[Nathan Baker <baker@bi...>]

Hello --

> I am trying to create the input file to cmpute the electrostatic  
> potential of a protein. The APBS calculation will be useful to run a  
> Brownian Dynamics to understand the features of a complex between  
> the protein and a polysaccharide.
>
> I have been reading carefully how to create an input file but I am  
> not an expert and I find difficult to find the right flags to insert  
> in it.
> Please can you give me guidelines to "which parameters to include in  
> the file" and "how to chose the right flags for those parameters".

PDB2PQR (http://pdb2pqr.sf.net/) will generate input files for you  
that can be modified/customized for your particular application.  This  
should provide a starting point that you can expand upon using the  
APBS documentation.

> As well, which parameters and flags to insert in the .in file are  
> the best for a saccharide?

I'm not aware of any particular parameters for this but hopefully  
someone on the APBS mailing list might have a suggestion.

Good luck,

Nathan

> Thanks in advance for your precious help. I will appreciate is so  
> much.
>
> All the Best,
> Davide

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