AMBER Archive (2009)

Subject: Re: [AMBER] Chirality error in pdb

From: case (
Date: Wed Aug 26 2009 - 06:52:18 CDT

On Wed, Aug 26, 2009, xiawei wrote:
> Hi, everyone:I have tried to calculated a protein structure with cyana
> andthen refine it in amber7 with energy minimization.However, the amber
> output pdb file contained the chirality error for the THR CB atom.For
> THR, CB chirality should be R-form, after amber, most of the THR became
> S-form!
> But in original cyana pdb, no chirality errors were found.I think
> the calculation in amber caused the problem, can anyone give me some
> suggestions?Thanks in advance!

It is indeed unusual for energy minimization to invert chirality, but it
certainly possible if there are bad contacts in the starting structure.

The "makeCHIR_RST" script can create chirality constraints to prevent such
behavior, but you might want to try to track down the source of the problem as


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