AMBER Archive (2007)

Subject: Re: AMBER: RESP calculation of modified nucleotides

From: Raviprasad Aduri (rpaduri_at_chem.wayne.edu)
Date: Mon Feb 26 2007 - 10:56:47 CST


Dear Mathew,
Thats absolutely right. In your antechamber file, you have the whole
nucleoside mono phosphate, so you just need to enter the charge values from
your calculation and the charges for the sugar and phosphate from the AMBER.
Best of luck
Raviprasad Aduri

At 10:17 PM 2/25/2007, you wrote:
>Dear Raviprsad,
>
>thanks for your help.
>Once I have obtained the charges by 2 stage RESP fitting, can I remove
>the charges of the methyl group and use the charges of sugar-phosphate
>group for the normal nucleotide. Is it right?
>
>
>Thanks
>
>Mathew
>
>
>rpaduri_at_chem.wayne.edu wrote:
>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
>
>Raviprasad Aduri
>
>Quoting mathew k varghese :
>
> > 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_at_yahoo.co.in
> >
> > ===========================================================================
> >
> > ---------------------------------
> > Here's a new way to find what you're looking for - Yahoo! Answers
>
>
>
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>/\/\athew
>
>Mathew K Varghese
>Research Scholar
>School of Pure and Applied Physics
>M.G.University
>Kottayam, Kerala
>India
>
>email mathew_kvarghese_at_yahoo.co.in
>
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>
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