Dear all,
My apology in advance if this is very trivial questions here.
So, I have a protein, lets say protein a, which is a dimer. I am studying
the interaction of this protein with another protein, lets say protein b,
and I have already built up the structure with homology modeling. I am
interested in using PBSA and GBSA to calculate free energy changes well as
decomposition energy of the dimer complex as well as the complex between
the protein a (in dimer form) and protein b. Basically I am interested in
all the protein-protein interactions: dimer of a and each of a with b.
I have done these kind of calculations many times BUT with the complex
involving only two proteins, one is treated as receptor and one is as
ligand.
How do I even get started with complex with four protein chains? How do I
modify commands for tleap, MMPBSA,GBSA and all that for four protein
chains?? What do I have for receptors or ligands?
I would really appreciate any inputs.
Thank you in advance!!
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Received on Sat Sep 17 2016 - 13:00:02 PDT
