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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> Running DOCK</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=283"> </A>Running DOCK</H2><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=285"> </A>Starting a DOCK Run</H6><P CLASS="Body"><A NAME="pgfId=287"> </A>You are now ready to run <A NAME="marker=6603"> </A><A HREF="Manual.15.html#18568" CLASS="XRef">DOCK</A>. Since dock can use a substantial amount of CPU time, it is a good idea to check whether there are other jobs running on the same machine. Consider any other users sharing your computers when deciding whether to start more than one run at a time. Be aware of any policies your site has regarding submitting background jobs.</P><P CLASS="Body"><A NAME="pgfId=1576"> </A>The easiest way to select dock parameters is to run dock interactively. Do this by typing dock -i dock.in. You will be prompted for a value for each parameter. Any value you enter will be stored in the file dock.in. This file does not need to exist beforehand. If it does exist, then dock will extract all the relevant parameters it can find from the file. For each parameter, dock will supply a default value. If you want to use the default value, just hit return. The following tables list recommended values for running dock in two different ways: first to dock a single ligand, and second to dock a database of ligands. If you are viewing this manual on-line, then click on any of the keywords to view the reference entry for it.</P><H3 CLASS="Table"><A NAME="pgfId=2020"> </A>Table 2. Recommended dock parameters for a new user.</H3><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=7417"> </A>2A: <A HREF="Manual.19.html#41860" CLASS="XRef">General</A></H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7421"> </A>Keyword</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7423"> </A>Suggestions</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7429"> </A><A HREF="Manual.19.html#22201" CLASS="XRef"></A>flexible_ligand</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7431"> </A>no; try later</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7433"> </A><A HREF="Manual.19.html#34562" CLASS="XRef"></A>orient_ligand</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7435"> </A>yes; searches ligand orientations</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7441"> </A><A HREF="Manual.19.html#35823" CLASS="XRef"></A>score_ligand</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7443"> </A>yes; scores each ligand orientation</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7445"> </A><A HREF="Manual.19.html#36933" CLASS="XRef"></A>minimize_ligand</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7447"> </A>no; try later</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=45367"> </A><A HREF="Manual.19.html#37217" CLASS="XRef"></A>multiple_ligands</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=45369"> </A>no</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=45552"> </A><A HREF="Manual.19.html#10903" CLASS="XRef">random_seed</A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=45554"> </A>0 is fine</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=2207"> </A> </P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=7456"> </A>2B: <A HREF="Manual.19.html#40650" CLASS="XRef">Orientation Search</A></H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7713"> </A>Keyword</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7715"> </A>Suggestions</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7464"> </A><A HREF="Manual.19.html#40677" CLASS="XRef"></A>match_receptor_sites</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7466"> </A>yes; matches ligand to site points</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=45562"> </A><A HREF="Manual.19.html#27719" CLASS="XRef"></A>random_search</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=45564"> </A>no</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7809"> </A><A HREF="Manual.19.html#34261" CLASS="XRef">ligand_centers</A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7811"> </A>no</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7472"> </A><A HREF="Manual.19.html#37805" CLASS="XRef"></A>automated_matching</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7474"> </A>yes; otherwise need to enter geometric match parameters</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7476"> </A><A HREF="Manual.19.html#32044" CLASS="XRef"></A>maximum_orientations</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7478"> </A>500; number of orientations to try</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7480"> </A><A HREF="Manual.19.html#20966" CLASS="XRef"></A>write_orientations</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7482"> </A>yes; to write out multiple orientations for single molecule</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7824"> </A><A HREF="Manual.19.html#23984" CLASS="XRef"></A>rank_orientations</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7826"> </A>yes; to save the top scoring orientations</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7820"> </A><A HREF="Manual.19.html#18391" CLASS="XRef"></A>rank_orientation_total</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7822"> </A>10; to save the top 10 orientations</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=2678"> </A> </P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=7564"> </A>2C: <A HREF="Manual.19.html#26630" CLASS="XRef">Scoring</A> </H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7725"> </A>Keyword</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7727"> </A>Suggestions</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7572"> </A><A HREF="Manual.19.html#34124" CLASS="XRef"></A>intermolecular_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7574"> </A>yes</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7576"> </A><A HREF="Manual.19.html#41535" CLASS="XRef"></A>gridded_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7578"> </A>yes</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7580"> </A><A HREF="Manual.19.html#22380" CLASS="XRef"></A>grid_version</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7582"> </A>4</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7584"> </A><A HREF="Manual.19.html#42188" CLASS="XRef"></A>bump_filter</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7586"> </A>yes</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7588"> </A><A HREF="Manual.19.html#26093" CLASS="XRef"></A>bump_maximum</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7590"> </A>3</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7592"> </A><A HREF="Manual.19.html#36064" CLASS="XRef"></A>contact_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7594"> </A>no</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7596"> </A><A HREF="Manual.19.html#15150" CLASS="XRef"></A>chemical_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7598"> </A>no</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7600"> </A><A HREF="Manual.19.html#23338" CLASS="XRef"></A>energy_score</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7602"> </A>yes</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7934"> </A><A HREF="Manual.19.html#19771" CLASS="XRef">atom_model</A></P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7936"> </A>u; for united atom model</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7604"> </A><A HREF="Manual.19.html#10779" CLASS="XRef"></A>vdw_scale</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7606"> </A>1</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7608"> </A><A HREF="Manual.19.html#36768" CLASS="XRef"></A>electrostatic_scale</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7610"> </A>1</P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=2803"> </A> </P><TABLE><CAPTION><H3 CLASS="Table-Sub"><A NAME="pgfId=7618"> </A>2D: <A HREF="Manual.19.html#12854" CLASS="XRef">Input</A> </H3></CAPTION><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7729"> </A>Keyword</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=7731"> </A>Suggestions</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal">?? 快捷鍵說明
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