AMBER Archive (2009)
Subject: Re: [AMBER] Peptide bond broken
From: Syed Tarique Moin (tarisyed_at_yahoo.com)
Thanks a lot
Syed Tarique Moin
--- On Fri, 7/10/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
From: FyD <fyd_at_q4md-forcefieldtools.org>
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 http://q4md-forcefieldtools.org/Tutorial/leap.php