I you are sure about the interaction sites and the orientation, I will suggest you to build manually the complex and use the resulting model as template and build a new model. But this time use the "strongest" optimization routine (see the manual it is routine 3 or 1 I don't remember". Also depend on the result you may have to eliminate some restraint that may bias the final model.

------------------------------------
Eric Feyfant, Ph.D.
Senior research Scientist
Computational Chemistry
Wyeth Research
200 Cambridge Park Drive
Cambridge, MA 02140
tel: +1 617 665 5656
fax: +1 617 665 5682
email: efeyfant@wyeth.com

>>> "Himanshu Grover" <hgrover_00@iiita.ac.in> 6/30/2004 8:04:44 AM >>>

hi,
being a new user, I am facing many problems with modeller. now consider
a situation in which i want to model only one particular domain/protein
in a protein-protein complex, since the structure for the other
domain/protein is available, but then i want to optimize the binding
region of the modelled domain taking into context, the other domain as
well... is it possible that i use the optimization routine of modeller
for the same, only after putting both the proteins of the complex into
proper interacting/binding orientation, so that energy minimization can
be performed taking into context the entire complex and not just the
modelled part
thanks, for helping out...

sincerely.
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