Re: [modeller_usage] wrong topology for the ligand?

[Modeller Caretaker <>]

On Tue, Nov 16, 2004 at 02:08:00AM -0500, Youbin Tu wrote:
>      I am using MODELLER7V7 to build a ligand-enzyme complex, I created 
> the ligand and modified the library files. Everything worked well 
> except the ligand in the final result seems too weird, for example the 
> benzene is not planar and there are many bonds between 2 atoms which 
> should only have one bond theoritically. 

For non-standard residues (such as ligands) Modeller can only do as well
as the parameters you give it, just as with any molecular mechanics
package. If the ligand looks weird, you've almost certainly got an
incomplete parameter set (and Modeller may warn you about this,
depending on the circumstances).

If you give Modeller no parameters, it will guess them from the current
template structure. See http://salilab.org/modeller/7v7/manual/node30.html.
In the case of benzene, this will restrain your C-C bonds to their
distances in the original structure, but it probably won't enforce
sufficient constraints to keep planarity.

If flexibility of the ligand isn't too important, you should use a
'block' residue and keep the original geometry unchanged. This is also
covered at the above URL.

>      I thought maybe it is my problem when building the ligand. But 
> when I tried to use GDP which  already existed in the library file. The 
> final results still have the same problem. 

You may have conflicting restraints in this case.

Alicia's reply is largely correct. Modeller writes only xyz information
into output PDBs, and no connection data; this is why viewing packages
have to guess at the connectivity and sometimes get it wrong. Modeller
uses the CHARMM (not CHARMm) 22 parameter set, and the coverage of
residues other than aminoacids is rather sparse.

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