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

From: anu chandra <>
Date: Fri, 21 Aug 2015 16:58:51 +0100


Thanks for the reply. I just carried out a trial calculation of SASA using
molsurf and the results look little weird. My systems contains dimeric
protein - Protein A ( residue 1-290) and protein B (291-560). Using
molsurf, I just tried to calculate SASA of protein A in presence and
absence of Protein B. For this trial, I generated topology file for dimer
(protein A- protein B) and monomer (protein A) separately and try to
calculate SASA of protein A in both case with single frame in pdb format ,
as shown below,

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. I
expected there should be a decrease in SASA of protein A in dimer due to
the presence of protein B since both share an interface area which is not
accessible. May I know what is going wrong with the SASA calculation here?

Many thanks


On Thu, Aug 20, 2015 at 7:25 PM, Jason Swails <>

> 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
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Fri Aug 21 2015 - 09:00:06 PDT
Custom Search