Hi, I am trying to learn protein-ligand docking using complex 3dau (protein+NADPH+MTX)
My first task is to calculate the binding energy of cofactor binding to a protein.
I did the following:
1.I relaxed the protein+cofactor+ligand (whole complex).
2.Then i generated the params file for the ligand and the cofactor. (Using the coordinates from the output of relaxed pdb)
3.Then i appended the generated cofactor pdb(from2) to protein pdb(protein coordinates got from otput of relax).
4.Then i used the dock application:
./ligand_dock.linuxgccrelease -database ~/rosetta-3.4/rosetta_database/ -s ~/input/3dau_plus_nap.pdb -in:file:extra_res_fa ~/input/NAP.params
I got a silent file as a output: silent.out; score= -507.698.
I calculated the score of the (only)protein pdb using ./score.linuxgccrelease : -330.170.
As i said, I have to calculate the binding energy of cofactor binding to the protein.
Will the difference in score of the protein and docked protein+cofactor give the binding energy?
If not, how do the binding energy calculation?
Also what are the ouputs of a typical dock run?
What are the information we can get from the silent.out?
How to convert the silent.out to .pdb.