Hi,
If you strip a trajectory prior to 'surf', the 'surf' command doesn't
know that things were stripped and considers the molecule as a whole.
If you want to get an estimation for how much a portion of a molecule
contributes to the overall surface area you will need to keep the
molecule intact and specify a mask to 'surf' containing the atoms you
are interested in.
Keep in mind however that the LCPO method is extremely approximate, so
vet your results carefully.
-Dan
On Wed, Oct 17, 2018 at 7:28 AM <g.bakrani.sci.ui.ac.ir> wrote:
>
> Hello all,
> I have trying to analyze the results of an association simulation
> trajectory, so i stripped water and ions first, and then stripped
> molecules in the box and have kept just one molecule. Then i ran surf
> command to survey accessible surface of interaction involved residues.
> May i know wheter the surf command consider the association and
> perform the analysis or just consider the molecule alone and calculate
> the surface of residues independent of association?
> Thanks for your kind help,
> Best regards.
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Received on Wed Oct 17 2018 - 07:30:02 PDT
