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<div>For not particularly "exotic" geometries CP2K should be able to get the proper connectivity.</div>What you've seen could be some sort of bug or wrong parameters in input. <div>Can you please post all the necessary file to reproduce the error (input file and PDB) ?</div><div>does it hang infinitely?<div><br class="webkit-block-placeholder"></div><div>teo</div><div><br></div><div><div><div>On 20 Jan 2008, at 23:34, Jack Shultz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Thanks Shawn,</div> <div> </div> <div>Before I go off and download that. I notice that CP2K CONNECTIVITY has a default <em>GENERATE</em> </div> <div><font face="Courier New">GENERATE</font>: Use a simple distance criteria. (Look at keyword BONDPARM) <br>I may be runing while should be walking...trying to create an CI_NEB for 2 H2O2-->2H2O+O2</div> <div>I tried GENERATE like so</div> <div> </div> <div><font size="2">&TOPOLOGY</font></div> <div><p>CHARGE_BETA</p><p>COORD_FILE_NAME 2H2O.pdb</p><p>COORDINATE PDB</p><p>CONNECTIVITY GENERATE</p><p>&END TOPOLOGY</p></div> <div>This gets a little bit hung on Generate</div> <div><br> GENERATE| Number of Torsions generated: 2</div> <div> GENERATE| Number of Impropers generated: 0</div> <div> GENERATE| Number of 1-4 interactions generated: 2</div> <div> </div> <div>Would you recomend generating with the plugin then or should I be able to do it with CP2K</div> <div> </div> <div class="gmail_quote">On Jan 20, 2008 5:18 PM, Shawn T. Brown <<a href="mailto:shawn...@gmail.com">shawn...@gmail.com</a>> wrote:<br> <blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">The programs VMD and NAMD has a program called psfgen. Check out the website <a href="http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/" target="_blank"> http://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/</a> for info.<br><br>Cheers,<br>Shawn <div class="Ih2E3d"><br><br><br> <div class="gmail_quote">On Jan 20, 2008 5:11 PM, Jack Shultz <<a href="mailto:jackyg...@gmail.com" target="_blank">jackyg...@gmail.com</a>> wrote:<br> <blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0pt 0pt 0pt 0.8ex; BORDER-LEFT: rgb(204,204,204) 1px solid"><p>Is there any GPL software for generating PSF ?</p><br><br></blockquote></div><br><br></div><br><br></blockquote></div><br><br> <br> <br></blockquote></div><br></div></div></body></html>