[gmx-users] Simulation a labeled protein

[Faezeh Nami]

Dear Itamar

Thank you for the reply.

If I modify Cys parameters in the *rtp file in order to add the Cys-label
parameters, it will be applied to other Cys in the protein as well. Isn't
it?

In case of modification of *itp file, should I modify all nr or qtot after
the Cys? What about bonds?

Best,
Faezeh

On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass <itamar.kass at monash.edu> wrote:

>  Hi Faezeh,
>
> You can modify the FF and add the Cys-label parameters to the *rtp and *hdb
> files, such that pdb2gmx will be able to use them. Another why is use the
> original pdb as a starting point and modify the output *gto, *itp and *top
> files.
>
> Just remember that in anycase, it is better to copy the files into your
> local directory so an change you made will not effect other simulations.
>
> Cheers,
> Itamar
>
>
> PS I can recommend on this site which can help you in the process
> http://compbio.biosci.uq.edu.au/atb/
>
>
> On 21/07/11 7:43 PM, Faezeh Nami wrote:
>
> Dear all
>
>  I am trying to simulate a protein which a label  (a small organic
> molecule) is covalently attached to a cysteine. Worth to say there is no
> label in the original pdb file of protein and it was attached to the Cys.
> using a software.
> Should I insert the label parameters into the conf.gro file or I need to
> modify a force field? If there is someone who has experiences in such
> systems, please have some advice.
>
>  Thanks in advance,
> Faezeh
>
>
>
>
>
> --
>
>
> "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu
> ============================================
>
>
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