Re: [AMBER] creating parameters for integrins

From: Nhai <>
Date: Thu, 17 Nov 2016 12:44:00 -0500

Rename: you can use parmed for this (need to write python code)

import parmed as pmd
parm = pmd.load_file('your.pdb')
parm.residues[10].name = 'HID' # as an example'new.pdb')

Of course there will be many other ways to do, but ParmEd is very flexible and handy for those things.


> On Nov 17, 2016, at 12:22 PM, Tsibela German Tebello Mofokeng <> wrote:
> 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.
> Regards
> Tebello
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Received on Thu Nov 17 2016 - 10:00:04 PST
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