Chain identifiers in NAMD simulation

From: Hrishikesh Dhondge (
Date: Wed Apr 06 2022 - 05:00:09 CDT


I have a doubt regarding the simulation in NAMD. If I have to use the amber
force field in NAMD, then I can create the system in the leap program
provided by AMBER. But the leap program renumbers the residues in the
simulation system. Chain identifiers are not used. There is a single list
of all atoms where atoms and residues are numbered sequentially starting
from 1 without any gaps.

So if I have a protein-RNA/DNA complex to simulate, will it affect the
simulation (missing information about chain or segment identifiers)?

Thanks in advance!

With regards
Hrishikesh Dhondge
PhD student,

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