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

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Sat, 8 Jan 2011 15:15:22 +0530 (IST)

As you said I generate the new template for phosphoaspartate in mol2 format
using antechamber as well as library for it, then I use this template and
library to change ASP 54 to phosphoaspartate in my PDB file.

This worked and now PDB file have phosphoaspartate but this residue is conneted
at its both ends via TER card.When I visualize this modified PDB it was ok.

But when I minimize this modofied PDB, phosphoaspartate is there but not bonded at
both ends.

Here I have follow the tutorial :- http://ambermd.org/tutorials/basic/tutorial4b/

So where is the problem please suggest me.

Here I am attaching PDB
1.Before minimization
2.After minimization



> 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

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Received on Sat Jan 08 2011 - 02:00:02 PST
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