AMBER: Leap question Kara Di Giorgio (Thu Jul 14 2005 - 10:10:12 CDT)
- Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 14:08:03 CDT)
- AMBER: Leap problem Kara Di Giorgio (Thu Jul 14 2005 - 19:06:50 CDT)
- AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000_at_126.com (Thu Jul 14 2005 - 21:38:08 CDT)
- AMBER: Energy decomposition parameters Angelo Pugliese (Fri Jul 15 2005 - 03:57:21 CDT)
- AMBER: P4 EM64T Intel Fortran Compile Problem Dawei Zhang (Fri Jul 15 2005 - 12:04:49 CDT)
- AMBER: Re: Problems with ptraj/rdparm Thomas E. Cheatham, III (Fri Jul 15 2005 - 14:22:28 CDT)
- AMBER: problem with protein ligand complex Claire Zerafa (Sat Jul 16 2005 - 11:31:56 CDT)
- AMBER: random-coil polymer Varsha Goyal (Sat Jul 16 2005 - 17:35:19 CDT)
- AMBER: AMBER-process_mdout.perl Praveena Gopal (Mon Jul 18 2005 - 02:26:19 CDT)
- AMBER: PMF calculations with TI using the sander Vitor Manuel Sousa F?x (Mon Jul 18 2005 - 02:30:59 CDT)
- AMBER: cap simulations questions Fabien CAILLIEZ (Mon Jul 18 2005 - 09:50:32 CDT)
- AMBER: segmentation fault in radial ptraj Kateryna Miroshnychenko (Mon Jul 18 2005 - 11:55:08 CDT)
- AMBER: Using Antechamber with Gamess and other molecular manipulations Charles Karney (Mon Jul 18 2005 - 12:28:20 CDT)
- AMBER: comparing md trajectories ayongye_at_chem.uga.edu (Mon Jul 18 2005 - 20:12:15 CDT)
- AMBER: pdb file and xleap Wai Keat Yam (Tue Jul 19 2005 - 05:06:50 CDT)
- AMBER: mm_pbsa question Matthew Davies (Tue Jul 19 2005 - 05:07:51 CDT)
- AMBER: Amber 7 Compiler Error Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 07:26:14 CDT)
- AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 15:14:30 CDT)
- AMBER: Trouble with Amber8 Dustin (Tue Jul 19 2005 - 15:16:10 CDT)
- AMBER: cap and ptraj Fabien CAILLIEZ (Tue Jul 19 2005 - 17:14:50 CDT)
- AMBER: FW: Andrew Box (Tue Jul 19 2005 - 21:07:44 CDT)
- AMBER: P4 EM64T Intel Fortran Compile Problem Zhang Bing (Wed Jul 20 2005 - 21:24:20 CDT)
- AMBER: Atom type :Si Ananda Rama Krishnan Selvaraj (Thu Jul 21 2005 - 14:02:23 CDT)
- AMBER: [OT] A nab programming question M. L. Dodson (Thu Jul 21 2005 - 15:07:09 CDT)
- AMBER: Question about Prep file opitz_at_che.udel.edu (Thu Jul 21 2005 - 15:52:41 CDT)
- AMBER: Error in MD mathew k varghese (Thu Jul 21 2005 - 22:53:08 CDT)
- AMBER: Lipid bilayer parameters nag raj (Fri Jul 22 2005 - 02:18:24 CDT)
- AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Fri Jul 22 2005 - 02:53:24 CDT)
- AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 09:09:34 CDT)
- AMBER: nucgen bdna types Stern, Julie (Fri Jul 22 2005 - 20:01:20 CDT)
- AMBER: mmpbsa test problem Suxin Zheng (Fri Jul 22 2005 - 20:41:11 CDT)
- AMBER: Lipid bilayer parameters and charmm force field parameters nag raj (Fri Jul 22 2005 - 22:15:35 CDT)
- Re: AMBER: Modeling of a radical Peter Gannett (Sat Jul 23 2005 - 09:21:25 CDT)
- AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Sun Jul 24 2005 - 20:50:45 CDT)
