From: FyD <>
Date: Sat, 11 Jun 2011 09:22:38 +0200

Dear Caterina,

> I want to calculate the charges of methyl-cytosine base using the RESP
> charge fitting procedure. I built my molecule (1,5-dymethylcytosine) and on
> the position 1 I put the cap (another methyl group). Assuming that the
> methyl-cytosine base has a charge of -0.0631 (the same as cytosine on AMBER
> FF03), my cap (the methyl on position 1) must to have a charge of +0.0631 so
> the whole residue will be neutral. How can I fix the charge on the
> methylgroup to +0.0631 in Antechamber?

I guess you have to prepare/adapt the RESP inputs by hand in your case
if you use Antechamber.

In your case, I would start from a dipeptide (for instance
ACE-CYM-NME) as defined originally in Cieplak et al. J.Comput. Chem.
1995, 16, 1357-1377.

If you use R.E.D. or R.E.D. Server the procedure is done as it follows.
- You prepare a P2N file (or a set of P2N files; in your case using
Ante_RED version 1.4 or 2.0 should lead to the same type of file; I
mean from a chemical equivalencing point of view).
- You define intra-molecular charge constraint(s) within the dipeptide
[and inter-molecular charge constraint(s) between the dipeptide and
methylammonium or acetate if you want to generate the terminal
fragments]; using the keywords INTRA-MCC (and INTER-MCC)
- You run R.E.D. III.4 or R.E.D. Server/R.E.D. IV and you get a mol2
file for each fragment you are interested in.

For the Duan et al. force field, your best bet is to use Gaussian 2003.

- If you use R.E.D. III.4 & if you want to derive RESP charges for the
Duan et al. force field see the 'Scripts/Corn2Duan.csh' script so that
when you define the RESP-A1 charge model in RED-III.4, charges are
these for the Duan et al. force field.

- If you use R.E.D. Server just pick up the RESP-A1B charge model (&
not RESP-A1A).

See the tutorials . as well
  R.E.D. Server

Finally, you can find examples of such an approach in R.E.DD.B.
See the project F-82 entitled "3-(2-naphthyl)-L-alanine" by A. Ziemys.
RESP inputs for the corresponding project are .
in "" see the section related to intra-molecular charge
constraint(s) and inter-molecular charge constraint(s).

See as well the RESP documentation we have adapted .
It should be further developed...

I hope this helps.

regards, Francois

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Received on Sat Jun 11 2011 - 00:30:02 PDT
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