AMBER Archive (2009)

Subject: Re: [AMBER] Peptide bond broken

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Jul 12 2009 - 21:35:35 CDT

On Fri, Jul 10, 2009, Syed Tarique Moin wrote:
>
> I have done parameterization of a metallic center of a protein. But
> during the minimization, the peptide bond between the aminoacid
> (attached to metal) and the next (to it) is broken. I am unable to find
> the reason behind it.

You don't provide enough information for anyone to be of much help. Metallo
centers are not "standard" parts of the Amber library, so you presumably
somehow created a bond between the metal and the amino acid in question. But
since we don't know how you did this, it is not possible to help much in
figuring out what went wrong.

You can use rdparm to print out the bonds in your system -- that can help you
make sure that you have what you want in the prmtop file.

...dac

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