VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Nov 22 2007 - 05:45:12 CST

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
>
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