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
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