Re: [AMBER] solvent accessibility

From: Daniel Roe <>
Date: Fri, 14 May 2021 14:04:20 -0400


Unfortunately the 'molsurf' command doesn't have a real per-atom
surface area calculation - it's one of the long-standing items on my
to-do list (that only gets longer and longer unfortunately). The LCPO
surface area calculation ('surf') can do per-atom, but it's quite
inferior to 'molsurf'.

Maybe there is an enterprising grad. student or post-doc who would
like to volunteer to add this to CPPTRAJ? :-)

Sorry I can't be more helpful,


On Tue, May 11, 2021 at 12:20 PM Cato, Lee <> wrote:
> I am trying to determine the solvent exposure for each residue on my protein.
> I believe molsurf is the most appropriate way to calculate this. However, I don't know how to calculate per residue rather than per atom. Is there a command that allows a per residue calculation of solvent accessibility?
> my current code:
> parm wt.prmtop
> trajin
> molsurf out test.dat
> run
> Thanks,
> Cato
> --
> Ph.D. Candidate
> Biochemistry, Cell, and Developmental Biology Program
> Ortlund Lab
> Emory University
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Received on Fri May 14 2021 - 11:30:03 PDT
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