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: #
> # AG-Klebe-Home: http://www.agklebe.de #
> ######################################################################
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras