<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Aug 24, 2012, at 2:40 AM, Miro Moman wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>Searching through the archives, I have found that performing DockPrep in batch mode is quite straightforward:<br><br><a href="http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html">http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html</a><br><br>I have also noticed that, when working from the GUI, energy minimisation involves a previous DockPrep step.<br><br>I would like to perform the energy minimisation of several protein-ligand complexes, can this be easily done in batch mode?<br></div></blockquote><div><br></div>You would just take the Dock Prep example you found and meld it with the example of how to loop through data files and perform commands on them, found here:</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html</a></div><div><br></div><div><blockquote type="cite"><div>Furthermore, I would also be interested of computing the binding energy both prior and after minimisation (possibly including APBS-computed electrostatic terms...). However, this is of secondary importance as it can be easily achieved with other tools.</div></blockquote><br></div><div>In the most recent daily builds there is a tool for computing an electrostatic potential volumetric data set using an APBS web service, but I'm a little hazy on whether this really helps you and I'm certainly no expert on accessing the tool via an API. If you feel it would be a big help, just say so and the programmer that worked on that (Conrad Huang) may be able to provide more info.</div><div><br></div><div>--Eric</div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span>
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