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

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Thu, 30 Dec 2010 22:18:54 +0530 (IST)

Thanks Jason for qiuck reply I will do it.

> 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!
> Jason
>
> Hope this helps,
> Jason
>
> On Thu, Dec 30, 2010 at 2:45 AM, Sangita Kachhap <sangita.imtech.res.in>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
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 30 2010 - 09:00:08 PST
Custom Search