<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "> Hi Jack,<div><br class="webkit-block-placeholder"></div><div>what you want to do is what many pharmaceutical (and not only) company (money) aim to do. The most efficient you do it and the more money you get back.</div><div>And where there's money the competition is always quite high ;-)..</div><div><br class="webkit-block-placeholder"></div><div>I'm not an expert of that but I would highly suggest you to have a look at what is going on out there.. With some effort I'm sure you can find</div><div>quite few informations.</div><div><br class="webkit-block-placeholder"></div><div>Regarding cp2k the only thing I can tell you is that we don't support at the moment any specific(automatic)-docking algorithm.</div><div><br class="webkit-block-placeholder"></div><div>Good Luck!</div><div>Teo</div><div><br><div><div>On 7 Jan 2008, at 15:50, Jack Shultz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div>Perhaps treat it in a couple scenarios:</div><div>1) Run molecular docking on transition state structures with a catalysts where the TSS model is derived in a reaction isolated from any catalysts.</div><div>2) Then another scenario, run a molecular docking between the substrate and an enzyme. Generate a quantum box to of approximate 30 atoms and simulate a reaction within that area, ignoring external influences</div><div> </div></span></blockquote></div><br></div></body></html>