Hello, I have downloaded the waterrefine_XPLOR directory from Jens Linge's FTP site, but I can't get the example to work; XPLOR does not read in the dihedral angles and stops. In fact, there is a line "! looking for the XPLOR bug: Are the dihedrals read in???" in read_data_test.xplor, so it seems that it's a known problem. When I removed the dihedrals from the calculation, no error messsages came up and a PDB came out, but the structure fell apart (of course).
Can anyone help me get this to work? In the end, I'd like to refine my 142 amino acid protein with a covalently bound organic ligand. I calculated my structure with a slightly modified version of the sa.inp that comes with XPLOR-NIH, using unambiguous NOEs, dihedrals, and RDCs. I'm using XPLOR-NIH 2.16.0 on an Intel Mac running OS X 10.4.10. Thanks, Martin [Biozentrum, Universit?t Basel, Switzerland] ORIGINAL MESSAGE: From: Haydyn David Thomas Mertens <hmertens <at> unimelb.edu.au> Subject: Re: structure refinement in explicit solvent like water Newsgroups: gmane.science.biology.xplor-nih.general Date: 2005-12-01 22:41:30 GMT (1 year, 33 weeks, 3 days, 7 hours and 29 minutes ago) Hi guys, Jens Linge and Michael Nilges have some water-refinement scripts in X-plor format available at: ftp://ftp.pasteur.fr/pub/BIS/linge/ The scripts are a conversion of the original explicit solvent refinement used in ARIA 1.2, but can be updated by changing a few parameters according to the article: Linge, J.P., Williams, M.A., Spronk, C.A., Bonvin, A.M. and Nilges, M. (2003) Refinement of protein structures in explicit solvent. Proteins 50, 496?506. Hope this helps. Haydyn >> I noticed a post on this maillist at Sep. 12, 2003 looking for a script >> to >> refine protein structure in explict solvent but did not find any >> response to >> that one. I did not find an example in the xplor-nih distribution >> either. I am >> wondering whether anyone has one at hand and would like to share. > -- Haydyn D.T. Mertens, Ph.D. Bio21 Molecular Science and Biotechnology Institute The University of Melbourne, Victoria, 3010, Australia tel:+61 3 83442273, email:hmertens <at> unimelb.edu.au ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
