Re: odd display of ambpdb generated files

From: Richard W Dixon <>
Date: Tue 17 Apr 2001 09:26:45 -0400

I also suspect that the atom label is justified too far to the left.
Specifically, (note spacing and alignment)

     1HG2 ILE
     HG21 ILE

The first two forms are handled by Insight in the way you would want (but do
generate a "template mismatch"). The third causes Insight to assume you have
mercury in your pdb file and to perform a distance based bond check. The colat
(Color by atom) command should also generate weird results (purple atoms) in
this case. There are not too many fixes for this other than convincing ambpdb
to conform to Insight's expectations, or visualizing with some other, more
understanding, program. If you don't need a builder, there are many other
options out there. Since Insight relabels and reorders the atoms to conform to
its interpretation of V2.0 of the PDB format specs whether you want it to or
not, I tend to avoid mixing amber and insight for anything unless I am forced.


Richard Dixon
Abbott Bioresearch Center (formerly BASF)

Elsa Sousa Henriques <> on 04/16/2001 01:49:03 PM

Please respond to
To: Jake Isaacs <rjisaa0
cc: AMBER list <amber
Subject: Re: odd display of ambpdb generated files

Jake Isaacs wrote:
> When I use InsightII to view a pdb file created from prmtop
> and inpcrd via ambpdb, multiple anomalous bonds appear.
> What might be the cause and solution for this?

Assuming that your pdb is for a protein or a DNA (i.e. with
standard residues InsightII recognizes), are there only heavy
atoms or did you include hydrogens also? My experience is that
since there are no unique labelling for the H's (e.g. a 3HA in
AMBER might be a 2HA in InsightII), many of the AMBER H's will
be unknown atoms to InsightII ... thus the anomalous bonds.

Hope it helps,

       獿'amore che muove il sol e l 'altre stelle

                    Dante Alighieri
                     (La Divina Commedia)
Elsa F. Sousa Henriques e-mail:
Dept. Quimica, FCUP phone: +351-22-6082827
Rua do Campo Alegre, 687 fax: +351-22-6082959
4169-007 PORTO
Received on Tue Apr 17 2001 - 06:26:45 PDT
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