http://wiki.docking.org/index.php?title=OUTDOCK_3.7&feed=atom&action=historyOUTDOCK 3.7 - Revision history2024-03-29T12:47:53ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=OUTDOCK_3.7&diff=6304&oldid=prevFrodo: Created page with " = 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..."2014-02-25T04:33:10Z<p>Created page with " = 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..."</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 ---> deprecated keyword ignored: molecules_maximum <br />
WARNING ---> 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 />
<pre> ***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 />
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'''Explanation of columns'''<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 />
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== setnum ==<br />
<br />
<br />
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== matnum ==<br />
<br />
<br />
== rank ==<br />
<br />
<br />
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== cloud ==<br />
<br />
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= Energy Terms = <br />
== elect == <br />
<br />
== vdW ==<br />
<br />
== psol ==<br />
<br />
== asol ==<br />
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== inter ==<br />
<br />
<br />
== rec_e ==<br />
<br />
<br />
== rec_d ==<br />
<br />
== r_hyd ==<br />
<br />
== Total ==<br />
<br />
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Back to [[DOCK 3.7]].<br />
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[[Category:Manual]]<br />
[[Category:DOCK 3.7]]</div>Frodo