[AMBER] creating parameters for integrins

From: Tsibela German Tebello Mofokeng <1754789.students.wits.ac.za>
Date: Thu, 17 Nov 2016 19:22:03 +0200

Dear Amber Users

I would like to edit a pdb file (ID =1DZI) to indicate that the Co2+ ion in
the metal-ion dependent adhesion site(MIDAS) of integrin A2B1 forms the
following coordinations:

1. A direct coordination to SER, GLU and ASP through their hydroxyl oxygen.
3. Indirect coordination through water molecules with THR and ASP.

My challenge is renaming the above mentioned amino acid residues to reflect
this interactions e.g. if HIS forms a bond with a metal then it is renamed
to HID as outlined in the following tutorial(link).


My main objective is to generate parameters for the Co2+ ion in this
complex while defining all its bonds using the guidelines outlined in the
above mentioned link.

Another alternative is to use xleap to create a library, but my computer
does not support a graphical interface so I am restricted to tleap and
antechamber to create the parameters.

Your help is highly appreciated.

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Received on Thu Nov 17 2016 - 09:30:02 PST
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