[gmx-users] PenG/CepC OPLSAA

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 6 23:29:43 CEST 2009

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.


> 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


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