<div>Hi Andrea,</div>
<div> </div>
<div>I think two 20 ns simulations of wild- and mutated protein won't *guarantee* that your results are significant, but, of course, they can be!</div>
<div>MD suffers from sensitivity to initial conditions, that gets worse with "short" simulations, as you know.</div>
<div> </div>
<div>I think you have to have an idea of the relaxation time of the process you are interested in.</div>
<div>One thing is to study side-chain isomerizations, another is motions involving the protein backbone.</div>
<div> </div>
<div>PCA is related to the covariance matrix of atom coordinates and can also be used in the dihedral space.</div>
<div>Check the papers on the cosine content of principal components, for instance. They can give you an idea of the "extent" of your simulation...</div>
<div> </div>
<div>Regards.</div>
<div> </div>
<div>Pedro.<br><br> </div>
<div><span class="gmail_quote">2007/4/2, <a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</a> <<a href="mailto:spitaleri.andrea@hsr.it">spitaleri.andrea@hsr.it</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi all,<br>I am performing a MD study using as starting point a protein whose<br>structure has been determined by nmr. the md of wild type has show few
<br>structural changes of some sidechains after 20ns. Afterfwards, using the<br>same starting point but mutating a PRO to LEU, I have perfomed a similar<br>MD. The structural behaviour of the mutate protein is a bit different
<br>(fair enough) from the wt. However, I was wondering whether it should be<br>more fair perform a MD for the mutate protein using the as starting<br>point the equilibrated structure (after 20ns) of the wt.<br>Second, performing different MD on the wt and the mutate protein, how
<br>may compare properly the results (a part of rmsd, energies, sas, hbond,<br>etc..)? Is it logic to perform a PCA on the energies values? Any<br>suggestion are welcome.<br><br>Thanks in advance<br><br>Regards<br><br>andrea
<br><br>Andrea Spitaleri PhD<br>Dulbecco Telethon Institute<br>c/o DIBIT Scientific Institute<br>Biomolecular NMR, 1B4<br>Via Olgettina 58<br>20132 Milano (Italy)<br><br><br><br>********************************************************************
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