From: beckloni_at_umdnj.edu
Date: Mon May 10 2004 - 10:48:22 CDT
Brian,
Thanks but I figured it out. Turns out there was a problem with Sybyl when
it rebuilt the molecule to save it. I had to re-connect the crystals and
then rename the atom types to receive all the coordinate charges. Thanks
though.
Nicholas Quoting Brian Bennion <brian_at_youkai.llnl.gov>:
>
> 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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