Sajad Ahrari wrote:
dear users
is it rational to do a simulation on a structure witch is not complete?
i mean pdb structure doesn't cover whole of the protein but it's active
core domain.
may be i should be asking this question somewhere else, but i thought
some of you may have concerned with such case and in fact i didn't
really know where to ask it!
It depends on your aims. If you can answer the question of interest while still
neglecting, i.e. missing termini, and you can prove that the missing residues do
not play any functional role in the dynamics of the active domain, then maybe
you can simulate it. But that is a lot of assumptions. It's certainly been
done, but it may require lots of justification and prior proof that no ill
effects will exist.
Note that this only applies to missing termini. Anything missing within the
sequence will cause pdb2gmx to fail, and even if you force it without building a
suitable model, mdrun will fail due to a physically unrealistic simulation.
-Justin
thanks in advance!
sajad
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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