surf or molsurf are in cpptraj
On May 23, 2014, at 8:16 AM, Jason Swails <jason.swails.gmail.com> wrote:
>
> 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 - 06:30:03 PDT
