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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML EXPERIMENTAL 970324//EN"><HTML><HEAD><META NAME="GENERATOR" CONTENT="Adobe FrameMaker 5.5/HTML Export Filter"><LINK REL="STYLESHEET" HREF="Manual.css"><TITLE> Input Parameters</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=8491"> </A>Input Parameters</H2><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=6832"> </A>File Format</H3><P CLASS="Body"><A NAME="pgfId=8653"> </A>Input parameters may be supplied in a text file. There are few simple format rules for this file.</P><TABLE><CAPTION><H3 CLASS="Table"><A NAME="pgfId=8546"> </A>Table 2. <A NAME="40687"> </A>Format of Input File</H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=8550"> </A>Rule</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=8552"> </A>Consequence</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=8560"> </A>Parameter names must be the first word on a line to be recognized.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=8567"> </A>Any character or word preceding a parameter effectively comments it out.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17680"> </A>The word following a recognized parameter name is interpreted as the parameter value.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17701"> </A>Comments can appear on the same line, after a parameter and value.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17721"> </A>Blank lines are allowed.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17708"> </A>Comments can appear on separate lines.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17723"> </A>Empty files are allowed.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17716"> </A>Missing parameters will be flagged (batch mode) or requested (interactive mode).</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17693"> </A>The order of parameters is irrelevant.</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=17668"> </A> </P></TD></TR></TABLE></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=8654"> </A>Parameters</H3><P CLASS="Body"><A NAME="pgfId=8726"> </A>dock has a large number of input parameters because of its wide array of functionality. Parameters are read in hierarchically, with the most general parameters first. They are also ordered according to broad classes of functionality in order to make the process of selection more intuitive. For instance all scoring-related parameters are requested together. Since only the relevant parameters are requested based on preceding selections, it is recommended that initial parameter selection be done interactively to generate a sensible input file as painlessly as possible.</P><P CLASS="Body"><A NAME="pgfId=8750"> </A>The following list of parameters are grouped according to the order they are requested at run time. Again, many parameters are listed here that will not be requested during your particular run.</P><P CLASS="Body"><A NAME="pgfId=19054"> </A>The default values listed here may be different from those provided during a particular run, because dock tries to recommend sensible parameter values based on preceding selections.</P><H3 CLASS="Table"><A NAME="pgfId=19180"> </A>Table 3. dock input Parameters</H3><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=19298"> </A>3A: <A NAME="41860"> </A>General </H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19081"> </A>Parameter</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19083"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19085"> </A>Default</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19087"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="4"><P CLASS="Normal"><A NAME="pgfId=26464"> </A>Parameters in this category determine the general behavior of the dock run. Each option can be used in isolation and many in combination to allow dock to perform a diverse repertoire of tasks. If none of these flags are selected, then dock simply reads in a single molecule and writes it out, which is useful for file format conversion.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=19102"> </A>flexible_ligand<A NAME="22201"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19104"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19106"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19111"> </A>Flag to allow <A HREF="Manual.19.html#33669" CLASS="XRef">Ligand Flexibility</A>.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=19114"> </A>orient_ligand<A NAME="34562"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19116"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19118"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19123"> </A>Flag to perform an <A HREF="Manual.19.html#40650" CLASS="XRef">Orientation Search</A>.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=19138"> </A>score_ligand<A NAME="35823"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19140"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19142"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19147"> </A>Flag to perform <A HREF="Manual.19.html#26630" CLASS="XRef">Scoring</A> of orientations or conformations.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=19150"> </A>minimize_ligand<A NAME="36933"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19152"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19154"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19156"> </A>Flag to perform local score <A HREF="Manual.19.html#22570" CLASS="XRef">Minimization</A> of orientations or conformations.