Faezeh Nami wrote:
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?
Set the name of your modified residue to something unique (in both the input
coordinate file and the .rtp entry).
In case of modification of *itp file, should I modify all nr or qtot
after the Cys? What about bonds?
What .itp file do you want to modify? Making changes to the pdb2gmx output is a
bad idea. You'll have to change any and all subsequent atom numbers, and that
extends to all of the bonded parameters as well, and you will have to add lots
in. This procedure is very error-prone. I would suggest building (and
thoroughly checking) an .rtp entry for your modified residue.
-Justin
Best,
Faezeh
On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass <[email protected]
<mailto:[email protected]>> 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
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| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376 <tel:%2B61%203%209902%209376>
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Virginia Tech
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