AMBER Archive (2007)

Subject: Re: AMBER: RESP calculation of modified nucleotides

From: Raviprasad Aduri (rpaduri_at_chem.wayne.edu)
Date: Wed Feb 28 2007 - 15:11:34 CST

Dear Mathew,
In my opinion, you can start with your pdb file or else using Gauss view
you can attach the optimized geometry of the base to the Sugar-Phosphate
(which is little tricky). If the geometry is not drastically changed before
and after optimization, I think you should be OK using the coordinates from
the pdb file.
Best of luck
Raviprasad Aduri

At 03:55 AM 2/28/2007, you wrote:
>Dear Raviprasad,
>
>I am trying doing the parametrisations of the modified nucleotides with
>your suggestions. I have one doubt,
>After optimisation the geometry of the base is slightly changed. So should
>I take the optimised base and replace the methyl group with the
>sugar-phosphate group and do the parametrisations or can I take the
>coordinates as extracted from the pdb file.
>
>Thanks for all the help.
>
>Mathew
>
>Raviprasad Aduri <rpaduri_at_chem.wayne.edu> wrote:
>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
> > >
> > >
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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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>/\/\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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