AMBER Archive (2009)

Subject: Re: [AMBER] Peptide bond broken

From: Syed Tarique Moin (
Date: Mon Jul 13 2009 - 08:20:02 CDT

Thanks a lot


Syed Tarique Moin

--- On Fri, 7/10/09, FyD <> wrote:

From: FyD <>
Subject: Re: [AMBER] Peptide bond broken
To: "AMBER Mailing List" <>
Date: Friday, July 10, 2009, 11:58 PM

Dear Syed Tarique Moin,

> 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.

In this type of complex a difficulty is to set up the molecular topology. I strongly suggest you to use Ante_R.E.D. for that; Ante_R.E.D. should generate the correct topology (independently of the number of connectivities between the metal & the bioorganic atoms) for your complex _if_ your initial Cartesian coordinate set is correct.

Then, you need to connect your complex to your protein. Here you have to to define head/tail in your complex. You can also use the "bond" command in LEaP.

Before MD, to see if your 'whole protein + complex' has the correct topology - do not solvate your molecule ;-), you might use the "savemol2" command as shown in
Then, you can study the connectivities in the @<TRIPOS>BOND section to see if the bond you suspect to be missing is really missing.

regards, Francois

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