VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Nov 22 2007 - 14:25:46 CST

Thanks for responding on a holiday! Happy Thanksgiving! We cracked it - the psfgen wasn't totally error free. I'm not sure why it generated a psf file anyway, but when we fixed the errors in residue numbering [wrong numbers left over from a previous run with almost but not quite the same structure], it solvated. It took piping the psfgen messages to a file so we could conveniently look at everything to locate the problem.
 
Thanks again!
Irene> Date: Thu, 22 Nov 2007 12:45:12 +0100> From: mef_at_ddt.biochem.umn.edu> To: einew_at_hotmail.com> Subject: Re: vmd-l: solvate crashes> CC: vmd-l_at_ks.uiuc.edu> > Irene,> > Could you please give us more details about the system you're trying> to solvate? Is it very big? What version of VMD are you using and> under which OS?> > Michel> > 2007/11/22, Irene Newhouse <einew_at_hotmail.com>:> >> > I've run into an odd occurrence: after a successful psfgen, my pdb/psf> > files crash in solvate. When I say the psfgen is 'successful', I mean that I> > have 2 files, which, when I load them into VMD look right, though I haven't> > checked on a micro level. Psfgen only produced errors referring to 'poorly> > guessed' H, capping groups, or a few side chain atoms missing from the pdb,> > which is based on x-ray data, which have some missing atoms. I can use> > sequence viewer to check the sequence & that looks good. I can use the Tk> > console & measure the minmax positions for the protein only. I've tried both> > to solvate using the command line from the Tk console & using the solvate> > plugin via the Extensions/Modeling tabs. The result is the same: VMD> > disappears from view, leaving behind a file solvate.log containing nothing.> >> > Has anyone run into this before? Usually my hair-tearing problems are in> > psfgen, & once that works, I'm more or less home free.> >> > Thanks!> > Irene Newhouse> >> > ________________________________> > Your smile counts. The more smiles you share, the more we donate. Join in!
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