AMBER Archive (2009)

Subject: Re: [AMBER] Antechamber: stuck at bondtype

From: David A. Case (
Date: Wed Jun 17 2009 - 08:28:15 CDT

On Wed, Jun 17, 2009, Jack Shultz wrote:

> I am trying to convert a pdb file to mol2 using antechamber....
> example from the tutorial 5 seems to work ok (sustiva.pdb)
> The current pdb I am trying to convert just gets stuck at the
> bondtype. There are about 110 residues in this protein.

This is way outside the design of antechamber. Basically, antechamber
was coded to look at small organic molecules, and you are asking it to
determine bond types (and later, atom types) for an entire protein. It's
not clear why you would want to do this: for proteins in Amber, you should
use the standard protein libraries.

So, my main question is: why do you want to do this? That is, what are you
going to use the output mol2 file for?


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