W:A liitle help with Insight

From: "Ritin, , Sharma" <sritin [] ibab.ac.in>
Subject: W:A liitle help with Insight
Date: Mon, 27 Jun 2005 03:02:50 -0400

 Hello bioinformaticians,
 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.
 My ligand is a nonapeptide and has a -S03H group attached to tyrosine aswell as
 -NH2  attached to phenylalanine. I am using CVFF forcefield. My receptor is
 purely made of amino acids.
 Anyone who has faced similar difficulty, please let me know the solution. If
 anyone has good tutorials on performing minimization, interactive and automated
 docking using insight than please send me the link or material.
 Any help in this regard will be highly appreciated.
 Respond ASAP
 Yours sincerely
 Ritin Sharma
 X-Ray Crystallography and Biophysics Lab
 Dept. of Physcis,Indian Institute od Science
 Bangalore, INDIA
 Email: sritin [] ibab.ac.in