Re: CCL:W:A liitle help with Insight

"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
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