Re: RE: [modeller_usage] wrong topology for the ligand?

[Modeller Caretaker <>]

On Wed, Nov 17, 2004 at 05:25:09AM -0500, Youbin Tu wrote:
>    Thanks for your reply, which help me a lot. 
>    But for my specific situation, the ligand I am trying to use is 
> phenacetin  which did not exist in the template pdb file. Or to say, we 
> created it so as to make it docked in the active site by using some NMR 
> restraints. We expected to see some interactions between the ligand and 
> the active site which will make the active site show a differnt look 
> from what it is when no ligand is bound. 

Yes - if there is no template, you will have to define parameters for
the ligand.

>    Now I was really confused, if the ligand can not have correct 
> connectivity, how can we expect to see the interactions between the 
> ligand and the enzyme?

You misunderstand me. Modeller knows the connectivity - it reads it from
the topology file - but it doesn't write it to the final model PDB file,
so your PDB viewer cannot read the connectivity.

>    Again, why the ligand does not show  correctly, you know , we build 
> the phenacetin in Builder module in InsightII  and output it as a RTF 
> file, then append it to the top_heav.lib file.

The RTF file only defines the topology. It doesn't define the
parameters. These need to be put into par.lib. This is the case for any
molecular mechanics package, not just Modeller.

>    Another question is whether does the RTF file provide enough 
> connectivity information for the ligand?

Certainly. All connectivity for the ligand is included in the RTF
(residue topology file) but you need the parameters as well. If
InsightII has parameters defined for your ligand, you will need to save
them as well, and put them into Modeller's par.lib file.

Note that the topology only defines bonding interactions, i.e. covalent
bonds within the ligand or protein. Interactions between the ligand and
the protein are non-bonding, and are not described here - you'd use VDW
or electrostatic interactions for that.

> Or is it because of the special restraints we applied in MODELLER  which
> make the connectivity changed?

They won't change your topology, but of course, if you have a bond
interaction which clashes with a user restraint, Modeller will try to
compromise.

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