Re: AMBER: RESP calculation of modified nucleotides

From: FyD <>
Date: Sun, 25 Feb 2007 18:49:55 +0100


> One good starting point to learn about RESP charge fitting is the following
> website ""
> As far as the methyl group charge constrain is concerned, you can add up the
> charges of the phosphate and sugar moeity for normal nucleotide (from AMBER)
> and use that value.
> The way you constrain the methyl group is as follows:
> Lets say the charge constrain you want to use is 0.09e and the
> methyl atoms are
> 10,11,12 and 13 in your gaussian file. Then at the end of your resp
> input file
> you need to add a line that looks like this
> 4 0.09
> 1 10 1 11 1 12 1 13
> What this tells the resp program is that there is a charge constrain of 0.09e
> for 4 atoms in molecule 1 and the atom numbers for which this
> constrain should
> be applied to are 10,11,12 and 13.

You can also use R.E.DD.B. were you will find many examples of RESP inputs.

For instance, for the F-59 project, you get the 2
corresponding RESP inputs
And the inter-molecular charge constraints are described in those inputs...

You can also get examples of intra-molecular charge constraints for
many other R.E.DD.B. projects.

regards, Francois

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Received on Wed Feb 28 2007 - 06:07:09 PST
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