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
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Dec 30 2010 - 09:00:08 PST
