Re: [AMBER] Residue chirality

From: Jason Swails <>
Date: Tue, 9 Jul 2013 08:45:06 -0400

On Tue, Jul 9, 2013 at 5:21 AM, Karl N. Kirschner <> wrote:

> Hi,
> At one time there was a bug concerning this in tleap (and g/sleap??),
> and I am not sure if it was ever corrected. If I recall correctly, the only
> work-around I found was to construct the enantiomer using an external
> editor (e.g. PyMol) and load it into xleap. This preserved the connectivity
> and dihedral angles.

Why not just create the enantiomer inside tleap itself? For instance to
translate GLU its D-enantiomer:

transform GLU { {1 0 0} {0 1 0} {0 0 -1} }

This seems a bit easier than building a residue elsewhere and ensuring that
the naming convention is done 'correctly' for tleap to recognize the
correct parameters.

That said, I typically avoid letting tleap build entire sidechains whenever

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Jul 09 2013 - 06:00:04 PDT
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