Hi,
You could do this using LCPO surface area with cpptraj. To calculate
the contribution to the overall SASA by different residues you could
use this input:
parm protein.parm7
trajin trajectory.nc
surf R1 :1 out sasa.dat
surf R2 :2 out sasa.dat
surf R3 :3 out sasa.dat
...
You will get an output file (sasa.dat) that will contain the SASA of
residues 1, 2, and 3, etc in columns:
#Frame R1 R2 R3 ...
Note that here R1, R2, and R3 are just labels, you can name them
whatever you want.
Hope this is helpful.
-Dan
On Tue, Mar 6, 2012 at 6:08 AM, Beale, John <John.Beale.stlcop.edu> wrote:
>
> I need to compute and plot the SASA on a per-residue basis for my peptide. Can someone provide me with a method for doing this?
>
> Thanks!
>
> John
>
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> Department of Neurology, Washington University School of Medicine
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
> bealej.neuro.wustl.edu<mailto:bealej.neuro.wustl.edu>
>
>
>
>
>
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Received on Tue Mar 06 2012 - 04:30:03 PST
