Hi all,
I want to run NEB on a protein+drug system, where my one end state is drug bound to the protein (state 1) and the other end state is drug unbound (away) from the protein (state 2).
I am following Amber tutorial on Antechamber to generate drug parameters using gaff2 forcefield. This essentially means I am isolating my drug and generating it's .mol2 file, which is then being used to generate .frcmod and .lib files.
I am using implicit solvent for my simulations, so the parameters I generated by using the method I described above should work fine for my state 2 (where the drug is isolated and away from the protein). But I am worried if it is correct to use these parameters for state 1 as well because the drug environment changes in state 1.
I would like to know the thoughts of the amber community on this, what is recommended to be done? Is it fine if I go ahead with the same parameters for state 1 as well? If not, how can I generate correct drug parameters in a protein surrounded environment?
Thanks,
Madhur Aggarwal
IIIT Hyderabad
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Received on Fri Jan 03 2020 - 10:30:02 PST
