2011/9/21 Horacio Pérez-Sánchez <horacio.um.es>
> We have developed a fast and accurate new GPU based SASA calculation
> method. It can bring information about SASA per atom and also grid per atom
> necessary to graphically render the molecular surface. We would like to know
> in Amber:
>
Is it just for visualization, or can you get gradients to do dynamics with
it as well?
>
> a) where could we find information about the SASA method it uses so we can
> test speed and accuracy increment with our method
>
There are 2 methods for calculating SASAs in Amber: LCPO (implemented in
cpptraj, sander, and nab). The second is a recursive algorithm that uses
icosahedra to approximate the SA term. This is accessible through sander
using the gbsa=2 option in the input file (see the Amber manual).
> b) same question for the method Amber uses to graphically render the
> molecular surface
>
Amber doesn't really do graphical stuff much. The only GUI program in our
suite is xleap, which doesn't display surfaces as far as I know. I use VMD,
using either their built-in SURF routine or MSMS to render the surface.
HTH,
Jason
> Thanks in advance,
> Horacio
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 21 2011 - 11:00:02 PDT
