AMBER Archive (2009)

Subject: Re: [AMBER] atom types in pdb files

From: David A. Case (
Date: Mon Apr 13 2009 - 15:25:04 CDT

On Mon, Apr 13, 2009, Dan Kaps wrote:

> The residue names match those in the .prepin files; however, the atom
> names to not. Unfortunately the atoms in the .prepin files are in
> different orders than those in the .pdb files...what a mess...any
> suggestions?

Well, the order of atoms within a residue in the PDB file is irrelevant.
But the atom names in the PDB file do have to match those in the prepin
file. If you create your prepin/mol2 files using antechamber and starting
from a PDB file, then the names will match. If you use another path, then
you'll have to find some other way to get the names to match, e.g. by
hand-editing the pdb file....


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