AMBER Archive (2009)

Subject: Re: [AMBER] Peptide bond broken

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

Thanks a lot

Regards

Syed Tarique Moin

--- On Fri, 7/10/09, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

From: FyD <fyd_at_q4md-forcefieldtools.org>
Subject: Re: [AMBER] Peptide bond broken
To: "AMBER Mailing List" <amber_at_ambermd.org>
Cc: q4md-fft_at_q4md-forcefieldtools.org
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 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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber