Dear list,
I have a tetramer with one ligand bound to each monomer. I want to calculated the binding energy between the two dimers in the tetramer with ligands boundIn my trajectory, all the four ligands are numbered later than the four monomers. But MMGBSA only takes residues with continuous numbers as mark. Is there a way to renumber the trajectory for MMGBSA calculation?
My case is different with offsetting the residue number discussed in the below post.
http://archive.ambermd.org/201703/0344.html
I tried the same way by manually change the residue number, and then use tleap to generate the prmtop file. When I use cpptraj to process my trajectory, it runs but the output trajectory was damaged, the structure was messy.
Thanks,
Ming
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Received on Thu Sep 02 2021 - 00:30:02 PDT
