Dear Tony,
We got your files with the problem described below.
Your Modeller run did not give you not only the hetatm but any output since it
reported an error in the *.log file. It was complaining about the alignment.
This is the most usual problem, users must pay attention to it. The log file
clearly says, that there is a discrepancy in the number of residues among the
seq.s and the pdb files: the number of residues are different in all cases.
there are several problems:
1., you forgot to indicate in the header of each pir format alignmnet seq. that
the number of residues is one resides longer, since you wanted to include a
heteroatom as well. (e.g. see below ,instead of 500 you need 501)
2., Modeller learns from the pdb templates what kind of atom or residue to be
read in: you indicated in the sequence that there is a "zn" hetatm, which is
misleading. In the pir format you have single letter codes: Modeller thought
you have 2 additional residues, a "z" and an "n". You need only to put "." to
show that something else to be read in from the pdb files at that position. If
you wants to have specificly Zn than you a., have to put "z" in the sequence,
and b., ZN2 in the PDB files. The CHARMM atom types are listed in
$MODINSTALL/modlib/restyp.lib.
Modeller clearly complained that you have too many residues in the sequences
(in all of them) i.e. z, n, and "." as well for a single hetatm.
i.e. e.g.:
original:
>P1;1glu_B
structureX:1glu_znf_b: 458: B : 500: B: Glucocorticoid Receptor: : :
GSCKVFFKRAVEGQ-HNYLCAGRNDCIIDKIRRKN-------CPACRY-RKC/.zn*
correct:
>P1;1glu_B
structureX:1glu_znf_b: 458: B : 501: B: Glucocorticoid Receptor: : :
GSCKVFFKRAVEGQ-HNYLCAGRNDCIIDKIRRKN-------CPACRY-RKC/z*
the corrected alignment file with your top script now produces structures to
me, though you need figure out additional marginal problems. e.g. your
templates at certain positions are too different etc.
good luck for the future,
andras
> > >
> > > A.J.Pemberton wrote,
> > >
> > > > Dear users,
> > > >
> > > >I have set my steering file to activate the HETATM usage (modeller 4):
> > > >
> > > >SET TOPOLOGY_MODEL = 1, HETATM_IO = on, HYDROGEN_IO = on, WATER_IO = on
> > > >
> > > >as per FAQ question 15
> > > >
> > > >but modeller is not giving me HETATMs is the pdb output, why?
> > > >
> > > >Regards,
> > > >
> > > >Tony
> > > >
> > > >*********************************************************************
> > > >Mr. A.J.Pemberton Tel: +121-414-3388
> > > >c/o Dept. Rheumatology, Fax: +121-414-3982
> > > >Medical School, E-mail:
> > > >The University of Birmingham,
> > > >Birmingham B15 2TT.
> > > >U.K.
> > > >*********************************************************************
> > >
> > >
> > > I have the same problem !!!
> > >
> > >
> > > Antonello Romani
> > >
> > >
> > >
> > >
> > > ___________________________________________________________________________
> > > Antonello Romani
> > > Istituto di Patologia Generale
> > > Plesso Biotecnologico Integrato
> > > Facolta' di Medicina e Chirurgia
> > > Universita' degli Studi di Parma
> > > via Volturno 39
> > > 43100 Parma
> > >
> > > Tel: +39 0521 903 764
> > > Fax :+39 0521 903 742
> > >
> > > E-Mail :
> > >
> > >
> > > ___________________________________________________________________________
--
,
Andras Fiser, PhD # phone: (212) 327 7206
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras