Hi,
as far as I know there is no good GB model for protein/nucleic acid
complex in AMBER. Our lab is working on a version for nucleic acid and
it can be combined with current igb8 parameters for the complex. We
are trying our best to introduce the new GB pars to next AMBER
release.
Hai Nguyen
On Thu, Oct 24, 2013 at 8:53 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear all,
>
> We are attempting some MMGBSA calculations on a protein-nucleic acid
> complex and we'd like to get some feed-back on the generalized born
> parameters.
> For the record, we are using ff99SB/ildn/nmr force field variant.
>
> I know that generally igb=1 has been tested and recommended on nucleic
> acids. According to the original work by Vickei Tsui and Dave Case,
> igb=1 + mbondi radii with the parameter changes highlighted in the
> AmberTools manual is the preferred combination for nucleic acids.
>
> I also know that for proteins igb=5 and the new igb=7 and igb=8 +
> mbondi2 are performing better.
>
> My question is: what about state-of-the-art for protein-nucleic acid
> complexes ? Is anybody willing to share some latest experiences and some
> new relevant references about the choice of parameters ?
>
> Thanks for any insights,
>
> Best wishes
> Vlad
>
>
>
> --
> Dr. Vlad Cojocaru
> Max Planck Institute for Molecular Biomedicine
> Department of Cell and Developmental Biology
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
>
>
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Received on Thu Oct 24 2013 - 12:00:03 PDT
