Thank you Hai, I will try it out.
On 17 November 2016 at 19:44, Nhai <nhai.qn.gmail.com> wrote:
> 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
> parm.save('new.pdb')
>
> Of course there will be many other ways to do, but ParmEd is very flexible
> and handy for those things.
>
> Hai
>
> > On Nov 17, 2016, at 12:22 PM, Tsibela German Tebello Mofokeng <
> 1754789.students.wits.ac.za> 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).
> >
> > http://ambermd.org/tutorials/advanced/tutorial20/mcpb.htm
> >
> > 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Nov 18 2016 - 00:00:03 PST
