Dear Amber users,
I am trying to calculate the binding free energy change for the protein
complex I am working with. The system contains protein A-ligand complexed
with protein B and protein C. I also have another system of unliganded
protein A complexed with protein B and protein C. Now, I am trying to
calculate the binding free energy change in protein A with B and C. I have
few queries here regarding setting up the complex for the MMPBSA.py
calculation.
In all calculation, I will be considering Protein A ( with or without
ligand) as receptor.
1. If I want to calculate the free energy between protein A with protein B,
do I need to consider protein C in the complex and receptor? i.e.,
Complex : protein A+protein B+protein C
Receptor : protein A+protein C
Ligand : protein B
2. Do I need to consider ligand bound to the protein A as a part of
receptor while using protein A as the receptor?
Many thanks in advance
Anu
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Received on Mon Oct 12 2015 - 09:30:04 PDT
