AMBER Archive (2009)

Subject: Re: [AMBER] convert .mol2 file to .pdb with atomtype definitions

From: David A. Case (
Date: Tue Mar 17 2009 - 11:00:19 CDT

On Tue, Mar 17, 2009, Pansy Patel wrote:
> I would like to convert a .mol2 file into a .pdb file.
> The 'antechamber' in Amber is designed to convert single residues.
> My file is a DNA structure model in .mol2 format with another small organic molecule interacting with it.
> I tried to use babel to convert the file
> but all the atoms are termed RES which is not the right atom type
> Is there some way that I can generate atom types for the DNA part of the mol2 file using amber or any other accessible software ?

Have you tried using LEaP: use loadmol2 followed by savepdb? You may
have to do some experimentation and hand editing (either of the input or
output file), but it may get you close.


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