Hello!
I want to do homology modelling including information from ligands to model the active site of a protein. I started with hemoglobin as the heme substrate and its topology are already defined in the Modeller4 libraries. As restraints I want to use knowledge based pair potentials between protein and ligand atoms derived from complexes in the PDB and express these restraints as splines.
In the top-file, I include the following SPECIAL_RESTRAINTS routine: ######################### SUBROUTINE ROUTINE = 'special_restraints' SET DYNAMIC_MODELLER = on SET CONTACT_SHELL = 6.00 READ_ATOM_CLASSES ATOM_CLASSES_FILE = 'atmcls-special.lib' READ_PARAMETERS FILE = 'special-pairpot.lib', ADD_PARAMETERS = on END_SUBROUTINE #########################
In the file "atmcls-special.lib" I grouped the protein atoms (ATMGRP A001 - A012) and the HEME atoms (A041 - A058) according to SYBYL atom classifications.
In the file "special-pairpot.lib" I try to express these pair-potentials as splines. The file looks like this: ######################### MODELLER12 VERSION: USER FORMAT R 10 25 1 31 2 31 0 A001 A041 1.0 0.0 6.0 0.25 -0.05 0.05 values R 10 25 1 31 2 31 0 A002 A041 ... . . . #########################
When I run Modeller it reads the "special-pairpot.lib"-file but then tells me "rdparf__E > increase MATTACNS" and exits.
Does anyone know what went wrong? I am not sure if my parameters in the "special-pairpot.lib"-file are set correctly.
Thank you very much for your help,
Andreas
-- ###################################################################### # Andreas Evers # # # # Research group for Drug Design & X-ray Crystallography # # Institute of Pharmaceutical Chemistry # # Philipps-University of Marburg # # Marbacher Weg 6 phone2 +49-6421-28-25072 # # D-35032 Marburg FAX: +49-6421-28-28994 # # email: Andreas.Evers@mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ######################################################################