Dear Mathew
You are absolutely right. You need to constrain your methyl group to
0.1053e. What it does is that it will force the overall base charge to be
-0.1053e and so when you add the sugar-phosphate to the base, the total
charge will be -1.0e.
Best of luck
Raviprasad Aduri
At 06:35 AM 3/2/2007, you wrote:
>Dear Raviprasad,
>
>In the preveous mail I made some mistakes. Sorry.
>
>I have almost corrected the problem. There were some errors in my resp inputs.
>
>When I used the values 0.092541 to constrain the charges of methyl group,
>I got values near to -1. But when I used the value of the
>sugar-phosphate(-0.8947), the total charge becomes 0. Should I use the
>value 0.1053 instead(1-0.8947)
>
>Thanks
>
>Mathew
>
>mathew k varghese <mathew_kvarghese.yahoo.co.in> wrote:
>Dear Raviprasad,
>
>
>When I have used the value of sugar-phosphate group for restraining the
>methyl group,
>I got the total charge as 0. , but I expect a value of -1. as that of the
>normal residues.
>
>As you have suggested, I looked the total charge of the constrained
>molecules, but it is not equal to the constraints I have used. But in the
>tutorial given in the antechamber site also, these are not the same. So I
>think it is right. How can we make sure that the charges exactly matches?
>
>Thanks for all the help.
>
>Mathew
>
>Raviprasad Aduri <rpaduri.chem.wayne.edu> wrote:
>Dear Mathew,
>That deviation is little more than what I expect. One way to rectify that
>is to use the exact charge constraint. What I mean by that is add up the
>charges of the sugar and phosphate (that you got from AMBER) and use that
>value as a constraint for the methyl group. One more thing when you do the
>RESP fit it is always a good thing to make sure that your constraint has
>been taken into account. The way you do it is that when you add the charges
>of the methyl group (from your resp1_output.1 and resp2_output.2) they
>should be exactly equal to the constraint value you used.
>I hope this helps.
>Best of luck
>Raviprasad Aduri
>
>At 09:33 AM 3/1/2007, you wrote:
> >Dear Raviprasad,
> >
> >I have almost done with the parametrisation of the modified nuclotides,
> >with your help.
> >I have one more qestion.
> >
> >The added methyl group is charge constrained with the value you have
> >suggested(0.092541). After the parametrisation, the total charge of the
> >residues are slightly greater than -1 ie, -1.0845, -1.0951 etc (for
> >different residues). Are these reasonable values? Or should I use some
> >other charge constraints?
> >
> >
> >
> >Thanks for all the help
> >
> >
> >Mathew
> >Raviprasad Aduri wrote:
> >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 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.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.yahoo.co.in
> > > > >
> > > > >
> > >
> ===========================================================================
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> > > >
> > > >Mathew K Varghese
> > > >Research Scholar
> > > >School of Pure and Applied Physics
> > > >M.G.University
> > > >Kottayam, Kerala
> > > >India
> > > >
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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.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.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.yahoo.co.in
>
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>Here's a new way to find what you're looking for -
><http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>Yahoo!
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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.yahoo.co.in
>
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>
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Received on Sun Mar 04 2007 - 06:07:56 PST
