<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Sep 4, 2012, at 5:40 AM, Miro Moman wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>When energy minimising protein-ligand complexes, I have observed that Chimera seldom, if ever, complains about missing parameters.<br><br>However, when I try to generate a Pmrtop file for the same complexes, quite often sLeap is unable to complete the request due to its inability to recognise certain atom types..<br><br>Provided that the minimization engine (MMTK) is using the Amber force filed, I was wondering:<br><br>Are parameters computed in the same way?<br><br>If not, what are the differences? Maybe a different forcefield version?<br></div></blockquote><div><br></div>Parameters are not computed in the same way for Write Prmtop / sleap as they are for Minimize Structure / MMTK.</div><div><br></div><div>For Write Prmtop, Chimera relies on sleap's built-in parmchk to generate missing parameters. sleap runs parmchk on a per-residue basis. This means that parameters can be missing for bonds/angles/torsions that cross the boundary between the non-standard residue and any connected residues. Since many non-standard residues are not connected to other residues (e.g. they are ligands), this isn't as big a problem as one might think, but it is still a problem.</div><div><br></div><div>For Minimize Structure, Chimera finds the entire connected chain that contains the non-standard residue and runs parmchk on that. In fact, it runs it on all such chains at once. This means that for structures that contain many chains with non-standard residues, the parmchk process can take a <i>long</i> time. Nonetheless, the parmchk will produce a complete set of parameters. We hope to make Chimera run parmchk on a per-chain basis sometime soon (parmchk execution time seems to scale exponentially with the number of atoms involved).</div><div><br><blockquote type="cite"><div>In addition, is there a way to inspect the parameters that have been generated for minimising a given ligand or non-standard residue?</div></blockquote><br></div><div>There is always a way. Well, almost always. There is this time at least! You would need to edit Chimera's Python code so that it doesn't remove the parmchk output once it's done with it.</div><div><br></div><div>For Write Prmtop, there is a _clean function defined near line 95 of <your Chimera>/share/WritePrmtop/__init__.py. You would add these lines at the beginning of the function to show the temp folder name in the reply log and to prevent it from being removed:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print tempDir</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>return</div><div>(indented appropriately)</div><div><br></div><div>Similarly, for Minimize Structure, there is a _removeTempDir function defined near line 301 of <your Chimera>/share/MMMD/MMTKinter.py. Add these lines near the beginning of that function:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print self.tempDir</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>return</div><div>(also indented appropriately)</div><div><br></div><div>The frcmod file left in the temp dir has the generated parameters. Other parameters are just the standard ones provided with the force field chosen.</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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