abelius wrote:
Dear All,
I would like to work on the R61 DD-peptidase enzyme complexed with
penicillin G and cephalosporin C. The antibiotics are covalently bound
and up till now I used gromacs/oplsaa for simulations on the apo enzyme
but I'm struggling with the FF parametrization of the antibiotics.
Can someone help me?
Read the primary literature for the force field and derive parameters in a
compatible way. There is no way around it - parameterization is an extremely
difficult task, but without doing it properly, your results will be
questionable, at best, and completely wrong, at worst.
-Justin
Thank you in advance,
Abel
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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