Hi Madhu --

We do not yet have any apolar parameters that have been specifically optimized for protein-protein interactions.  We do have some that are useful for protein solvation forces with the AMBER force field; these are described in our earlier paper (http://dx.doi.org/10.1073/pnas.0600118103) and can be set with the bconc, srad, press, and gamma in the APOLAR section of an APBS input file.

I hope this helps.



On Wed, May 13, 2009 at 6:08 AM, Madhumalar Arumugam <madhumalar@bii.a-star.edu.sg> wrote:
Dear users,
I am trying to calculate apolar contributions to binding of two protein
monomers.  I had looked at example inputs in the directory alkanes and
born. The parameters in both the inputs are different.
It is not clear to me how I should decide about the input parameters for
protein of my interest.
which parameters file I need to inculde for proteins (parm.dat)?

Is there any other place I can get example input files for the
apolar energy contribution for protein-protein interaction?

Thanks for any help.

Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Director, Molecular Biophysics Graduate Program
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/