[apbs-users] Regarding the Swanson et.al (Genetic Algorithm) optimised radii usage

[V.S. Sandeep Inakollu]

Hi All,

I am try to define the solute surface with Swanson et.al (Genetic Algorithm)  optimised radii using APBS software. I am a new user of APBS and I am ambiguous about how to implement it for my molecule, acetophenone.

When I tried to create a PQR file with the swanson FF using PDB2PQR tool, all my jobs are died (since my ligand is small molecule, acetophenone). I am not sure how to proceed further. I would be appreciated, if anyone could help me out with the protocol set up.

Thanks, Sandeep Inakollu

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Venkata Sai Sandeep Inakollu, M.S (Pharm.)

PhD Scholar,

School of Chemistry,

University of Wollongong,

Australia.

Mobil# : +61-406100693

E-Mail: sandeep.p...@gmail.com

vi...@uowmail.edu.au

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[Baker, Nathan]

Hello --

Can you provide more information about the calculation you are trying to perform?  The input files would be particularly useful.

Thanks,

-- 

Nathan Baker

Director, Advanced Computing, Mathematics, & Data Division — Pacific Northwest Natl Lab

Visiting Faculty, Division of Applied Mathematics — Brown University

+1-509-375-3997 — http://www.dam.brown.edu/people/baker/