VMD-L Mailing List
From: Irene Newhouse (einew_at_hotmail.com)
Date: Thu Nov 22 2007 - 04:02:33 CST
- Next message: L. Michel Espinoza-Fonseca: "Re: solvate crashes"
- Previous message: John Stone: "Re: problem with loading trajectories in timline plugin"
- Next in thread: L. Michel Espinoza-Fonseca: "Re: solvate crashes"
- Reply: L. Michel Espinoza-Fonseca: "Re: solvate crashes"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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.
www.windowslive.com/smile?ocid=TXT_TAGLM_Wave2_oprsmilewlhmtagline
- Next message: L. Michel Espinoza-Fonseca: "Re: solvate crashes"
- Previous message: John Stone: "Re: problem with loading trajectories in timline plugin"
- Next in thread: L. Michel Espinoza-Fonseca: "Re: solvate crashes"
- Reply: L. Michel Espinoza-Fonseca: "Re: solvate crashes"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]