Re: [AMBER] changing chirality with ParmEd?

From: Osman, Roman <>
Date: Tue, 21 Feb 2017 21:39:13 +0000


You probably meant CB not CA!


On Feb 21, 2017, at 4:33 PM, Carlos Simmerling <<>> wrote:

another option that may work better for a protein is to edit the PDB file,
deleting all of the side chain atoms on this amino acid except the CA and
HA. Then, change chirality by swapping the coordinates of these 2 atoms.
Save and load it into Leap, which should rebuild any missing atoms. Of
course it won't have an ideal conformation and may have steric clashes, but
it's a starting point for minimization (and very careful checking of the

On Tue, Feb 21, 2017 at 4:26 PM, Lachele Foley <<>> wrote:

You mean change L to D?

If so, then you can edit the coordinates: pick one coordinate (say, x)
and multiply all the values by -1. That will give you a mirror image.
Do this in a pdb file or a restart file, etc. Of course, that will
disrupt its relationship to other residues, so you might need to do
other stuff.

On Mon, Feb 20, 2017 at 2:42 PM, Hai Nguyen <<>> wrote:
AFAIN, there's not.


On Mon, Feb 20, 2017 at 10:14 AM, Thomas Pochapsky <<>>

Is there a straighforward way to change the chirality of specific amino
acid residues using parmed?

Tom Pochapsky

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:-) Lachele
Lachele Foley
Athens, GA USA
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Roman Osman
Professor of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
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Received on Tue Feb 21 2017 - 14:00:05 PST
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