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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> > >/\/\athew
> > >
> > >Mathew K Varghese
> > >Research Scholar
> > >School of Pure and Applied Physics
> > >M.G.University
> > >Kottayam, Kerala
> > >India
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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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>
>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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Received on Sun Mar 04 2007 - 06:07:47 PST
