Amber Archive Jul 2005 By Thread
- Re: AMBER: Create new Unit FyD (Thu Jun 30 2005 - 17:25:02 PDT)
- AMBER: least square fit of snapshots in md trajectory to a reference frame Ye Mei (Thu Jun 30 2005 - 19:56:08 PDT)
- AMBER: question about spline in sander -- array size of eed_cub Cordova, Luis E. (Thu Jun 30 2005 - 21:33:25 PDT)
- AMBER: question about leaprc.gaff and xxx.top Vijay Manickam Achari (Thu Jun 30 2005 - 22:52:15 PDT)
- AMBER: how to make cluster files? Ananda Rama Krishnan Selvaraj (Fri Jul 01 2005 - 00:10:05 PDT)
- AMBER: Stacking energy Angelo Pugliese (Fri Jul 01 2005 - 01:32:34 PDT)
- AMBER: molecular dynamics simulation of protein containing Mg2+ cation Ye Mei (Fri Jul 01 2005 - 02:33:31 PDT)
- AMBER: cavity volume Anthony Cruz (Fri Jul 01 2005 - 05:46:24 PDT)
- AMBER: Replica exchange Anthony Cruz (Fri Jul 01 2005 - 07:33:46 PDT)
- AMBER: Temperature varible in MMPBSA script JunJun Liu (Fri Jul 01 2005 - 06:59:05 PDT)
- AMBER: please help us on partial charge calculation of PT complex using RESP peng79.email.unc.edu (Fri Jul 01 2005 - 08:10:31 PDT)
- AMBER: questions about topology file Fabien CAILLIEZ (Fri Jul 01 2005 - 08:49:20 PDT)
- Re: AMBER: parallel error Peter Varnai (Fri Jul 01 2005 - 08:51:18 PDT)
- Re: AMBER: example script for hbond calculation Thomas E. Cheatham, III (Fri Jul 01 2005 - 09:10:07 PDT)
- AMBER: (no subject) Varsha Goyal (Fri Jul 01 2005 - 14:46:55 PDT)
- AMBER: loading DNA-RNA hybrid in xleap cbala.igib.res.in (Sat Jul 02 2005 - 08:36:59 PDT)
- AMBER: Question about Lennard-Jones Parameters in Topology file Linda Prengaman (Sat Jul 02 2005 - 11:15:51 PDT)
- AMBER: MM-PBSA-big energies John (Sun Jul 03 2005 - 14:31:56 PDT)
- AMBER: estimation of interface size Ye Mei (Sun Jul 03 2005 - 19:19:55 PDT)
- AMBER: Loading a macmodel file complex Yogesh Sabnis (Mon Jul 04 2005 - 08:02:49 PDT)
- AMBER: pmemd - bug report Petr Kulhanek (Mon Jul 04 2005 - 09:33:05 PDT)
- AMBER: nucgen and nukit dthomas.chem.uwa.edu.au (Tue Jul 05 2005 - 07:55:44 PDT)
- Re: AMBER: nucgen and nukit Bill Ross (Tue Jul 05 2005 - 09:33:04 PDT)
- AMBER: restart file Harianto Tjong (Tue Jul 05 2005 - 11:49:20 PDT)
- Re: AMBER: 10-12 potential and create atom type David A. Case (Tue Jul 05 2005 - 15:03:09 PDT)
- AMBER: DNA strands separate ivan.mmb.pcb.ub.es (Wed Jul 06 2005 - 03:39:24 PDT)
- AMBER: how to average the structure along md trajectory Ye Mei (Wed Jul 06 2005 - 06:51:56 PDT)
- AMBER: AMBER on Mac OS X Varsha Goyal (Wed Jul 06 2005 - 07:55:12 PDT)
- AMBER: box size in explicit water Lwin, ThuZar (Wed Jul 06 2005 - 09:39:47 PDT)
- AMBER: sander problem Anthony Cruz (Wed Jul 06 2005 - 16:05:44 PDT)
- AMBER: problem with addIons Lwin, ThuZar (Wed Jul 06 2005 - 14:41:25 PDT)
- Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends Ilyas Yildirim (Wed Jul 06 2005 - 15:24:45 PDT)
- AMBER: question about sander minimization error drugdesign (Thu Jul 07 2005 - 01:37:51 PDT)
