bulid psf for structure already with hydrogens

From: Ching Wong (wongcw_at_TITAN.SFASU.EDU)
Date: Wed Jul 19 2006 - 14:02:32 CDT

Hi all, sorry to bother.

I am trying to build psf file for a pdb (x-ray structure with hydrogens
added according to pKas).

I try to take out the segment and guesscoord commands but it wouldn't
work, but I don't want to add any hydrogens at all. Any idea of what
the script should be?



Mine is

package require psfgen
        topology top_all27_prot_lipid.inp
        alias atom ILE CD1 CD
(I try to take out this part, but it doesn't work)
        segment A {pdb 56Ac2m.pdb}
        patch DISU A:34 A:120
        patch DISU A:168 A:171
        patch ASPP A:114
        patch ASPP A:140
        patch ASPP A:239
        patch GLUP A:162
        patch GLUP A:201
        coordpdb 56Ac2m.pdb A

        writepdb new.pdb
        writepsf new.psf


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