Hello,
I have a doubt regarding the use of the amber force field with 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,
LORIA - INRIA Nancy
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Received on Wed Apr 06 2022 - 03:30:03 PDT