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=26379"> </A>multiple_ligands<A NAME="37217"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=26381"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=26383"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=26388"> </A>Flag to process <A HREF="Manual.19.html#17976" CLASS="XRef">Multiple Ligands</A>.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=26367"> </A>chemical_screen<A NAME="35897"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=26369"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=26371"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=26376"> </A>Flag to perform <A HREF="Manual.19.html#31142" CLASS="XRef">Chemical Screening</A> (<A HREF="Manual.19.html#37217" CLASS="XRef">multiple_ligands</A> must be selected, but not <A HREF="Manual.19.html#34562" CLASS="XRef">orient_ligand</A> or <A HREF="Manual.19.html#35823" CLASS="XRef">score_ligand</A>).</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=19162"> </A>parallel_jobs<A NAME="14818"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19164"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19166"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19170"> </A>Flag to perform docking as <A HREF="Manual.19.html#23238" CLASS="XRef">Parallel Jobs</A> orchestrated by a server dock job (<A HREF="Manual.19.html#37217" CLASS="XRef">multiple_ligands</A> must be selected).</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=19173"> </A>random_seed<A NAME="10903"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19175"> </A>integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19177"> </A>0</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19179"> </A>Integer to seed the random number generator.</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=8652"> </A> </P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=21902"> </A>3B: <A NAME="33669"> </A>Ligand Flexibility </H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21924"> </A>Parameter</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21926"> </A>Type</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21928"> </A>Default</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21930"> </A>Description</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="4"><P CLASS="Normal"><A NAME="pgfId=26427"> </A>Ligand flexibility parameters can be used in various combinations to relax an input conformation, to perform a conformational search of a molecule, or to perform a completely flexible docking of a molecule. See <A HREF="Manual.f.html#31662" CLASS="XRef">Conformation Search on page 32</A> for more discussion.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=22304"> </A>anchor_search<A NAME="28389"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22306"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22308"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22310"> </A>Flag to organize rigid segments into concentric layers around an anchor. Only the anchor is included in initial scoring/orienting. The outer segments are reattached in a subsequent conformation search.</P><UL><LI CLASS="Bullet"><A NAME="pgfId=22317"> </A>yes = <A HREF="Manual.f.html#37908" CLASS="XRef">Anchor-First Search</A> is performed.</LI><LI CLASS="Bullet"><A NAME="pgfId=22321"> </A>no = <A HREF="Manual.f.html#15938" CLASS="XRef">Simultaneous Search</A> of all torsions is performed prior to other processing.</LI></UL></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=22324"> </A>multiple_anchors<A NAME="18588"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22326"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22328"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22330"> </A>Flag to select several anchors for a molecule.</P><UL><LI CLASS="Bullet"><A NAME="pgfId=22331"> </A>yes = All rigid segments meeting <A HREF="Manual.19.html#34097" CLASS="XRef">anchor_size</A> criteria will be tried independently as anchors.</LI><LI CLASS="Bullet"><A NAME="pgfId=22335"> </A>no = The largest segment is used.</LI></UL></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=22338"> </A>anchor_size<A NAME="34097"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22340"> </A>integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22342"> </A>10</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=22344"> </A>Minimum number of heavy atoms for an anchor if <A HREF="Manual.19.html#18588" CLASS="XRef">multiple_anchors</A> requested. If no segment satisfies this value, then the largest segment is used.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=27185"> </A>write_partial_structures<A NAME="22766"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=27187"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=27189"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=27191"> </A>Flag to write out all partially-built structures during the anchor-first search. This option is useful to monitor the intermediate stages of a flexible ligand dock run. The structures from each cycle of growth are written to a separate file, with each file name constructed as shown in <A HREF="Manual.f.html#41750" CLASS="XRef">Table 6. on page 34</A>.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Parameter"><A NAME="pgfId=21933"> </A>torsion_drive<A NAME="29408"> </A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21935"> </A>boolean</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21937"> </A>no</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21939"> </A>Flag to perform a conformational search by driving each torsion through a set of low-energy dihedral values read from the <A HREF="Manual.19.html#20042" CLASS="XRef">flex_drive_file</A>.</P></TD>⌨️ 快捷键说明
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