Dear Manuel,Many thanks for the prompt reply and advice, I willtry to follow your suggestions. I have one more query, kindly elaborate histograming the water populations or share any example/link.
Thanks,Saman
On Thursday, September 22, 2016 9:49 AM, mmaestre <mmaestre.gate.sinica.edu.tw> wrote:
Hi Saman,
Check out the GIST or GRID features in cpptraj (the GIST tutorial on the amber website is really good: http://ambermd.org/tutorials/advanced/tutorial25/). If you're only interested in checking the number of waters, I think just using either the "hbond" command or a combination of "closest" and "distance" in cpptraj, should work. You could use that either for histograming the water populations, or as a dataset to apply via "filter", to obtain the snapshots in your trajectory which are in your favorite hydration state.
I hope this helps,
Manuel
-----Original message-----
From:Saman Yousuf ali <
saman.yousufali64.yahoo.com>
To:AMBER Mailing List <
amber.ambermd.org>
Date:Thu, 22 Sep 2016 12:24:38
Subject:[AMBER] Plot activesite water vs time.
Dear All,
I have a trajectory file and I would like to plot the number of water molecules within a distance from a ligand in time or study thermodynamicproperties of the water clusters over trajectory. I've been trying to figure out how to do it via cpptraj but I couldn't find anything.
I hope you can help me.
Thanks,Saman
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Received on Wed Sep 21 2016 - 22:30:03 PDT
