<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000"><div class="im"><blockquote type="cite"><div style="font-size:12pt;font-family:arial,helvetica,sans-serif">
<div>Dear Gromacs users</div>
<div>I have encountered in pdb data bank with Human interferon
crystal structure:</div>
<div>PDB ID : 1ITF</div>
<div><a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF" target="_blank">http://www.rcsb.org/pdb/explore/explore.do?structureId=1ITF</a></div>
<div><br>
</div>
<div>It is mentioned that it contains 24 structures. I opened
the file and saw there are 24 models there.</div>
<div><br>
</div>
<div>Now if I want to do some simulations on this protein, how
should I know which model to select</div>
</div>
</blockquote>
<br></div><div class="im">You get 24 model because that structure was not determined by X-Ray diffraction, but by NMR. With the structure calculation from the X-Ray data you obtain a single converged structure, whereas by NMR you get an ensemble of all conformations that have been detected in your sample solution.<br>
</div></div></blockquote><div><br></div><div> You can use any of the 24 structures, since you are going to perform a MD run. During your running, the other 23 conformations are likely to be visited. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
<br>
<blockquote type="cite">
<div style="font-size:12pt;font-family:arial,helvetica,sans-serif">
<div> and when doing pdb2gmx, I should delete the other models?</div>
</div>
</blockquote>
</div></div>Yup, just use one model.</blockquote></div><br>