Hi all,
I have been testing the ability of taking a sphere of a protein around a ligand, and positionally restrain the specified alpha carbons. I was hoping to keep non connected protein chains from drifting apart. I have been able to run these md/fep jobs, but I get huge interaction energies for the ligand, which has no positional restraints on it. I also don't restrain any atoms within the rvdw, rcoulomb and rlist radii. Am I thinking this is a possibility when it is physically impossible to simulate?
Currently I am selecting all residues around the ligand that have an atom within 20 Angstroms. I then save this as a pdb file and then run it through pdb2gmx, manually create a posres.itp file for each "chain" with their first and last residue's alpha carbon. Once I turn off these positional restraints the FEP energies drop down to "normal" levels.
Does anyone have an idea what is happening?
And if you do, can you please give a recommendation?
Thank you,
TJ Mustard
musta...@onid.orst.edu
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