Solvation free energy calculation with MM/GBSA

From: Neelanjana Sengupta (
Date: Wed Sep 23 2015 - 06:51:28 CDT

Dear NAMD community,

We would like to calculate the solvation free energy, using the Generalised
Born Surface Area (MM-GBSA) method, of a protein-nanosurface system that
has been simulated with NAMD; we have the PSF file and the DCD files.

Could you suggest how to go about this? (The APBS method will only allow
the PBSA method).

We are investigating options where we convert our trajectories to the AMBER
format and use the utilities available there, but this is very messy...

Thanks in advance.


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