AMBER Archive (2009)

Subject: RE: [AMBER] parameterization of protein-ligand complex

From: Jeff Yeo (
Date: Mon Sep 14 2009 - 10:03:25 CDT


I extracted the ligand from the docked protein-ligand complex file, by deleting all atoms which belong to the protein. It was saved as 'myligand.pdb'. Next, I created the .pdb file which contains only the atoms of the protein and saved it as 'protein.pdb'.
As described previously, I used the 'myligand.pdb' to generate the Gaussian03 input file. However, after Gaussian has completed its run, I realized that the Cartesian coordinates of the Gaussian-treated ligand has shifted and therefore the ligand is no longer inside the binding pocket of 'protein.pdb'. I am totally puzzled by why and how this has occured since I used the ligand coordinates from the docked protein-ligand complex file.
Moreover, although I have loaded the myligand.frcmod file during the tLeap session, it still complains that the atoms in the ligand portion of the concatenated file have missing parameters.
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