Re: odd display of ambpdb generated files

From: Michael Cooney <>
Date: Tue 17 Apr 2001 12:56:36 -0400 (EDT)

One more suggestion: when I use carnal instead of ambpdb to generate pdb
files from crd or rst files, Insight usually displays the structures
normally, i.e. with no strange bonds. If it is possible to use carnal,
then, this may work better.

Michael Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602 USA

On Tue, 17 Apr 2001, Bill Ross wrote:

> 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.
> Leap should be able to read Insight pdb's ok, and it might
> even be able to translate an ambpdb file into something
> that Insight would read properly:
> > x = loadpdb ambpdb.pdb
> > savepdb x insight.pdb
> Leap can rearrange the molecules, tho if the prmtop was generated
> by leap, this may be unlikely.
> Bill Ross
Received on Tue Apr 17 2001 - 09:56:36 PDT
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