On Thu, 2014-02-06 at 09:41 +0000, Nahoum Anthony wrote:
> Hi,
>
> I was wondering if someone would have guidance as the correct/best way to
> parameterise the linking residue between two proteins that are covalently
> conjugated together through an amide bond between the side chain nitrogen of
> the lysine of one protein to the (glycine) C-terminus carboxyl of the other
> protein ?
I would create some model compounds in which the lysine is capped at all
3 linking positions and use a RESP protocol (R.E.D. is designed for this
-- see
http://q4md-forcefieldtools.org/) to derive charges, constraining
the capping groups to have a net 0 charge (to keep the net charge on the
lysine residue 'correct'.
It may be that this residue has already been built -- R.E.D. runs a
database that would be worth looking through to see if these lysine
charges have already been derived.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Feb 06 2014 - 05:00:03 PST
