<font color='black' size='2' face='Arial, Helvetica, sans-serif'><font color="black" face="Arial, Helvetica, sans-serif" size="2">
<div> <font size="2"><font face="Arial, Helvetica, sans-serif">Hi Bartosz,<br>
<br>
</font></font>The<font color="black" face="Arial, Helvetica, sans-serif" size="2">re
are many potential reasons for a segmentation fault error in dock. My
understanding is that a segmentation fault occurs when the program
attempts to use unallocated memory causing the variable to be truncated
when copying or removing the variable. <br>
<br>
This often occurs when the input is unexpected. </font><font color="black" face="Arial, Helvetica, sans-serif" size="2">For example:</font><br>
<font color="black" face="Arial, Helvetica, sans-serif" size="2">(1) File names are too long. See: http://mailman.docking.org/pipermail/dock-fans/2011-January/002472.html<br>
(2) The input files (like multimol2) is not in expected format.<br>
etc.<br>
<br>
Step #1: use the verbose flag and examine the growth statistics and see where the molecule is failing. <br>
Compare with molecules the succeed.<br>
See: http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GrowthTreeAndStatistics<br>
Step #2: See if the molecules that are failing have any thing in common; Like they all contain a specific atom type. <br>
<br>
<div> I hope this helps,</div>
</font>
</div>
<div> <br>
</div>
<div style="clear:both">Trent E. Balius<br>
Graduate Student, Rizzo Group,<br>
Department of Applied Mathematics and Statistics,<br>
Stony Brook University.<br>
Office: Math Tower 3-129, Phone: (631) 632-8519<br>
<font size="2"><font face="Arial, Helvetica, sans-serif">URL:
http://www.ams.sunysb.edu/~tbalius/</font></font><br>
</div>
<div> <br>
</div>
<div> <br>
</div>
<div style="font-family:arial,helvetica;font-size:10pt;color:black">-----Original Message-----<br>
From: Bartosz Siemiński <sieminb@yahoo.pl><br>
To: dock-fans@mailman.docking.org<br>
Sent: Wed, Jun 22, 2011 6:58 am<br>
Subject: [Dock-fans] segmentation fault<br>
<br>
<div id="AOLMsgPart_3_1a5ad640-cde8-4efd-9a9f-3b9264114353">
<table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font: inherit;" valign="top">Hi all.
<div>Seems like I need your help. I wanted to re-dock ligands from different runs of DOCK Blaster, using DOCK6.4. I got my results for one set of 50 molecules. For another (using the same parameters), I got "segmentation fault" error. I noticed, that only some of those molecules were causing this problem, so I successfully docked the rest. For those "problematic" ones I adjusted many parameters trying to dock them anyway: grid size/spacing, enlarging sphere cluster, min_anchor_size, max_ligand_orientation, etc. I scouted dock-fans archive, found that contact score might be the problem, got rid of this scoring method - it didn't help.</div>
<div>I even made same tests on a different linux distribution just to make sure it's not the case (latest Ubuntu and Fedora releases).<br>
<div>
<div><br>
</div>
<div>Please tell me whats the possible/probable cause of this
error (even if there are many).</div>
</div>
</div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div><br>
</div>
<div>Bartosz Siemiński</div>
</td></tr></tbody></table>
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