Re: [AMBER] Solvent accessible surface area (SASA) calculation in CPPTRJ

From: David A Case <>
Date: Fri, 21 Aug 2015 13:36:59 -0400

On Fri, Aug 21, 2015, anu chandra wrote:
> trajin dimer.pdb # here, solvent and ions are removed beforehand
> molsurf proteinA :1-290 1.out
> trajin proteinA.pdb # here, proteinB is removed from dimer.pdb
> molsurf out 2.dat
> Unfortunately, in both case the SASA of protein A looks exactly same.

No, this is expected. Using the ":1-290" mask asks molsurf to just compute
the area of those residues.

If you want the buried surface area, load the dimer.pdb file, and do three
molsurf calculations: one with :1-290, one with :291-end, and one with
everything. A + B - (AB) will give you the buried area.

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Received on Fri Aug 21 2015 - 11:00:04 PDT
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