Dear Itamar<div><br></div><div>Thank you for the reply.</div><div><br></div><div>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?</div>
<div><br></div><div>In case of modification of *itp file, should I modify all nr or qtot after the Cys? What about bonds? </div><div><br></div><div>Best,</div><div>Faezeh<br><br><div class="gmail_quote">On Thu, Jul 21, 2011 at 5:51 AM, Itamar Kass <span dir="ltr"><<a href="mailto:itamar.kass@monash.edu">itamar.kass@monash.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#FFFFFF" text="#000000">
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 href="http://compbio.biosci.uq.edu.au/atb/" target="_blank">http://compbio.biosci.uq.edu.au/atb/</a><div><div></div><div class="h5"><br>
<br>
On 21/07/11 7:43 PM, Faezeh Nami wrote:
<blockquote 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>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div><pre 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: <a href="tel:%2B61%203%209902%209376" value="+61399029376" target="_blank">+61 3 9902 9376</a>
| Fax: <a href="tel:%2B61%203%209902%209500" value="+61399029500" target="_blank">+61 3 9902 9500</a>
| E-mail: <a href="mailto:Itamar.Kass@monash.edu" target="_blank">Itamar.Kass@monash.edu</a>
============================================</pre>
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