<br>Dear Leila<br>Ok,But you have to separate your ions from your general pdb file(protein+ions) in the form of pdb,<br>in the other words you need to obtain the pdb files for your ions separately and then paste it to PRODRG server.because your protein has more than 300 atoms alonly.<br>
I hope it can help you<br><br><br><div class="gmail_quote">On Sat, Oct 16, 2010 at 12:00 PM, leila karami <span dir="ltr"><<a href="mailto:karami.leila1@gmail.com">karami.leila1@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear mohsen ramezanpour<i>
</i><pre style="font-family: arial,helvetica,sans-serif;"><font size="2">yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but </font><br style="font-family: arial,helvetica,sans-serif;">
</pre><font size="2"></font><pre style="color: rgb(0, 0, 0); font-family: arial,helvetica,sans-serif;"><font size="2">ERRDRG> Too many atoms in this molecule (should be <=300).
PRODRG> Program terminated unsuccessfully, sorry!
</font></pre><br>
<br>--<br>
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