Thanks for these two references ... I am trying to simulate a zinc ion (Zn++) binding domains .. Actually the study involves grafting the Zinc ion domain onto some other protein to check whether it binds to ions or not and what will be the effect of ion binding onto the topology of the other protein to which the zinc ion binding domain is attached .....<br>
<br><div class="gmail_quote">On Thu, Feb 17, 2011 at 11:15 PM, Marc Baaden <span dir="ltr"><<a href="mailto:baaden@smplinux.de">baaden@smplinux.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
Hi,<br>
<br>
As mentioned by others, there's really lots of literature out there. I<br>
thought I mention a recent study we carried out, because it actually<br>
helped discover some new ion binding sites based on MD. By re-examining<br>
crystal structures based on these results, we could even find<br>
experimental evidence for those ions being there. [1]<br>
<br>
But actually you didn't tell us which ions you want to simulate?<br>
Monovalent ions should be sort of ok, although there are differences<br>
among the forcefields (some original KCl used to crystallize).<br>
Di-valent ions, in particular Ca2+, are much more tricky. Higher<br>
charged ones are a nightmare. The higher the charge, the more likely<br>
you might want things like polarization in your simulation.<br>
<br>
There are also some specific forcefields finely parameterized for ions<br>
based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh<br>
and Piquemal.<br>
<br>
Good luck,<br>
Marc<br>
<br>
[1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis<br>
<a href="http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000" target="_blank">http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000</a><br>
<br>
[2] SIBFA (Sum of Interactions Between Fragments Ab initio computed)<br>
<a href="http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html" target="_blank">http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html</a><br>
<div class="im"><br>
<br>
<a href="mailto:bharat.85.monu@gmail.com">bharat.85.monu@gmail.com</a> said:<br>
>> Thankx for the reply ...<br>
>> Can you refer some papers which can be helpful for me to do MD<br>
>> simulation of proteins with ions ... It will be of great help.. I<br>
>> searched the gromacs user list but couldn't get much material..<br>
<br>
<br>
<br>
</div>--<br>
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris<br>
mailto:<a href="mailto:baaden@smplinux.de">baaden@smplinux.de</a> - <a href="http://www.baaden.ibpc.fr" target="_blank">http://www.baaden.ibpc.fr</a><br>
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