- AMBER: Replica Exchange Anthony Cruz (Thu Jul 07 2005 - 08:27:51 PDT)
- AMBER: tyrosyl charges Ozlem Demir (Thu Jul 07 2005 - 10:07:24 PDT)
- AMBER: Release of R.E.D-II FyD (Thu Jul 07 2005 - 10:58:54 PDT)
- AMBER: problems with bonds in sander Fabien CAILLIEZ (Thu Jul 07 2005 - 11:18:19 PDT)
- AMBER: how is truncated octahedron box calculated Lwin, ThuZar (Thu Jul 07 2005 - 13:38:05 PDT)
- AMBER: building nucleic acids mathew k varghese (Thu Jul 07 2005 - 21:07:03 PDT)
- Re: AMBER: building nucleic acids Bill Ross (Fri Jul 08 2005 - 12:05:15 PDT)
- AMBER: LCPO SASA parameters for other elements when using gbsa=1 option David.Maxwell.di.mdacc.tmc.edu (Fri Jul 08 2005 - 13:10:00 PDT)
- AMBER: infinite DNA Stern, Julie (Fri Jul 08 2005 - 14:44:25 PDT)
- AMBER: glc0358.vip.sina.com (Fri Jul 08 2005 - 23:22:45 PDT)
- AMBER: simulation with Mg2+ ions and counter ions Ye Mei (Fri Jul 08 2005 - 23:54:16 PDT)
- AMBER: glc0358.vip.sina.com (Sat Jul 09 2005 - 00:03:23 PDT)
- AMBER: how to see the box lines Ananda Rama Krishnan Selvaraj (Sat Jul 09 2005 - 11:10:50 PDT)
- AMBER: molecular dynamics Vijay Manickam Achari (Sat Jul 09 2005 - 19:55:55 PDT)
- AMBER: Leap compilation issues justin litchfield (Sun Jul 10 2005 - 18:41:50 PDT)
- Re: AMBER: Leap compilation issues Bill Ross (Sun Jul 10 2005 - 19:11:43 PDT)
- AMBER: Critical PMEMD 8 Bugfix Robert Duke (Mon Jul 11 2005 - 05:38:59 PDT)
- AMBER: MM_PBSA help, please opitz.che.udel.edu (Mon Jul 11 2005 - 08:55:47 PDT)
- AMBER: Ptraj and order of operations Furse, Kristina Elisabet (Mon Jul 11 2005 - 17:26:09 PDT)
- AMBER: MD simulation on a protein solvated by a combination of some water models ? B $BIp;V (Mon Jul 11 2005 - 21:10:12 PDT)
- AMBER: doubt on the value of Pressure on MD run Ananda Rama Krishnan Selvaraj (Tue Jul 12 2005 - 01:21:07 PDT)
- AMBER: Anal - problems with energy analysis Yogesh Sabnis (Tue Jul 12 2005 - 01:33:30 PDT)
- AMBER: molsurf error in MM/PBSA calculation JunJun Liu (Tue Jul 12 2005 - 06:43:55 PDT)
- AMBER: TI - frcmod file Oliver Hucke (Tue Jul 12 2005 - 12:21:44 PDT)
- AMBER: question replica exchange acceptance ratio Zhuang (Tue Jul 12 2005 - 14:01:19 PDT)
- AMBER: Comparison of AMBER against DL-POLY Devashish Kumar (Tue Jul 12 2005 - 15:32:03 PDT)
- AMBER: Amber 8: create topology for solvent - PBC box size problem Angela Liu (Wed Jul 13 2005 - 11:41:04 PDT)
- AMBER: Amber 8: heterogeneous multiple copy LES method Angela Liu (Wed Jul 13 2005 - 11:47:08 PDT)
- AMBER: lib file for nonstandard residue Eric Hu (Wed Jul 13 2005 - 16:52:19 PDT)
- AMBER: units of mwcovar matrix befor conversion Kateryna Miroshnychenko (Thu Jul 14 2005 - 01:18:28 PDT)
- Re:AMBER: MD simulation on a protein solvated by a combination of some water mod B $BIp;V (Thu Jul 14 2005 - 02:56:39 PDT)
- AMBER: Modeling of a radical L Jin (Thu Jul 14 2005 - 03:46:20 PDT)
- AMBER: Apologies - LMOD website down Istvan Kolossvary (Thu Jul 14 2005 - 07:39:54 PDT)
- AMBER: Leap question Kara Di Giorgio (Thu Jul 14 2005 - 08:10:12 PDT)
