AMBER Archive (2009)

Subject: Re: [AMBER] Can I use only a single point calculation to derive RESP charges?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat May 09 2009 - 01:00:36 CDT

Dear Josmar,

> I intend to derive RESP charges for NAD and NADP using REDIII.

I do not know which version you use. Just know the version III.2 is
the last version available for download: we strongly recommended to
use this last version (bug corrections, new features etc...). You can
also use R.E.D. Server which interfaces R.E.D.-IV.

> Since the crystallographic structures for both molecules complexed
> with the protein are available, can I use that conformation to
> derive RESP charges doing only a single point calculation?

Personnally, I would vote for optimizing by QM X-ray structures.
However, in the case of such cofactors - with negative charge(s) - it
is unlikely the structure after optimization will be similar to the
that taken from the X-ray structure. This is mainly because of the
computational conditions used in the geometry optimization as well as
the lack of the environment of the cofactor (that in the X-ray
structure). So you need to find a way to solve this problem...

> Is there any on-line database where I can find the parameters for
> such common cofactors?

We have developed a common strategy using R.E.D.-IV for many cofactors.
See the message http://archive.ambermd.org/200812/0329.html in the
Amber mailing list. I can send you the corresponding force field
libraries in the Tripos mol2 file format to your personal email
address if you tell me the cofactor(s) you need, their total charge as
well as the force field you plan to use. We have a version for the
Duan et al. and Hornack et al. force fields.

These data will be available in R.E.DD.B. However, because of the
numerous molecular fragments generated by R.E.D.-IV, R.E.DD.B. needed
to be reconstructed. Consequently, R.E.DD.B. is currently unavailable
these days. However, the new version is going to be opened Monday.
Then, we will be able to feed R.E.DD.B. with very large projects...

regards, Francois

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