Hi Andrew,
Have a look at the last section of tutorial B1 which has the command you are looking for in cpptraj:
http://ambermd.org/tutorials/basic/tutorial1/section6.htm
Note though that a simple average in cartesian space might not be that meaningful. For example the average of a methyl group freely rotating is to have all the hydrogens on a point along the axis of rotation.
More useful might be to RMS fit everything and perhaps plot the differences, look at RMSF's for example. Or indeed do some cluster analysis on your trajectory. I'd suggest looking through some of the tutorials on the AMBER website: http://ambermd.org/tutorials/
In particular you might find tutorial B3, C0 and C1 useful.
All the best
Ross
> On Dec 17, 2015, at 2:35 PM, Andrew Bostick <andrew.bostick1.gmail.com> wrote:
>
> Dear all,
>
> I did 20 ns MD simulation on my system (protein-ligand complex).
>
>
> I want to have the average structure of the protein-ligand complex from the
> last 5 ns of MD trajectory.
>
>
> How to do that?
>
>
> Any help will highly appreciated.
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Received on Thu Dec 17 2015 - 15:00:06 PST