- Re: AMBER: lib file for nonstandard residue Bill Ross (Thu Jul 14 2005 - 12:08:03 PDT)
- AMBER: Leap problem Kara Di Giorgio (Thu Jul 14 2005 - 17:06:50 PDT)
- AMBER: Can GB and MS work correctly together in mmpbsa? zhli_2000.126.com (Thu Jul 14 2005 - 19:38:08 PDT)
- AMBER: Energy decomposition parameters Angelo Pugliese (Fri Jul 15 2005 - 01:57:21 PDT)
- AMBER: P4 EM64T Intel Fortran Compile Problem Dawei Zhang (Fri Jul 15 2005 - 10:04:49 PDT)
- AMBER: Re: Problems with ptraj/rdparm Thomas E. Cheatham, III (Fri Jul 15 2005 - 12:22:28 PDT)
- AMBER: problem with protein ligand complex Claire Zerafa (Sat Jul 16 2005 - 09:31:56 PDT)
- AMBER: random-coil polymer Varsha Goyal (Sat Jul 16 2005 - 15:35:19 PDT)
- AMBER: AMBER-process_mdout.perl Praveena Gopal (Mon Jul 18 2005 - 00:26:19 PDT)
- AMBER: PMF calculations with TI using the sander Vitor Manuel Sousa F?x (Mon Jul 18 2005 - 00:30:59 PDT)
- AMBER: cap simulations questions Fabien CAILLIEZ (Mon Jul 18 2005 - 07:50:32 PDT)
- AMBER: segmentation fault in radial ptraj Kateryna Miroshnychenko (Mon Jul 18 2005 - 09:55:08 PDT)
- AMBER: Using Antechamber with Gamess and other molecular manipulations Charles Karney (Mon Jul 18 2005 - 10:28:20 PDT)
- AMBER: comparing md trajectories ayongye.chem.uga.edu (Mon Jul 18 2005 - 18:12:15 PDT)
- AMBER: mm_pbsa question Matthew Davies (Tue Jul 19 2005 - 03:07:51 PDT)
- AMBER: pdb file and xleap Wai Keat Yam (Tue Jul 19 2005 - 03:06:50 PDT)
- AMBER: Amber 7 Compiler Error Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 05:26:14 PDT)
- AMBER: Trouble with Amber8 Dustin (Tue Jul 19 2005 - 13:16:10 PDT)
- AMBER: Compiling Amber7 wint Intel Fortran v8 Compiler Stephen P. Molnar, Ph.D. (Tue Jul 19 2005 - 13:14:30 PDT)
- AMBER: cap and ptraj Fabien CAILLIEZ (Tue Jul 19 2005 - 15:14:50 PDT)
- AMBER: FW: Andrew Box (Tue Jul 19 2005 - 19:07:44 PDT)
- AMBER: P4 EM64T Intel Fortran Compile Problem Zhang Bing (Wed Jul 20 2005 - 19:24:20 PDT)
- AMBER: Atom type :Si Ananda Rama Krishnan Selvaraj (Thu Jul 21 2005 - 12:02:23 PDT)
- AMBER: [OT] A nab programming question M. L. Dodson (Thu Jul 21 2005 - 13:07:09 PDT)
- AMBER: Question about Prep file opitz.che.udel.edu (Thu Jul 21 2005 - 13:52:41 PDT)
- AMBER: Error in MD mathew k varghese (Thu Jul 21 2005 - 20:53:08 PDT)
- AMBER: Lipid bilayer parameters nag raj (Fri Jul 22 2005 - 00:18:24 PDT)
- AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Fri Jul 22 2005 - 00:53:24 PDT)
- AMBER: SHAKE error Agata Jurkiewicz (Fri Jul 22 2005 - 07:09:34 PDT)
- Re: AMBER: a bimolecular reaction Yong Duan (Fri Jul 22 2005 - 10:44:23 PDT)
- AMBER: nucgen bdna types Stern, Julie (Fri Jul 22 2005 - 18:01:20 PDT)
- AMBER: mmpbsa test problem Suxin Zheng (Fri Jul 22 2005 - 18:41:11 PDT)
- AMBER: Lipid bilayer parameters and charmm force field parameters nag raj (Fri Jul 22 2005 - 20:15:35 PDT)
- Re: AMBER: Modeling of a radical Peter Gannett (Sat Jul 23 2005 - 07:21:25 PDT)
