[AMBER] Hydrogen bond calculataion

From: richa anand <richaaanand.gmail.com>
Date: Wed, 14 Dec 2016 12:31:08 +0530

Dear Amber users,

I want to calculate number of hydrogen bonds between donor and acceptor
irrespective of the hydrogen atom donated in each frame. For example

Acceptor Donor-hydrogen Donor Frames Frac.
Avg. dist.

RU_247.O2P ARG_52.HH12 ARG_52.NH1 98387 0.9839 2.8620
RU_247.O2P ARG_52.HH11 ARG_52.NH1 2 0.0000 3.4335

in above example there are two hydrogen bond interaction between RU_247.O2P
and ARG_52.NH1. Each interaction has different number of occurrence. From
this data I cant analyse in which frame interaction one was present or
absent and in which frame interaction two was present or absent.

I want result in the format given below:

Acceptor Donor Frames Avg.dist
RU_247.O2P ARG_52.NH1 ----- -----

If I simply add occurrence of both interaction to know the real occurrence
of interaction between RU_247.O2P ARG_52.NH1, then there is a possibility
of redundancy of adding the frames. Can anybody help me to change the
source code of CPPTRAJ to find out the expected result that I want. I know
this change should be done in printing the "nframes" action command in
CPPTRAJ, but unable to do it.

Any help is appreciated.


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Received on Tue Dec 13 2016 - 23:30:03 PST
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