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Hi Faezeh, <br>
<br>
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.<br>
<br>
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.<br>
<br>
Cheers,<br>
Itamar<br>
<br>
<br>
PS I can recommend on this site which can help you in the process
<a class="moz-txt-link-freetext" href="http://compbio.biosci.uq.edu.au/atb/">http://compbio.biosci.uq.edu.au/atb/</a><br>
<br>
On 21/07/11 7:43 PM, Faezeh Nami wrote:
<blockquote
cite="mid:CADBssj1auVqCDttuVvLi_B_Pib-8ywgjF2YLppiC63LqzCZrFw@mail.gmail.com"
type="cite">Dear all
<div><br>
</div>
<div>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.</div>
<div>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. </div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div>Faezeh <br>
<div><br>
</div>
<div><br>
</div>
</div>
<br>
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<br>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
"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: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================</pre>
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