- AMBER: fit Yong Xu (Mon Jul 25 2005 - 04:04:57 CDT)
- AMBER: ptraj-acceptor mask format Peter Gannett (Mon Jul 25 2005 - 14:10:47 CDT)
- AMBER: antechamber Dustin (Mon Jul 25 2005 - 15:30:40 CDT)
- AMBER: nucgen H5T H3T Stern, Julie (Mon Jul 25 2005 - 20:55:52 CDT)
- AMBER: potential of mean force calculation along reaction coordinates Ye Mei (Tue Jul 26 2005 - 02:04:00 CDT)
- AMBER: Lipid parameters nag raj (Tue Jul 26 2005 - 05:55:22 CDT)
- AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Tue Jul 26 2005 - 08:25:53 CDT)
- AMBER: why not minimize snapshots before MM/PBSA calculations JunJun Liu (Tue Jul 26 2005 - 10:02:00 CDT)
- RE: AMBER: Tutoial 8 (Case Study) Ross Walker (Tue Jul 26 2005 - 12:03:37 CDT)
- AMBER: Thermodynamic Integration for conformational changes? Grzegorz Jezierski (Tue Jul 26 2005 - 12:33:00 CDT)
- AMBER: new residue Douali, Latifa (Tue Jul 26 2005 - 19:50:51 CDT)
- RE: AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 02:20:27 CDT)
- AMBER: cutoff in ANAL Madjid Taghdir (Wed Jul 27 2005 - 03:06:54 CDT)
- AMBER: prepi format and question about it Ilyas Yildirim (Wed Jul 27 2005 - 04:20:00 CDT)
- AMBER: Protein residue numbering Sukjoon Yoon (Wed Jul 27 2005 - 06:52:42 CDT)
- AMBER: [FWD] water minimalization problems blakrose_at_gazeta.pl (Wed Jul 27 2005 - 10:46:47 CDT)
- AMBER: How to insert a protein in lipid bilayer nag raj (Wed Jul 27 2005 - 11:56:07 CDT)
- AMBER: pbsa problem Suxin Zheng (Wed Jul 27 2005 - 14:47:29 CDT)
- AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 15:58:36 CDT)
- AMBER: Minimized structure Yam (Wed Jul 27 2005 - 22:02:03 CDT)
- AMBER: nucgen error (U not generated) mathew k varghese (Wed Jul 27 2005 - 22:28:51 CDT)
- AMBER: dihedral term in prmtop file Ye Mei (Thu Jul 28 2005 - 09:38:55 CDT)
- AMBER: Division by zero in sander Caleb S Howe (cshowe_at_Princeton.EDU) (Thu Jul 28 2005 - 09:57:00 CDT)
- AMBER: Fatal Error on loading a pdb in xLeap Kara Di Giorgio (Thu Jul 28 2005 - 10:10:45 CDT)
- AMBER: ambpdb core dump Peter Gannett (Fri Jul 29 2005 - 06:27:46 CDT)
- AMBER: ptraj output missing opitz_at_che.udel.edu (Fri Jul 29 2005 - 10:05:19 CDT)
- AMBER: temperature keep increasing in high temp. Hwankyu Lee (Fri Jul 29 2005 - 16:27:04 CDT)
- AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 19:10:46 CDT)
- AMBER: Failed sander runs for large systems Pratul K. Agarwal (Fri Jul 29 2005 - 21:41:44 CDT)
- AMBER: RESTARTED DUE TO LINMIN FAILURE Sukjoon Yoon (Sat Jul 30 2005 - 01:00:24 CDT)
- AMBER: Amber parameters for ADP zgleo (Sat Jul 30 2005 - 00:22:19 CDT)
- AMBER: questions about MG ions JIANING WANG (Sun Jul 31 2005 - 18:12:36 CDT)
- AMBER: AMBER8 crashes machine(nodes) under IBM compiler, Suse Linux, amd IBM loadleveler Soo (Sun Jul 31 2005 - 21:45:01 CDT)
Last message date: Sat Dec 31 2005 - 12:51:27 CST
Archived on: Sat Dec 31 2005 - 12:51:45 CST
393 messages sorted by:
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