Dear amber community,
I am planning to run an MMPB/GBSA analysis for an
AMBER-derived protein-DNA complex with a single trajectory protocol method.
In my MD trajectories, I observed ion-mediated interaction between protein
and DNA . How to include this ion type of interaction in free energy
calculation. Is it a good idea to retain ions during the extract coordinate
step or should I strip the ions?. I would kindly appreciate your
suggestions.
Thanks in advance,
Pranita Patil
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Received on Mon May 24 2021 - 23:00:02 PDT
