VMD-L Mailing List

From: Sruthi Sudhakar (sruthisudhakarraji_at_gmail.com)
Date: Fri Jul 26 2024 - 07:13:21 CDT

Hi,

I have tried to replicate the procedure given in the "Dynamical networks in
tRNA: protein complexes" on the 2 protein systems- Wildtype and a single
amino acid mutated system. I face some confusion regarding how the
community assignment happens. For eg: in the case of WT, community 1 has
residues 1-25
2 has 35-40, and 3 has 220-240. At the same time, in the mutant, community
1 has 0-25, but 2 has 301-305, 3 has 58-70, and so on. I do understand
that there will be changes. The problem is that residues 35-40 remain in
the same community as in WT, however, the community number is now not 2 but
5. This has happened with many such residues. Could anyone please help
regarding this? Why is there a shuffle in the residues?I am unable to
figure out how to properly compare these. Is there any fix- manual or
otherwise for this?

In the PNAS publication, the communities mostly has the same residues and
therefore any deviations are easier to map. Here it is very confusing. I
have used every 100 frames from my 500 ns MD simulation for the analysis.

Regards,
Sruthi Sudhakar