AMBER Archive (2009)

Subject: Re: [AMBER] Peptide bond broken

From: Shubhra Gupta (shubhg_at_iiar.res.in)
Date: Sun Jul 12 2009 - 23:17:31 CDT

Was there any warning when you were generating the topological and
coordinate files.
If yes, try to avoid that.

Shubhra

On Mon, Jul 13, 2009 at 7:35 AM, case <case_at_biomaps.rutgers.edu> wrote:

> 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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