On Thu, 2015-08-20 at 17:35 +0100, anu chandra wrote:
> Dear Amber users,
>
> I have carried out a simulation of dimeric protein (Protein A- Protein B)
> and I am trying to calculate the exposed area (SASA) of Protein A in
> presence and absence of ligands. I have noticed that there are two
> different SASA methods - surf and molsurf - available in CPPTRAJ. Is it
> right to using these methods for calculating the SASA in my case?.
Yes.
> If so,
> which one of these methods can give a more reliable data?
I think the "molsurf" algorithm is better. "surf" uses LCPO, which is a
bit odd. It's advantageous for MD in that it has analytical gradients,
but for just computing SASA I think molsurf does a better job.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 20 2015 - 11:30:04 PDT
