From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jul 23 2006 - 19:47:03 CDT
It should work fine if you remove just the guesscoord command.
On Jul 19, 2006, at 2:02 PM, Ching Wong wrote:
> 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?
>
> Thanks.
>
> Jas
>
> 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
> guesscoord
>
> writepdb new.pdb
> writepsf new.psf
>
>
> -------
> Jasmine
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