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.