AMBER Archive (2008)

Subject: AMBER: drug/protein interaction modeling setup

From: Sean Johnston (sean.johnst_at_gmail.com)
Date: Mon Oct 20 2008 - 15:10:52 CDT

Hey all you AMBER users,

I'm trying to get LEaP to help me out with this liganded protein
interaction, and I can't seem to make it all work out. I extracted the
ligand from the pdb file, putting hydrogens on so I could put it into
antechamber and assign atom labels and bond/angle parameters. After getting
my prepin file, I loaded everything into LEaP and proceeded to load in the
protein. I first tried in tleap, but that gave me really weird topology and
coordinate files, and then when I did it in xleap, I noticed that the
coordinates had changed somewhere along the line, so now the ligand wasn't
anywhere else near the protein. Is there something in LEaP or antechamber
that would mess with the coordinates of the ligand/protein? Thanks for the
help, and I could provide a couple more specifics... I'm late for band!

Oh, and is there a standard way to make this work? Am I going about it
correctly?

-Sean Johnston

Sean Johnston
johnstos_at_stolaf.edu
sean.johnst_at_gmail.com

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