AMBER: 5 Ligands and 1 Protein

From: Colby C <>
Date: Wed, 20 Jun 2007 13:07:33 -0500

I am trying to prepare files for SANDER to run energy minimization of a
large protein with 5 ligands in 5 separate binding sites. We ran
antechamber with each of the 5 ligands and it made the 5 prepin files.
These files don't seem to have any missing parameters after running
parmchck. We are not sure how to combine these ligands with the large
protein. In xleap we tried to input each ligand but the xyz was all
wrong. Ultimately we just want to put all 5 ligands in the protein and
minimize the whole system.

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Received on Sun Jun 24 2007 - 06:07:13 PDT
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