Hi,
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
Anu
On Thu, Aug 20, 2015 at 7:25 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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 Fri Aug 21 2015 - 09:00:06 PDT
