Re: [AMBER] how to add phosphate group in protein

From: Jason Swails <>
Date: Thu, 30 Dec 2010 09:42:28 -0700

You will have to create a new residue that is phosphoaspartate and create a
new residue template for it (either mol2, amber prep, or OFF library) and
assign a new name to that residue in your template (i.e. PAS or something).
 Then you'll have to change every ASP that you want to phosphorylate in your
PDB file to the name PAS and leap will automatically add any missing atoms
from the template.

To create the new library, consider using R.E.D. tools or
antechamber/parmchk to help you. R.E.D. has a lot of helpful tutorials that
address exactly what you want to do (and may even have this residue already
parameterized in its database).

Good luck!

Hope this helps,

On Thu, Dec 30, 2010 at 2:45 AM, Sangita Kachhap <>wrote:

> Hello amber users
> I have a protein in unphosphorylated form and I have to do MD simulation of
> its
> phosphorylated
> form.So how I can add phosphate group to Asp of this protein.
> With regard
> Sangita Kachhap
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Dec 30 2010 - 09:00:06 PST
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