- AMBER: Adding residues to a DNA sequence Kara Di Giorgio (Sun Jul 24 2005 - 18:50:45 PDT)
- AMBER: fit Yong Xu (Mon Jul 25 2005 - 02:04:57 PDT)
- AMBER: ptraj-acceptor mask format Peter Gannett (Mon Jul 25 2005 - 12:10:47 PDT)
- AMBER: antechamber Dustin (Mon Jul 25 2005 - 13:30:40 PDT)
- AMBER: nucgen H5T H3T Stern, Julie (Mon Jul 25 2005 - 18:55:52 PDT)
- AMBER: potential of mean force calculation along reaction coordinates Ye Mei (Tue Jul 26 2005 - 00:04:00 PDT)
- AMBER: Lipid parameters nag raj (Tue Jul 26 2005 - 03:55:22 PDT)
- AMBER: Periodic box imaging using ptraj Grzegorz Jezierski (Tue Jul 26 2005 - 06:25:53 PDT)
- AMBER: why not minimize snapshots before MM/PBSA calculations JunJun Liu (Tue Jul 26 2005 - 08:02:00 PDT)
- RE: AMBER: Tutoial 8 (Case Study) Ross Walker (Tue Jul 26 2005 - 10:03:37 PDT)
- AMBER: Thermodynamic Integration for conformational changes? Grzegorz Jezierski (Tue Jul 26 2005 - 10:33:00 PDT)
- AMBER: new residue Douali, Latifa (Tue Jul 26 2005 - 17:50:51 PDT)
- RE: AMBER: An atom name with 4 characters is not compatible with Leap ? Arnoult, Eric [PRDFR] (Wed Jul 27 2005 - 00:20:27 PDT)
- AMBER: cutoff in ANAL Madjid Taghdir (Wed Jul 27 2005 - 01:06:54 PDT)
- AMBER: prepi format and question about it Ilyas Yildirim (Wed Jul 27 2005 - 02:20:00 PDT)
- AMBER: Protein residue numbering Sukjoon Yoon (Wed Jul 27 2005 - 04:52:42 PDT)
- Re: Re: AMBER: how to reduce box size and delete excess solvent hj zou (Wed Jul 27 2005 - 06:36:40 PDT)
- AMBER: [FWD] water minimalization problems blakrose.gazeta.pl (Wed Jul 27 2005 - 08:46:47 PDT)
- AMBER: How to insert a protein in lipid bilayer nag raj (Wed Jul 27 2005 - 09:56:07 PDT)
- AMBER: pbsa problem Suxin Zheng (Wed Jul 27 2005 - 12:47:29 PDT)
- AMBER: convert_trajectory Wei Chen (Wed Jul 27 2005 - 13:58:36 PDT)
- AMBER: Minimized structure Yam (Wed Jul 27 2005 - 20:02:03 PDT)
- AMBER: nucgen error (U not generated) mathew k varghese (Wed Jul 27 2005 - 20:28:51 PDT)
- AMBER: dihedral term in prmtop file Ye Mei (Thu Jul 28 2005 - 07:38:55 PDT)
- AMBER: Division by zero in sander Caleb S Howe (cshowe.Princeton.EDU) (Thu Jul 28 2005 - 07:57:00 PDT)
- AMBER: Fatal Error on loading a pdb in xLeap Kara Di Giorgio (Thu Jul 28 2005 - 08:10:45 PDT)
- AMBER: ambpdb core dump Peter Gannett (Fri Jul 29 2005 - 04:27:46 PDT)
- AMBER: ptraj output missing opitz.che.udel.edu (Fri Jul 29 2005 - 08:05:19 PDT)
- AMBER: temperature keep increasing in high temp. Hwankyu Lee (Fri Jul 29 2005 - 14:27:04 PDT)
- AMBER: mm_pbsa Wei Chen (Fri Jul 29 2005 - 17:10:46 PDT)
- AMBER: Failed sander runs for large systems Pratul K. Agarwal (Fri Jul 29 2005 - 19:41:44 PDT)
- AMBER: Amber parameters for ADP zgleo (Fri Jul 29 2005 - 22:22:19 PDT)
- AMBER: RESTARTED DUE TO LINMIN FAILURE Sukjoon Yoon (Fri Jul 29 2005 - 23:00:24 PDT)
- AMBER: questions about MG ions JIANING WANG (Sun Jul 31 2005 - 16:12:36 PDT)
- Last message date: Mon Aug 01 2005 - 06:53:00 PDT
- Archived on: Fri Mar 12 2010 - 05:59:46 PST
