# Re: AMBER: RESP calculation of modified nucleotides

Date: Sat, 24 Feb 2007 16:49:10 -0500

Dear Mathew,

One good starting point to learn about RESP charge fitting is the following
website
"http://amber.scripps.edu/antechamber/ac.html"

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 find more information on RESP from AMBER manual as well.
I hope this helps.
Best of luck

Quoting mathew k varghese <mathew_kvarghese.yahoo.co.in>:

> Dear Raviprsad and other amber users,
>
>
> We have done the Gaussian calculations of the modified nucleotides by
> replacing the sugar and phosphate by methyl group. We got the ESP from the
> gaussian output and sucessfully produced the RESP inuts.
>
> How can I costrain the methyl charges? Are we taking only the charges for the
> base atoms and using the charge values of sugar and phosphate from the normal
> nucleotides? The How can we costruct the parameters for the complete modified
> nucleotide to load into LEaP?
>
> Thanks for the help
>
> Mathew
>
>
>
>
> /\/\athew
>
> Mathew K Varghese
> Research Scholar
> School of Pure and Applied Physics
> M.G.University
> Kottayam, Kerala
> India
>
> email mathew_kvarghese.yahoo.co.in
>
> ===========================================================================
>
> ---------------------------------
> Here’s a new way to find what you're looking for - Yahoo! Answers

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 25 2007 - 06:07:59 PST
Custom Search