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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> Output</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=14528"> </A>Output</H2><P CLASS="Body"><A NAME="pgfId=14269"> </A>dock reports several kinds of information as output which is either written to screen in interactive mode or written to file in batch mode. Each section of the output is discussed below.</P><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14271"> </A>Heading</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=14549"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14550"> </A> UUUUUUUUU CCCCCCC SSSSSSS FF/ FFF/</P><P CLASS="Normal"><A NAME="pgfId=14551"> </A> UU/ UU/ CC/ CC/ SS/ SS/ FF/ FFF/</P><P CLASS="Normal"><A NAME="pgfId=14552"> </A> UU/ UU/ CC/ CC/ SS/ FFFFF/</P><P CLASS="Normal"><A NAME="pgfId=14553"> </A> UU/ UU/ CC/ CC/ SS/ FF/ FF\</P><P CLASS="Normal"><A NAME="pgfId=14554"> </A> UU/ UU/ CC/ CC/ SS/ SS/ FF/ FF\</P><P CLASS="Normal"><A NAME="pgfId=14555"> </A> UUUUUUUUU/ CCCCCCC/ SSSSSSS/ FF/ FF\</P><P CLASS="Normal"><A NAME="pgfId=14556"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14557"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14558"> </A>University of California at San Francisco, DOCK 4.0</P><P CLASS="Normal"><A NAME="pgfId=14559"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14560"> </A>__________________Job_Information_________________</P><P CLASS="Normal"><A NAME="pgfId=14561"> </A>launch_time Wed Mar 19 12:05:01 1997</P><P CLASS="Normal"><A NAME="pgfId=14562"> </A>host_name mycomputer</P><P CLASS="Normal"><A NAME="pgfId=14563"> </A>memory_limit 126062592</P><P CLASS="Normal"><A NAME="pgfId=14564"> </A>working_directory /usr/people/user</P><P CLASS="Normal"><A NAME="pgfId=14565"> </A>user_name user</P><P CLASS="Normal"><A NAME="pgfId=14566"> </A> </P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=14539"> </A>The heading lists general information about the current job. The launch_time, host_name and working_directory fields are useful to help the user archive the run conditions. The memory_limit field refers to the amount of RAM in bytes available to the job. This is can at most be equal to the physical memory of the computer, but may be less if limits have been imposed on the users shell. If the job requires more RAM than is available, then execution is stopped and an error message is reported.</P><P CLASS="Body"><A NAME="pgfId=14368"> </A> </P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14537"> </A>Parameters</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=14401"> </A>________________General_Parameters________________</P><P CLASS="Normal"><A NAME="pgfId=14403"> </A>flexible_ligand no</P><P CLASS="Normal"><A NAME="pgfId=14404"> </A>orient_ligand no</P><P CLASS="Normal"><A NAME="pgfId=14405"> </A>multiple_ligands yes</P><P CLASS="Normal"><A NAME="pgfId=14406"> </A>score_ligand no</P><P CLASS="Normal"><A NAME="pgfId=27138"> </A>chemical_screen no</P><P CLASS="Normal"><A NAME="pgfId=14407"> </A>parallel_jobs no</P><P CLASS="Normal"><A NAME="pgfId=14408"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14409"> </A>____________Multiple_Ligand_Parameters____________</P><P CLASS="Normal"><A NAME="pgfId=14410"> </A>ligands_maximum <infinity></P><P CLASS="Normal"><A NAME="pgfId=14411"> </A>initial_skip 0</P><P CLASS="Normal"><A NAME="pgfId=14412"> </A>interval_skip 0</P><P CLASS="Normal"><A NAME="pgfId=14413"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14414"> </A>____________________File_Input____________________</P><P CLASS="Normal"><A NAME="pgfId=14415"> </A>ligand_atom_file old.mol2</P><P CLASS="Normal"><A NAME="pgfId=14416"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14417"> </A>____________________File_Output___________________</P><P CLASS="Normal"><A NAME="pgfId=14418"> </A>ligand_none_file new.pdb</P><P CLASS="Normal"><A NAME="pgfId=14374"> </A> </P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=14571"> </A>All input parameters are echoed into the output. In fact, the output file may be used as an input file for another run. This is a useful technique to clean up an old, cluttered input file and make a tidy, well-organized input file.