AMBER Archive (2002)

Subject: Re: model molecules for getting charges of DNA

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Sun Jun 09 2002 - 14:47:04 CDT

Jiyoung:

Amber did 2 stages of RESP combining
deoxyribonucleoside and DMP (dimethylphosphate). It
also used equivalence on the partial charges of sugar
and phosphate groups (except C1' and H1') from A, C,
G, T. The method was described in:

Cieplak et al, J. Comp. Chem, 16:1357 (1995).

Qing Zhang

Department of Chemistry
New York University

--- Jiyoung Heo <jyheo_at_wag.caltech.edu> wrote:
> Dear Amber developers,
>
> I am wondering what was the model compound to get
> the charges for DNA
> base. I assume that it could be 1-methylpyrimidine
> or 9-methylpurine.
> Was it deoxyribonucleoside?
> I am trying to get the charges for a non-standard
> base.
> When I looked at your all_nuc94.in, the sugar and
> phosphate parts have
> common charges except C1' and H1'. How did you
> re-distribute your
> residual charge of base part after you got the
> charges from QM
> calculation?
>
> Jiyoung

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