[AMBER] Probability of Contact Formation

From: Aravind R via AMBER <amber.ambermd.org>
Date: Mon, 12 Jun 2023 21:50:57 +0530

Hi Amberites,
I would like to calculate the Probability of Contact Formation Qi defined
by the number of frames each ith contact in the protein present with and
without a conjugate. The value of Q i
was calculated by Qi = Ncont /N total, where Ncont is the number of
conformations in which the ith contact is formed, and Ntotal is the total
number of conformations in the sampled(trajectory length).
Then I would like to calculate DeltaQi.
DQi = QiWT - Qiconj, where Q iWT and Qiconj are the values of Qi of the
protein without and with a conjugate, respectively.
I have trajectories (cumulative 7.5 us data) for both conditions. Should I
use the native contacts command to calculate this? I do not need normalised
value, I need all the contacts which were present in the trajectory and how
many frames in which they were present.
Thanks in advance.
Aravind R
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Received on Mon Jun 12 2023 - 09:30:02 PDT
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