AMBER Archive (2009)

Subject: Re: [AMBER] Peptide bond broken

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Jul 11 2009 - 01:58:06 CDT

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
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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