VMD-L Mailing List
From: Roman Shevchuk (rmnshevchuk_at_gmail.com)
Date: Wed Jul 04 2012 - 06:42:06 CDT
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Dear users
I want to run simulation with namd and polarizable water model (
http://www.ks.uiuc.edu/Research/Drude/ ). But in original files water box
consists of 216 water molecules which is too few for my purposes.
I created pdb with larger water box and tried psfgen to create
corresponding *psf file with following commands:
topology swm4.top
segment BULK { auto none
pdb box.pdb
}
writepsf box.psf
But in the result box.psf doesn't have info about NUMLP and when I tried to
run namd I get an error:
FATAL ERROR: EOF ENCOUNTERED LOOKING FOR NUMLP IN DRUDE PSF FILE
As I understood current version of psfgen doesn't create info about lone
pairs. Is there a way to fix this?
Best, Roman
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