AMBER Archive (2009)

Subject: Re: [AMBER] MD simulations on a protein with FAD and NADH

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Feb 27 2009 - 02:24:37 CST

Hi Mannan,

> Is there any reference in which MD simulations on a protein which
> has  FAD and NADH.

Besides the Amber contrib reported by Ross - I can send you FF
libraries more or less for the cofactors (FAD, NAD, CoASH etc...) you
wish. When we developed these force field libraries we adopted a
global strategy for as many as possible cofactors (i.e. we did not
only studied FAD or NADH). The idea was not just to pick up one
structure, and to get charges for this particular structure but to
adopt a global/general charge derivation strategy (with FF library
building) for as many as possible cofactors.

See the list of available force field libraries described in the Amber
mailing list @ http://archive.ambermd.org/200812/0329.html

Just tell we if you wish to try those FF libraries, I can send them to
your personal email.

regards, Francois

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