AMBER Archive (2004)

Subject: Re: AMBER: RESP charge derivation

From: FyD (fyd_at_u-picardie.fr)
Date: Wed Aug 11 2004 - 11:55:57 CDT

> I have derived RESP charges for some base analogues. I used a methyl
> instead of sugar for the Gaussian calculations (# HF/6-31G* OPT POP=MK
> IOP(6/33=2) FChk=All Iop(6/33=2)). As a control a derived charges for
> methyl-G and compare them with the Amber charges for G. I got the
> results below. There are some differences. The question is, given the
> differences that I observed between the Amber charges of G and the
> calculated charges of m-G can I rely that the my charges are good?? The
> RESP was performed in 2 stages as described for Amber.

>From our tests, RESP atomic charges can present charge difference up to 0.07 e
if you generate the appropriate inputs. Now, I would not be surprised to see
charge difference up to 0.1 e depending on... so much parameters...

I would say that charge difference bigger than 0.1 e results from bad inputs or
the use of a different minimum to compute the MEP.

I would obviously suggest you to use R.E.D. with several orientations as I guess
a unique conformation is only possible with your methyl-base...

You can find a lot of information at
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm

- If you want to use R.E.D. for your methyl derivative, run first R.E.D.
- Then copy the input1 & 2 and espot file in a new directory and add the
restaint charges for your methyl group in the input1.
See
http://www.u-picardie.fr/labo/lbpd/RED/FAQ-I.htm#28
and
http://structbio.vanderbilt.edu/archives/amber-archive/2004/2696.phtml

Regards, Francois

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