AMBER Archive (2009)

Subject: Re: [AMBER] Chirality error in pdb

From: case (case_at_biomaps.rutgers.edu)
Date: Fri Aug 28 2009 - 06:33:41 CDT

On Fri, Aug 28, 2009, xiawei wrote:
>
> 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>..

Do the chriality restraints make a difference? How many steps of minimization
does it take to see this result? It is indeed rare for energy minimization to
move a structure very far, much less invert chirality. I assume(?) that you
have studied the starting cyana structures carefully, and that they have a
well defined chirality. Are there any missing protons that have to be added?
An error there could lead to the behavior you describe.

Please remember that readers on the list know almost nothing about your
situation: all you've said is that you have starting structures from cyana and
that you are using amber7. So the best you can expect is some very general
debugging advice.

...dac

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