Re: PSF file generation

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Mon May 10 2004 - 10:39:42 CDT

Hello,

Does psfgen complain or give any warnings as it is running?

Brian

On Sun, 9 May 2004 beckloni_at_umdnj.edu wrote:

> Greetings,
> I am attempting to generate a psf file for two different molecules,
> trypsin and a novel analogue. Unfortunately, the pgn file will only read
> the C and N terminus of the analogue, not the rest of the molecule. I have
> attempted to add the missing residues through such commands as residues and
> even alias residues but nothing seems to work. Is there something that I am
> doing wrong here?
> Here is my pgn file setup:
> package require psfgen
> topology top_all27_prot_tst.inp
> alias residue HIS HSE
> alias atom ILE CD1 CD
> segment TRP {
> pdb trp.pdb
> }
> patch DISU TRP:22 TRP:157
> patch DISU TRP:42 TRP:58
> patch DISU TRP:128 TRP:232
> patch DISU TRP:136 TRP:201
> patch DISU TRP:168 TRP:182
> patch DISU TRP:191 TRP:220
> coordpdb trp.pdb TRP
> segment ANA {
> pdb analogue.pdb
> first CTER
> last NTER
> }
> coordpdb analogue.pdb ANA
> guesscoord
> writepdb trpd.pdb
> writepsf trpd.psf
>
>
> Both of the segment file formats are out of SPDBV to rebuild the missing
> side chains. The analogue file was built as one single chain in Sybyl.
>
> Sincerely,
> Nicholas Beckloff
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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