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<blockquote type="cite" cite="mid:3FA16938.1000205@lulu.it.northwestern.edu">
The iron non-bond parameters are available at the AutoDock web site:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.scripps.edu/pub/olson-web/doc/autodock/parameters.html#PARAMETERS">
http://www.scripps.edu/pub/olson-web/doc/autodock/parameters.html#PARAMETERS</a>
<br>
<p>The parameters are derived from two different force fields, AMBER (1986)
and the Merck FF, MMFF [T. A. Halgren, (1992), "Representation of van der
Waals (vdW) Interactions in Molecular Mechanics Force Fields: Potential Form,
Combination Rules, and vdW Parameters", <i>JACS</i>, <b>114</b>, 7827-7843].
The combined AMBER (1986)/MMFF parameters represent a new and untested set
of parameters, so they should be used with caution. </p>
Look for the table with the
<pre><b><i><font size="-1">Rij, epsij, C12, C6</font></i></b></pre>
values. The AutoDock convention requires one-letter element symbols; therefore,
iron is " f ".<br>
<br>
Kind regards,<br>
<br>
Martina Bertsch, Ph.D. <br>
Northwestern University <br>
Feinberg School of Medicine <br>
Molecular Pharmacology and Biological Chemistry <br>
303 East Chicago Avenue <br>
Chicago, IL 60611 <br>
<br>
<br>
Anton Feenstra wrote:<br>
<blockquote type="cite" cite="mid:3F9FF1DF.3090505@chem.vu.nl">
<pre wrap="">nk yx wrote:<br></pre>
<blockquote type="cite">
<pre wrap="">Yes, the simulation goes well when a ligand is close to the heme.<br>But when the protein has no ligand, the free water is easy to collapse <br>nearby the heme.<br></pre>
</blockquote>
<pre wrap=""><!----><br>Strange. I have also simulated a P450 without ligand, which had water<br>in the active site instead. That didn't give any problems that I saw...<br><br></pre>
<blockquote type="cite">
<pre wrap="">I found the parameters(different to zero) for Fe2+ in OPLS force field. <br>Might I use the parameters for the Fe since I modified the charge from <br>+2 to +1.<br></pre>
</blockquote>
<pre wrap=""><!----><br>That would at least be a good initial guess, I think.<br><br><br></pre>
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