[gmx-users] Simulation a labeled protein

[Itamar Kass]

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
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| Monash University,
| Victoria 3800
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| Tel: +61 3 9902 9376
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| E-mail: Itamar.Kass at monash.edu
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