http://wiki.docking.org/index.php?action=history&feed=atom&title=OUTDOCK_3.7 2026-04-07T04:01:52Z Revision history for this page on the wiki MediaWiki 1.39.1 http://wiki.docking.org/index.php?title=OUTDOCK_3.7&diff=6304&oldid=prev 2014-02-25T04:33:10Z

<p>Created page with &quot; = Explanation of header = Here we explain line by line the meaning of the header in the OUTDOCK 3.7 file. DOCK v. 3.7, compiled 20140211 Version of program, date create...&quot;</p> <p><b>New page</b></p><div><br /> = Explanation of header = <br /> <br /> Here we explain line by line the meaning of the header in the OUTDOCK 3.7 file. <br /> <br /> <br /> DOCK v. 3.7, compiled 20140211<br /> Version of program, date created<br /> <br /> DOCK compiled for bitsize 64<br /> Architecture<br /> <br /> DOCK git commit: 2d29d656e1953ded8dbe941c88a758b43cc6220d<br /> Source code reference number<br /> <br /> CPU, Date, and Time: node-3-28.c.bkslab.org 20140224<br /> Which computer the program ran, and started on what date YYYYMMDD.<br /> <br /> WARNING ---&gt; deprecated keyword ignored: molecules_maximum <br /> WARNING ---&gt; deprecated keyword ignored: vdw_maximum<br /> Warnings that keywords ignored. <br /> <br /> <br /> Solvation type: context-dependent ligand desolvation<br /> Ligand desolvation treatment. Choices are None, Full, and Context-dependent<br /> <br /> &lt;pre&gt; ***WORK IN PROGRESS***<br /> Ligands will NOT be recombined (NO mix-n-match)<br /> Internal Distance Clashes checked<br /> Experimental premax scoring will NOT be used<br /> Clusters/Additional Match Spheres scoring will not be used<br /> No a* search, normal search used<br /> :dislim = 0.0500 maxnodes = 4 minnodes = 4<br /> Matching method number 2 will be used<br /> :disstep = 0.0500 dismax = 0.5000 matchgoal = 5000<br /> timeout = 10.00000 <br /> Receptor spheres: ../dockfiles/matching_spheres.sph<br /> Input ligand: /raid1/people/mattchu/database/testd/top10.db2.gz<br /> DelPhi/Qnifft gridsize is 99<br /> Receptor desolvation not being used<br /> vdW parms: ../dockfiles/vdw.parms.amb.mindock<br /> a maximum of 10.0 in vdw energy score is allowed for any flexible group<br /> a maximum of 10.0 in vdw energy score is allowed for the whole rigid component<br /> natmin = 4 natmax = 100<br /> number of poses saved during processing = 1<br /> number of poses written = 1<br /> hydrogens always written out<br /> trilinear interpolation is always done<br /> the ligand internal energy scaled by the factor 0.000000 <br /> Receptor grids for Group#: 1<br /> Desolvation grid: ../dockfiles/ligand.desolv.heavy<br /> Additional hydrogen desolvation grid: ../dockfiles/ligand.desolv.hydrogen<br /> DelPhi grid: ../dockfiles/trim.electrostatics.phi<br /> bumpmap filename: ../dockfiles/vdw.bmp<br /> vdw filename: ../dockfiles/vdw.vdw<br /> receptor energy: 0.0000<br /> Only poses with a score better than 1.0000000E+07 <br /> will be written to disk. Use with caution for retrospective calculations, <br /> Intended use is for prospective calculations. <br /> min grid limits: -4.540001 -2.193001 -35.89100 <br /> max grid limits: 23.96000 28.36152 -7.891000 <br /> first set of grids read successfully<br /> 12 colors used in receptor sphere file<br /> Receptor spheres: 45<br /> cluster 1 with 45 spheres<br /> 9001 9002 9003 9004 9005 9006 9007 9008 9009 9010 9011 9012 9013 9014 9015<br /> 9016 9017 9018 9019 9020 9021 9022 9023 9024 9025 9026 9027 9028 9029 9030<br /> 9031 9032 9033 9034 9035 9036 9037 9038 9039 9040 9041 9042 9043 9044 9045<br /> <br /> output file: test.mol2.gz <br /> maximum receptor sphere-sphere distance 12.23739<br /> &lt;/pre&gt;<br /> <br /> <br /> <br /> <br /> &#039;&#039;&#039;Explanation of columns&#039;&#039;&#039;<br /> = Non-energy terms =<br /> Here we explain what each of the columns means: <br /> == mol# ==<br /> <br /> == id_num ==<br /> ZINC ID or molecule code if not from ZINC. <br /> <br /> == flexiblecode ==<br /> <br /> == matched ==<br /> <br /> <br /> == nscored ==<br /> <br /> <br /> <br /> == time ==<br /> <br /> <br /> <br /> == hac ==<br /> <br /> <br /> <br /> == setnum ==<br /> <br /> <br /> <br /> == matnum ==<br /> <br /> <br /> == rank ==<br /> <br /> <br /> <br /> == cloud ==<br /> <br /> <br /> = Energy Terms = <br /> == elect == <br /> <br /> == vdW ==<br /> <br /> == psol ==<br /> <br /> == asol ==<br /> <br /> <br /> == inter ==<br /> <br /> <br /> == rec_e ==<br /> <br /> <br /> == rec_d ==<br /> <br /> == r_hyd ==<br /> <br /> == Total ==<br /> <br /> <br /> Back to [[DOCK 3.7]].<br /> <br /> <br /> [[Category:Manual]]<br /> [[Category:DOCK 3.7]]</div>

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