From: Roman Shevchuk (rmnshevchuk_at_gmail.com)
Date: Wed Jul 04 2012 - 06:42:06 CDT

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