Dear Jia,
> I am trying to simulate a peptide with a metal-containing complex. As
> shown in the attached picture, the gold atom (yellow ball) of
> phenanthroline-gold is bound to N and S atoms of HIS and CYS, respectively.
> I used to calculate the resp charge of non-standard residue by R. E. D. III.
> It works fine. But I have no experience to work on small molecules.
>
> I would like to know if it possible to obtain the RESP charge of such a
> heavy-metal contained complex which is bound to two residues?
You need to solve several problems in R.E.D.-III.x to get charges for
your Gold complex:
1) Add the "Au" atom in the source codes to authorize R.E.D. &
Ante_R.E.D. to use "Au"
2) Add which "radius" value you want to use for "Au"
3) Add which "theory level" you want to use during the geometry
optimization & MEP computation step
4) Select a target complex to be involved in charge derivation using
the RESP program. Here, you need to imagine how you could include your
complex in your whole molecule. You select a model & you use
constraint(s) during the RESP fit to make your model compatible with
the whole system: Once you understood the use of intra-molecular
charge constraint in dipeptide for instance you can easily apply the
same strategy to your Au complex (using two amino acid central
fragment).
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
I can help you setting these steps if you need...
The next version of the R.E.D. Tools source code is going to be
distributed under the GNU General Public License. We will see if we
can release III.4 next week.
regards, Francois
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Received on Thu Jun 24 2010 - 22:30:03 PDT
