[gmx-users] Simulation a labeled protein

Itamar Kass itamar.kass at monash.edu
Thu Jul 21 11:51:51 CEST 2011

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.


PS I can recommend on this site which can help you in the process 

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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