Subject: Re: CCL:W:A liitle help with Insight

From: Jeff Nauss <jnauss_at_accelrys.com>
Date: Mon, 27 Jun 2005 08:55:20 -0700

"Computational Chemistry List" <chemistry-request_at_ccl.net> wrote on 
06/27/2005 12:02:50 AM:

> I have modelled a protein(receptor) using modeller. Now i want to do
> some minimization on my receptor and ligand and later docking using 
> insight. But i have got stuck with fixing potentials and charges of 
> both my receptor and ligand. 
> I get various errors like "Partial charges not equal to formal 
> charges" , "open or undefined valencies", "cannot assign cvff 
> forcefeild". While running discover it complains of unfound 
> parameters in .out file and run is stopped. 

Ensure that you have add hydrogen atoms to your molecule.  Modeler 
typically does not place all hydrogens in your structure.  Thus as far as 
InsightII and Discover are concerned you do not have the correct 
chemistry.

> My ligand is a nonapeptide and has a -S03H group attached to 
> tyrosine aswell as -NH2  attached to phenylalanine. I am using CVFF 
> forcefield. 

The ligand modified as you have will probably be problematic.  I do not 
know if the CVFF force field has robust parameters for such modified amino 
acids.  It might but you need to have the correct chemistry for the 
ligand.  That includes hydrogens, correct bond orders, and explicit 
definition of formal charges.

If you have the CFF force field, that might perform better with respect to 
atom typing.  If not, you may need to develop your own parameters or 
search the literature.

> If anyone has good tutorials on performing minimization, 
> interactive and automated docking using insight than please send me 
> the link or material.

Look in the Pilot tutorials that come with InsightII.  Look under Help | 
Pilot_Tutorials.

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
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From: Donna Bassolino-Klimas <donna=at=stone.congenomics.com>
Date: Mon, 27 Jun 2005 18:21:58 -0400 (EDT)

> InsightII and Discover are concerned you do not have the correct 
  Also remember to add the hydrogens at neutral pH ... otherwise
  some will be charged and your resulting structure will have an
  overall charge.

  Donna

===================

Donna Bassolino-Klimas, Ph.D.
DBK Web Development
donna=at=dbkonline.com
www.dbkonline.com