Thanks will do that and get back.
rgds,
Prateeksha
On Fri, Mar 21, 2008 at 8:59 PM, <rpaduri.chem.wayne.edu> wrote:
> Dear Prateeksha,
>
> You need to generate a new residue for the protonated Adenosine. Once you
> have
> the force field files for this residue, you can use it along with the
> usual ff
> to carry out your simulations. You can find a detailed description of how
> to
> generate "prepin" and "frcmod" files for a modified nucleoside in the
> following
> article:
> "Aduri, R.et al., J. Chem. Theory Comput., vol. 3, 1464 - 1475, 2007"
> I hope this helps.
>
> Sincerely
> Raviprasad Aduri
>
> Quoting prateeksha s <prateeksha.s.gmail.com>:
>
> > Hi,
> >
> > I want to simulate protonated adenine. So which charge scheme one should
> use
> > for that?
> >
> > Also, I'm having troubles with xleap displaying the protonated adenine.
> The
> > un-protonated adenine displays fine. But, the Hs in protonated adenine
> are
> > not getting recognized.
> >
> > Please give your inputs.
> >
> > Thanks and cheers,
> > Prateeksha
> >
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 18 2008 - 21:12:54 PDT