</P><P CLASS="Body"><A NAME="pgfId=14573"> </A>This particular parameter list is nearly the shortest possible since most general parameters have been turned off. It is constructed automatically when dock is used to convert a molecule file format (see <A HREF="Manual.17.html#34053" CLASS="XRef">Molecule File Conversion on page 54</A>).</P><P CLASS="Body"><A NAME="pgfId=14586"> </A>If a parameter is not needed it is not reported in the output. The user can override this feature and force all parameters to be written out by using the -v flag (see <A HREF="Manual.17.html#20437" CLASS="XRef">Command-line Arguments on page 53</A>).</P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14419"> </A>Results</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=14462"> </A>_________________________Docking_Results_______________________</P><P CLASS="Normal"><A NAME="pgfId=14463"> </A>Name : ligand1</P><P CLASS="Normal"><A NAME="pgfId=14464"> </A>Description : ****</P><P CLASS="Normal"><A NAME="pgfId=14465"> </A>Orientations tried : 616</P><P CLASS="Normal"><A NAME="pgfId=14466"> </A>Orientations scored : 500</P><P CLASS="Normal"><A NAME="pgfId=14467"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14468"> </A>Best energy score : -59.02</P><P CLASS="Normal"><A NAME="pgfId=14469"> </A> Intramolecular energy score : 12.18</P><P CLASS="Normal"><A NAME="pgfId=14470"> </A> Intermolecular energy score : -71.20</P><P CLASS="Normal"><A NAME="pgfId=14471"> </A>RMSD of best energy scorer (A) : 2.39</P><P CLASS="Normal"><A NAME="pgfId=14472"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14473"> </A>Elapsed cpu time (sec) : 492.87</P><P CLASS="Normal"><A NAME="pgfId=14446"> </A> </P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=14594"> </A>The docking results of each molecule are output as above. In terse mode (-t flag) all results are printed on a single line.</P><P CLASS="Body"><A NAME="pgfId=14639"> </A>This particular output is from the flexible docking of a molecule.</P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14420"> </A><A NAME="38444"> </A>Performance</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=14477"> </A>______________________Docking_Performance______________________</P><P CLASS="Normal"><A NAME="pgfId=14478"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14479"> </A>Procedure timings time (s) percent</P><P CLASS="Normal"><A NAME="pgfId=14480"> </A>Read 0.11 0</P><P CLASS="Normal"><A NAME="pgfId=14481"> </A>Screen 0.00 0</P><P CLASS="Normal"><A NAME="pgfId=14482"> </A>Orientation Search 0.48 0</P><P CLASS="Normal"><A NAME="pgfId=14483"> </A>Orientation Score 49.90 10</P><P CLASS="Normal"><A NAME="pgfId=14484"> </A>Conformation Anchor 0.05 0</P><P CLASS="Normal"><A NAME="pgfId=14485"> </A>Conformation Peripheral 442.38 90</P><P CLASS="Normal"><A NAME="pgfId=14486"> </A>Other 0.02 0</P><P CLASS="Normal"><A NAME="pgfId=14487"> </A>Total 492.94 100</P><P CLASS="Normal"><A NAME="pgfId=14488"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14489"> </A>Minimizer usage minimum average maximum</P><P CLASS="Normal"><A NAME="pgfId=14490"> </A>Calls per molecule 4200 4200 4200</P><P CLASS="Normal"><A NAME="pgfId=22433"> </A>Score improvement per call 0 2.7e+10 8.7e+13</P><P CLASS="Normal"><A NAME="pgfId=14491"> </A>Vertices per call 1 3 6</P><P CLASS="Normal"><A NAME="pgfId=14492"> </A>Cycles per call 1 2 5</P><P CLASS="Normal"><A NAME="pgfId=14494"> </A>Iterations per cycle 1 15 100</P><P CLASS="Normal"><A NAME="pgfId=14457"> </A> </P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=14640"> </A>This section of the output is generated if the user used the -p command-line flag (see <A HREF="Manual.17.html#20437" CLASS="XRef">Command-line Arguments on page 53</A>). It is intended to help the user to understand the performance bottlenecks of a particular run and to make informed parameter choices. Since minimization can consume significant portions of cpu time, it is profiled in more detail.</P><P CLASS="Body"><A NAME="pgfId=14421"> </A>This particular output is from a flexible docking run in which a majority of the cpu time is spent during the peripheral conformation search.</P><P CLASS="Body"><A NAME="pgfId=22221"> </A> </P><DIV><H6 CLASS="New-Page"><A NAME="pgfId=7057"> </A> </H6></DIV></DIV><CENTER><P>⌨️ 快捷键说明
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