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Re: Modelling Heme

It is possible to transfer the heme group from the template to the 
target (model) using a "block" residue as suggested by Andras. But as 
Christoph pointed out the heme residue type is defined in the Modeller 
topology libraries, and the corresponding parameters are present in the 
parameter libraries. So (in theory) all you need to know is how to 
refer to the HEME residue in the alignment file. This you can figure 
out by looking at Modeller's residue type library (restyp.lib) where 
you will find the entry:

 31 | HEM                 | h | HEME | heme ligand

this tells you that Modeller uses 'h' as the one-letter code for the 
HEME residue. Now all you need to do is add the 'h' residues in the 
right places of your template and target sequences in the alignment, 
add "SET HETATM_IO = on" to the TOP file, cross you fingers, and re-run 
Modeller. If all is fine the heme group will appear in your model.

The difference between this approach and using a block residue is that 
the block residue is treated as a rigid object that is just copied from 
the template to the model, for example Modeller can not distort the 
block residue and the rest of the protein does not "feel" its presence 
beyond the protein - block residue distance restraints extracted from 
the template. This limitation dissapears when defining the heme group 
as a proper residue.

I hope this helps.



Roberto Sanchez, Assistant Professor
Structural Biology Program, Department of Physiology & Biophysics and
Institute for Computational Biomedicine, Mount Sinai School of Medicine 
Box 1677, 1425 Madison Avenue, New York, NY 10029
phone +1 (212) 659 8648, fax +1 (212) 849 2456

----- Original Message -----
From: fisera <>
Date: Thursday, February 14, 2002 1:12 am
Subject: Re: Modelling Heme

> please follow instructions from FAQ (Freq. Asked  Questions) point 16,
> Modeller manual
> http://salilab.org/modeller/manual/node29.html
> good luck 
> Andras
> Christoph Nimptsch wrote:
> > 
> > Dear Modellers,
> > 
> > I am trying to model a protein containing a heme group.
> > There is a residue type called heme in top_heav.lib, but I don`t 
> know how to
> > utilize it.
> > I am aware of changing my alignment to include HETATMs but I haven`t
> > succeeded yet.
> > 
> > Do I have to change the pdb-templates to include the heme 
> residue? How can I
> > make it clear that MODELLER 6v1 should use it?
> > 
> > Is it possible to receive the model with the heme group in it?
> > 
> > Thanks for any suggestions,
> > 
> > Christoph Nimptsch