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.k...@monash.edu
============================================
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