Set idecomp=1 (or 2 or 3). This will decompose the energetic contributions,
including the SASA. However, if you're using amber10, imin=5 and idecomp do
not play nicely with one another, since I think many variables fail to get
re-initialized after each frame is complete (so results become cumulative,
rather than resetting for individual snapshots).
Hope this helps,
Jason
On Tue, Oct 5, 2010 at 4:49 AM, hirdesh kumar <hirdeshs8.gmail.com> wrote:
> Hi All,
> I am interested in calculating the SASA contribution of 3-4 residues of my
> interest in each trajectory.. I have the file (mentioned below) but it
> calculates the SASA in general. How can I include the residue wise
> contribution.
>
> $AMBERHOME/exe/sander -O -i SASA.in -p prmtop -c mdcrd -o SASA.out
> &cntrl
> imin = 5,
> gbsa=2,
> surften=1
> /
>
> --
> Hirdesh
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Oct 05 2010 - 05:30:03 PDT
