Thanks for your rely.
I'm afraid it was not caused by the bad contacts in the original pdb file since
I have tried three different pdb from cyana and all have THR CB chirality errors after
amber 7, which is really strange>..
> Date: Wed, 26 Aug 2009 07:52:18 -0400
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] Chirality error in pdb
>
> 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
> well.
>
> ....dac
>
>
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Received on Wed Sep 02 2009 - 23:05:51 PDT
