Re: [AMBER] does surf command use for stripped trajectory?

From: Daniel Roe <>
Date: Wed, 17 Oct 2018 10:27:56 -0400


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.

On Wed, Oct 17, 2018 at 7:28 AM <> 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
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