Well, I thought that this is not a very simple matter, but for superficial aa-s it works nice, and even for more problematic aas there are visible changes.<br>The main problem is, that I have to deal with 1000s of mutations, so I have to do it in a high throughput manner... (as high-thorughput as it is reasonably possible)
<br><br><div><span class="gmail_quote">On 12/16/05, <b class="gmail_sendername">Ran Friedman</b> <<a href="mailto:ran@hemi.tau.ac.il">ran@hemi.tau.ac.il</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Hota,<br>
<br>
<div align="justify">I'd think that in order to observe structural
transformations upon mutations, you should first get your system
equilibrated (via EM, PR and at least 100ps unconstrained MD) and then
run pretty long MD simulations. Later, you can compare relevant
measures (e.g. contacts, hydrogen bonds, secondary structures) between
simulations of mutant and wt proteins. Also, bear in mind that no
matter how long your simulation is, the time scale for large structural
changes (e.g. large domain motions) will be longer. Hopefully, you'll
still be able to observe some changes under a reasonable simulation
time (at least several nanoseconds).<br>
<br>
As for the mutation itself, you can try to use programs that deal with
it, e.g. jackal (available from Prof. Barry Honig) or swisspdb viewer
rather than do it yourself. <br>
<br>
Good luck,<br>
Ran.<br>
</div>
<br>
Tamas Horvath wrote:<br>
<blockquote type="cite" cite="http://midc343d7080512160621o49d87e44l80f70d5ba058e3f3@mail.gmail.com"><div><span class="e" id="q_10834189330c4b3e_1">Hi!<br>
I want to calculate with gromacs, how certain mutations affect the
structure of a protein.<br>
<br>
In order to do so, 1st I "mutate" the protein in the pdb file. I use a
very simple algorithm, which places the new aa in the same orientation
as the old aa was, but it does not ensure that there is no spatial
clashes (though in most cases there is no such problem).
<br>
<br>
I run gromacs simulations on this new structure (based on the demo,
that comes with it)<br>
1st a cg+steep energy minimasition<br>
2nd a position restraining<br>
3rd a 20ps periodic simulated annealing, with temperatures: 300 320 320
300, and times: 0 2 4 6
<br>
4th simple 2ps md at 300K, and I get 10 structures from this run, which
then I compare to the wt structure<br>
<br>
What I'm asking is, that is it a reasonable approach? How may I modify
it to make it more reasonable?<br>
How may I detect if the protein is in it's favourable conformation?
(Mutations in the core may have extensive effects, which may need more
time to "settle")<br>
<br>
Any suggestions would be appreciated!<br>
<br>
Hota
<br>
<br></span></div>
+++++++++++++++++++++++++++++++++++++++++++<br>
This Mail Was Scanned By Mail-seCure System<br>
at the Te
<pre><hr size="4" width="90%">
_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailman/listinfo/gmx-users</a>
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.</pre>
</blockquote>
<br>
<pre cols="72">-- <br>------------------------------------------------------<br>Ran Friedman<br><a href="http://bioinfo.tau.ac.il/%7Eran" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://bioinfo.tau.ac.il/~ran
</a>
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
------------------------------------------------------<br></pre>
<br>_______________________________________________<br>gmx-users mailing list<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br><br></blockquote></div><br>