Hello!
Is it possible in MODELLER to change the weight of certain
parameters in the optimization process? I am doing homology modelling with
incorporation of ligand information as special restraints. The restraints
are expressed in terms of knowledge based distance dependent pair
potentials between protein and lingand atoms. These pair potentials are
expressed in terms of cubic splines.
I would like to try if I can improve my results by increasing the scaling
weight of my special restraints compared to the predefined restraints
which Modeller uses in the model building process.
my top file basically looks like this:
--------------------------------
INCLUDE SET ALNFILE = '../alis/1dlw_2d.pir'
SET KNOWNS = '1dlw'
SET SEQUENCE = 'fake'
SET ATOM_FILES_DIRECTORY = '../pdbs'
SET HETATM_IO = on
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
SET FINAL_MALIGN3D = 1
CALL ROUTINE = 'model'
STOP
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
---------------------------------
The file atmcls-special.lib contains the definitions of the atom groups I
use, the
file special-pairpot.lib contains the restraints for each protein - ligand
atom pair, e.g.:
---------------------------------
MODELLER12 VERSION: MODELLER FORMAT
R 10 60 1 31 2 66 0 L001 P001 1.00 0.00 5.90 0.10 -0.13 -0.05 10.00 9.99
9.95 9.89 9.80 9.68 9.55 9.39 9.21 9.02 8.80 8.57 8.33 8.07 7.80 7.53 7.25
6.96 6.67 6.38 6.09 5.80 5.51 5.23 4.96 4.69 4.44 4.06 3.95 3.59 3.07 2.62
2.26 1.86 1.40 0.95 0.61 0.38 0.17 0.01 -0.10 -0.18 -0.27 -0.36 -0.44
-0.49 -0.50 -0.51 -0.50 -0.50 -0.55 -0.62 -0.70 -0.75 -0.74 -0.73 -0.70
-0.66 -0.64 -0.64
.
.
.
------------------------------
... defines the distance distribution between protein and ligand C.3
atoms.
Thank you in advance 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: #
# AG-Klebe-Home: http://www.agklebe.de #
######################################################################