Re: [modeller_usage] hetatms placed far away from the backbone

[Modeller Caretaker <>]

On Wed, Oct 13, 2004 at 04:23:10PM +0200, Michael Knoll wrote:
> I'm trying to model a ZN-containing (two zn ions) protein with 
> modeller6v2.
...
> The model building results in a model where the overall structure of the 
> model looks almost good, but the zn atoms are PLACED FAR AWAY from the 
> model backbone.

Modeller may not be able to guess which restraints you need between your
hetatoms (Zn) and neighboring residues - you can check the restraints
file generated during modeling to see if any restraints were defined on
the Zn atoms. Most likely, you will have to add some user-defined
restraints to keep the geometry of the Zn-binding site. See, for
example, the tutorial for a similar system at

http://salilab.org/modeller/methenz/

The text for example 2 can be found at:
http://salilab.org/modeller/methenz/andras/node16.html

(The text applies to a rather old version of Modeller, but the example
TOP files, at ftp://salilab.org/tutorials/methenz/example2/, will work
with Modeller 7v7, and probably 6v2.)

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
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