Hi,
On Mon, Feb 22, 2016 at 9:34 PM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Dear all, I have run MD simulation using Amber12. Now I would like to check the occupancy of pi-stacking or hydrophobic interactions that the inhibitors make with the protein over the entire trajectories. I know cpptraj has the option for doing hydrogen bond analysis. Any suggestions for above mentioned interaction analysis?
There is no exact command in cpptraj for calculating stacking, since
the definition of what is "stacked" in MD simulations using a pairwise
additive FF can be somewhat arbitrary. Typically people use a
combination of geometric criteria; there is no shortage of examples of
stacking calculations in the literature. See e.g. this recent work
from Brown et al. (
http://pubs.acs.org/doi/abs/10.1021/ct501170h) and
references therein.
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Feb 23 2016 - 08:30:05 PST
