Hi Andreas,
yes, you could play with the MAKE_SCHEDULE command, to set up a new shedule: to scale up or down certain type of restraints during optimization. See the explanation in the manual. Also, for the existing schedules, see the $MODINSTALL6a/modlib/sched.lib file
You can define your own, ligand related restraint in one of the 32 type of restraint groups (preferably choose such a group which is not used, so your restraints will be the only one in that group) so you can vary them independently. For these groups see manual pp.75, table 2.4 . Do not worry about the names, most groups are not used in the process (check your actual log file for a report about them) and the names and groupings are somewhat arbitrary, but you can go for groups 27-31, that is about arbitrary distance or NMR distance restraints and usually empty.
Andras
Evers Andreas wrote: > > 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: Andreas.Evers@mailer.uni-marburg.de # > # AG-Klebe-Home: http://www.agklebe.de # > ######################################################################