[AMBER] Regarding protein - nucleic acid contacts

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Tue, 29 Jun 2021 16:14:17 +0530

Dear all,

In the following publication,
an analysis of something called "tight contacts" is done. The tight contact
is the contact of the ligand with the residues around it in 4 Å. My query
is that is it something similar to the native contacts command in the
CPPTRAJ. Our intention is to find the total number of polar, nonpolar
contacts of nucleic acids 1-15 of a system to the protein to which it is
interacting. We would like to have either the total number of polar, non
polar contacts separately or the total fraction of simulation time is a
particular contact occurring. There are 2 different sequences (15
nucleotides each) of which we need to do this calculation. So would the
native contacts be sufficient?

Sruthi Sudhakar
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Received on Tue Jun 29 2021 - 04:00:02 PDT
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