Re: [AMBER] How to express a right-handed amino acid in leap

From: Jason Swails <>
Date: Thu, 11 Oct 2012 16:03:04 +0200

On Thu, Oct 11, 2012 at 2:36 PM, Changqing Yan <>wrote:

> Dear all,
> As you know the usual amino acid created in Amber is left-handed. So anyone
> knows how to create a right-handed amino acid in leap? For example, I want
> to create a right-handed phe amino acid in a peptide sequence SVRPfVDRE.
> What should I do?

The templates are right-handed. If your starting PDB has a right-handed
PHE amino acid, then it will not switch the chirality to left-handed.

If, on the other hand, you want to use the templates in tleap and include a
right-handed helix, I have a way. You need to create a new residue as a
copy of PHE and then 'reflect' it through a mirror plane (that inverts

For instance:

dPHE = copy PHE
transform dPHE { {1 0 0} {0 1 0} {0 0 -1} }

And then use "dPHE" in place of PHE in your "sequence" command.


P.S. -- Make sure you visualize the result to make sure you have what you

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu Oct 11 2012 - 07:30:05 PDT
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