AMBER Archive (2009)

Subject: Re: [AMBER] Parametrizing charges for modified DNA bases

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Dec 07 2009 - 13:31:02 CST

Dear Bob,

You could use the R.E.D.-III.3 tools or R.E.D. Server/R.E.D.-IV
See http://q4md-forcefieldtools.org/

Tutorials are available @
http://q4md-forcefieldtools.org/Tutorial/
See in particular:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#14
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#18
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25

And examples in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/projects/F-58/
A more complex case:
http://q4md-forcefieldtools.org/REDDB/projects/F-60/

regards, Francois

> I would like to parametrize charges for DNA bases that contain some
> chemical modifications. The modifications are pretty simple and
> contain atom types that are already defined within the AMBER force
> field.
>
> In order to parametrize charges, however, I would like to follow the
> method used for the rest of the DNA bases. That is, I would like to
> fit the RESP charges to the bases while restraining the charges on the
> sugar group to certain values. That way, this base should be
> compatible with the rest of the bases in the AMBER force field. Is
> there software that will aid in this process?

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