On May 23, 2014, at 8:07 AM, Soumendranath Bhakat <bhakatsoumendranath.gmail.com> wrote:
> Hi All;
>
> I want to calculate SASA over time for protein-ligand complex. I have
> residues ranging from 1-560
>
> My cpptraj or ptraj inputs looks like that
>
> trajin md50.mdcrd
>
> surf R1 :1-560 out sasa.dat
>
>
> Can anyone please confirm if these SASA script looks good?
molsurf may be a better SASA estimator than LCPO (which is used by "surf"). I don't see any problems with your SASA command, but if you have doubts you should run the calculation and check that the resulting values make sense.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 23 2014 - 05:30:03 PDT
