Received: from rockvax.rockefeller.edu (rockvax.rockefeller.edu [129.85.1.21])
by net.bio.net (8.9.1a/8.9.1) with ESMTP id LAA21054
for <biosci-help at net.bio.net>; Fri, 13 Aug 1999 11:14:46 -0700 (PDT)
Received: from mriris.rockefeller.edu (mriris.rockefeller.edu [129.85.25.245])
by rockvax.rockefeller.edu (8.9.1/8.9.1) with SMTP id OAA18243
for <@rockvax.rockefeller.edu:biosci-help at net.bio.net>; Fri, 13 Aug 1999 14:08:29 -0400 (EDT)
Received: by mriris.rockefeller.edu (951211.SGI.8.6.12.PATCH1042/951211.SGI)
for biosci-help at net.bio.net id OAA27917; Fri, 13 Aug 1999 14:04:07 -0400
From: "Celine Francart" <francac at mriris.rockefeller.edu>
Message-Id: <990813140406.ZM27915 at mriris.rockefeller.edu>
Date: Fri, 13 Aug 1999 14:04:05 -0400
X-Mailer: Z-Mail (4.0.1 13Jan97)
To: biosci-help at net.bio.net
Subject: X-PLOR problem!
MIME-Version: 1.0
Content-Type: text/plain; charset=us-ascii
My name is Celine Francart. I am a post-doctoral associate at Rockefeller
University in New York.
I am dealing right now with the structure determination of a complex
protein-peptide by using XPLOR, however I've got a problem at the first step of
the distance geometry with the dg_sub_embed.inp.
I have generated for both the protein and the peptide the protein.psf,
protein.pdb, peptide.psf and peptide.pdb files. After changing residue numbers
in the peptide.pdb file in order to avoid duplicate numbers of residues, I used
the generate.inp as described in the manual in order to generate the
complex.psf and complex.pdb files:
generate.inp:
remarks file nmr/generate.inp
remarks Generate structure file for a protein
remarks using the SA parameter and topology files.
topology
@/TOPPAR/topallhdg.pro
end {*Read topology file *}
parameter
@/TOPPAR/parallhdg.pro
end
segment {*Generate protein *}
name="prot" {*This name has to match the *}
{*four characters in columns 73 *}
{*through 76 in the coordinate *}
{*file, in XPLOR this name is *}
{*name is referred to as SEGId. *}
chain
@/TOPPAR/toph19.pep {*Read peptide bond file *}
coordinates @prot.pdb {*interpret coordinate file to *}
end {*obtain the sequence *}
end
coordinates @prot.pdb
segment {*Generate protein *}
name="pept" {*This name has to match the *}
{*four characters in columns 73 *}
{*through 76 in the coordinate *}
{*file, in XPLOR this name is *}
{*name is referred to as SEGId. *}
chain
@/TOOPAR/toph19.pep {*Read peptide bond file *}
coordinates @pept.pdb {*interpret coordinate file to *}
end {*obtain the sequence *}
end
coordinates @pept.pdb
flags exclude vdw elec end
hbuild
selection=( hydrogen )
phistep=4
end
write coordinates output=complex.pdb end
write structure output=complex.psf end
stop
Getting these two complex.pdb and complex.psf files, I went on with the
dg_sub_embed.inp and always got the error message just after the powell
minimization:
X-PLOR> minimize powell
{*Regularization.*}
POWELL> nstep=100 drop=10. nprint=25
POWELL> end
POWELL: number of degrees of freedom= 5361
%ATMCHK-ERR: unknown coordinates for atom "prot-1 -GLY -CA "
%ATMCHK-ERR: unknown coordinates for atom "prot-1 -GLY -C "
%ATMCHK-ERR: unknown coordinates for atom "prot-1 -GLY -N "
%ATMCHK-ERR: unknown coordinates for atom "prot-2 -SER -N "
%ATMCHK-ERR: unknown coordinates for atom "prot-2 -SER -HN "
%ATMCHK-ERR: unknown coordinates for atom "prot-2 -SER -CA "
%ATMCHK-ERR: unknown coordinates for atom "prot-2 -SER -HA "...
At this time, I am quite sure the problem is coming from the complex.psf and
complex.pdb files, since I had no problem for running the same dg_sub_embed on
the protein alone or the peptide alone. However, by trying different ways to
get these pdb and psf files, I did not succeed yet. I would like to know if you
could help me to resolve this problem. Is the way I generated the complex files
the right one or did I do a mistake I missed?
Thank you very much for your help.
Sincerely yours
Celine Francart
--
Celine Francart
Laboratory of Physical Biochemistry, Box 163
The Rockefeller University
1230 York Avenue, New York, NY 10021
Office: FLX-B3 Phone: (212) 327 8274
Fax: (212) 327 7566
