AMBER Archive (2008)

Subject: Re: AMBER: drug/protein interaction modeling setup

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 20 2008 - 17:39:04 CDT

Once you have a prepin, the secret is to load it and then load your
pdb with protein and ligand coordinates. These pdb coordinates will
be applied to all residues, so the relative locations of protein and
ligand will be preserved. Ultimately the whole system will be shifted
when you solvate it, so do not get too attached to the coords in the
pdb.

Bill
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