VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Nov 22 2007 - 04:02:33 CST

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
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