AMBER Archive (2009)

Subject: Re: [AMBER] antechamber : missed atoms

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jan 27 2009 - 09:23:27 CST

On Mon, Jan 26, 2009, Khaled Barakat wrote:

> > I am trying to use Antechamber from Ambertools 1.2 to get parameters
> > for a set of ligands. The input pdb files for antechamber seem to be
> > OK . Attached is an example of these ligands along with
> > the NEWPDB.PDB generated by Antechamber. As you can see there are
> > some missing atoms in the NEWPDB.PDB file.

The ref.pdb file has a whole pile of atoms named "H". Atom names must
be unique.

Also, please visualize the file with something like Rasmol or VMD. Many
hydrogen atoms are in nonsensical positions. You will need to fix these
before feeding it to antechamber.

...dac

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