Hi Davood,<br><br>Although there could be many causes, in this case I'd suspect that there is a water molecule trapped inside the protein. This can be the result of solvation using genbox. An isolated water molecule can start to "rattle". It will get close to one side of the microcavity and "kicked" to the other side, where it will be overlapping more and "kicked" back even harder. This process can repeat itself until the overlaps can't be solved anymore and the system blows up, typically telling you the water molecule couldn't be settled. Check for isolated water molecules and delete them from the structure file if necessary.
<br><br>Hope it helps,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 5/27/06, <b class="gmail_sendername">davood ajloo</b> <<a href="mailto:ajloo2000@yahoo.com">ajloo2000@yahoo.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Dear gmx-users<br> We want to study interaction of ligand to enzyme. We constructed the gro and top file from Prodrg and add it to the end of enzyme gro and change the number of atoms. Some of calculation carried out until mdrun of
pr.mdp, but in this step we encontered to following error. what is the cause of it and how we can solve it.<br> Thanks a lot of.<br> <br> tep 5, time 0.01 (ps) LINCS WARNING<br> relative constraint deviation after LINCS:
<br> max 0.007443 (between atoms 3555 and 3557) rms 0.000281<br> bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 506 507 30.0 0.0999 0.0999 0.1000
<br> 1861 1862 37.0 0.0999 0.1000 0.1000<br> 2131 2132
30.4 0.0999 0.0999 0.1000<br> 2604 2605 35.4 0.0989 0.0997 0.1000<br> 2997 2998 36.5 0.0999 0.1000 0.1000<br> <br> t = 0.010 ps: Water molecule starting at atom 12011 can not be settled.
<br> Check for bad contacts and/or reduc<br></div><div><span class="ad"> <br> <br> <p>
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http://www.gromacs.org/mailing_lists/users.php</a><br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry
<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>