AMBER Archive (2009)

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

From: Pansy Patel (pdpatel_at_mail.ucf.edu)
Date: Tue Mar 17 2009 - 10:50:57 CDT

Hello, Amber:

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 ?

I use Amber9, and I don't have access to 'Sybyl'.

Thank you.

Pansy D. Patel

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