Re: Problem including substrate and heme - modeller_usage

3 Feb 1998


      The problem is that there is no MYR entry in the top_heav.lib or other
top*.lib libraries in the standard distribution.
Please check all the times that the entry of the molecule is present in
BOTH restyp.lib and top*.lib corresponding to your model (all atoms,
heavy atoms only, etc.).
Azat.
Jeffrey P. Jones wrote:
> 
> Thanks for your reply.  Both of these residues are in the library files, h & 5
> are the default single letter descriptors.  Any other suggestions?
> 
> Azat Badretdinov wrote:
> 
> > Hi, Jeffrey!
> >
> > Jeffrey P. Jones wrote:
> > >
> > > I am wondering what the format is for input in the alignment file of two
> > > molecules say heme (h) and myristic acid (5) distinct from the protein
> > > of interest.
> > >
> > > My guess is:
> > >
> > > AATLCLL(protein sequence)GT/h/5*
> >
> > Please read the corresponding example in FAQ in the manual, how to deal
> > with small molecules of non-aminoacid nature.
> >
> > The format is oK, but you have to specify in some library file what h
> > and 5 is (Hem is probably present in the standard library).
> >
> > Yours,
> > Azat.
> >
> > >
> > > The order they appear in the pdb file is AA/heme/myristate.
> > >
> > > Is this the format?  When I use it the myristic acid input is ignored.
> > >
> > > Jeff
> > >
> > > --
> > > Jeffrey P. Jones, Ph.D.
> > > Associate Professor of Pharmacology, Physiology
> > > Biochemistry and Biophysics
> > > (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html
> > > jpj@cyp.medicine.rochester.edu
> >
> > --
> > - Dr. Azat Badretdinov
> > - The Rockefeller Univ, Box 270
> > - 1230 York Ave, New York NY 10021, USA
> > - Phone: (212) 327 7206
> > - Fax: (212) 327 7540
> > - E-mail: azat@salilab.org
> > - WWW/URL: http://salilab.org/~azat
> 
> --
> Jeffrey P. Jones, Ph.D.
> Associate Professor of Pharmacology, Physiology
> Biochemistry and Biophysics
> (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html
> jpj@cyp.medicine.rochester.edu
--
- Dr. Azat Badretdinov 
- The Rockefeller Univ, Box 270 
- 1230 York Ave, New York NY 10021, USA
- Phone: (212) 327 7206
- Fax: (212) 327 7540
- E-mail: azat@salilab.org
- WWW/URL: http://salilab.org/~azat