[AMBER] QM/MM Protein-Ligand interaction w/cofactor

From: William Martin <wrmartin.umich.edu>
Date: Sat, 9 May 2015 15:35:30 -0400


New user of AMBER, poked through a few tutorials. Looking to do QM/MM MD
on a protein/ligand complex with a cofactor. Various places give
conflicting information on how to handle all of it (leave the ligand in,
take it out, leave the cofactor in, take it out, etc.). I'm not looking
for a step-by-step walkthrough (though if one exists that would be great!),
but a few guidelines would be super helpful. If it is important, a .pdb
exists for the protein with the ligand of interest in place, but future
studies will involve docking new molecules.

Thanks in advance!
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Received on Sat May 09 2015 - 13:00:03 PDT
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