AMBER Archive (2005)

Subject: Re: AMBER: Cu++ and RED

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Mon Feb 14 2005 - 23:30:47 CST

Dear Dupradeau,

Thanks for the info. I have found out that my problem
was with assignment of an carbon atom. Changing atom
type from C to CT for alpha-carbon of an aminoacid
enabled GAMESS to read +2 charge for the
AA-derivative-Cu(++) complex.

regards,

jenk.

--- FyD <fyd_at_u-picardie.fr> wrote:

> > I have been trying to compute RESP charges for an
> > aminoacid derivative in complex with Cu(+2). I use
> > Gamess and RED to compute partial atomic charges.
>
> Which version of R.E.D. do you use: version I or
> version II ?
> RESP charges for metal complexes are automatically
> derived _only_ with R.E.D.-II
>
> > However, I noticed that Gamess somewhat assigns
> (+1)
> > charge to the AA derivative - Cu complex but not
> (+2)
> > charge. The A.A. derivative itself has zero
> charge.
>
> Here, I am not sure I understand you. What is the
> total charge for your complex:
> Let's say it is +2. We can imagine some charge
> delocalisation making the partial
> charge of your copper quite strange. I got data from
> Sebastian F.A. about an
> iron-complex and we observed together important
> charge delocalisation for his
> complex. We even run some charge calculations with
> Piotr and we clearly
> observed that RESP charges are quite weird in some
> cases...
>
> > Is there anyway that I could set/modify RED
> parameters
> > so that (+2) charge is assigned to the AA
> > derivative-Copper complex ?
>
> I would first compare ESP and Mulliken charges
> computed by the QM soft, with the
> RESP charges obtained with R.E.D. Then, if you see
> some strange effects, you
> could add intramolecular restraints (IMR) to
> 'affect' the charge value of your
> copper. IMR are not automatically handled in
> R.E.D.-II. This means you have to
> proceed in two steps (i) run R.E.D.-II without IMR
> (ii) get the espot,
> input1/input2 files - add the IMR in input1, freeze
> the corresponding charges
> in the input2 and re-run resp manually using the 2
> aliases (resp1; resp2)
> defined @
> http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#27
>
> Adding IMR is directly related to the automatic
> generation of LEaP libraries for
> unusual aminoacids/sugar/nucleotide. This will be
> implemented in R.E.D.-III
> (using the 'tripos.mol2' format instead of the
> 'prep.in' one). Mulliken, ESP
> and RESP charges will be also compared (with
> statistics) to detect possible
> problems... We will start this very soon, now. This
> is quite straightforward to
> implement in R.E.D.-II. The 1st beta version of
> R.E.D.-III (without manual)
> should be available before next June...
>
> I hope this helps, regards,
>
> F.-Y. Dupradeau
> DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
> The Scripps Research Institute, La Jolla, CA, USA
> --
> http://www.u-picardie.fr/labo/lbpd/FyD.htm
>
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