Dear Sir,

Thank you very much for all previous replies. I am having some problems, please provide a solution to them.

1. Is the value of objective function obtained after complete process of MODELER , system size specific? I mean when I model a system of > 500 residues (target), it generates >50000 restraints (3 templates used) and final value of objective function is >20000, but when I model a part of the target , taking respectively aligned template portions, approx 150 residues (target), the restraints generated are around 9000 and final value of objective function comes to 2000 units. So, this shows that smaller the system , lower the final value of objective function, same restraints selected in both cases and assume no violations. Please comment

2. Also, how can one decide that such high values of objective function are acceptable or not, assume there are no violations? (Please specify if you have such experience/idea of Modelling bigger proteins.)

3. Thirdly, from documentation I came to understand that, that when one wants to generate non bonded pair restraints as static ones, he has to include them in MAKE_RESTRAINTS command and keep all DYNAMIC_SPHERE, LENNARD, COULOMB, etc off. Can you tell me which is better , non bonded restraints used as static or non bonded restraints as dynamic (generated automatically by MODELER on fly)?

Please explain.

Thank you very much in advance.

sincerely,

Vivek Sharma Graduate Student (Biochemistry/Biophysics) University of Helsinki.