AMBER: PDB files

From: Beale, John <>
Date: Mon, 30 Apr 2007 11:16:59 -0500

I am fairly new to AMBER and I have a question. I am trying to generate
pdb or mol2 files from a protein and a ligand that can be processed by
LeAP. I create the files by docking the ligand into the protein (Tripos
Surflex-Dock) and saving the complex as a pdb file. When I look at the
pdb file, in the section where the coordinates for the ligand are
listed, each set is listed with an atom type (H, O, C, S, for
instance.). There is no naming information in the file for the ligand
(e.g., there is no "H3, C5, N1 types of designations). There might be a
large number of hydrogens, for instance, but none possesses a unique
name. All of them are listed as "H". The same is true for oxygen,
nitrogen, and sulfur. Of course, when I try to run the pdb file into
LeAP the program tells me that there are a lot of atoms that possess no
unique designation, and the program doesn't allow me to save parameters.
I have processed all of my ligand structures through antechamber and
these files have the complete atom designations.


Is there a way to get my ligand pdb structures to have the proper AMBER
atom names, rather than just "H", "O", etc., when they come out of a
docking experiment?


John Beale

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Received on Wed May 02 2007 - 06:07:18 PDT
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