manual.1f.html
来自「最经典的分子对结软件」· HTML 代码 · 共 192 行
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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=1050"> </A>Output</H2><P CLASS="Body"><A NAME="pgfId=1062"> </A>The output of grid contains several types of information. Like dock, it outputs general information about the current job and echoes the parameters selected from the input file. In addition, it reports information about the receptor and the grids.</P><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14660"> </A>Receptor information</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=14717"> </A>Reading in coordinates of receptor.</P><P CLASS="Normal"><A NAME="pgfId=14718"> </A>Merging AMN 163 cap residue with THR1 1 residue.</P><P CLASS="Normal"><A NAME="pgfId=14719"> </A>Merging CXL 164 cap residue with ALA162 162 residue.</P><P CLASS="Normal"><A NAME="pgfId=14720"> </A>CHARGED RESIDUE THR1 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14721"> </A>CHARGED RESIDUE ARG9 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14734"> </A>CHARGED RESIDUE LYS51 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14735"> </A>CHARGED RESIDUE ARG52 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14736"> </A>CHARGED RESIDUE GLU56 : -1.000</P><P CLASS="Normal"><A NAME="pgfId=14737"> </A>CHARGED RESIDUE ARG57 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14741"> </A>CHARGED RESIDUE HIP77 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14742"> </A>CHARGED RESIDUE ASP78 : -1.000</P><P CLASS="Normal"><A NAME="pgfId=14754"> </A>CHARGED RESIDUE LYS127 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14760"> </A>CHARGED RESIDUE ASP146 : -1.000</P><P CLASS="Normal"><A NAME="pgfId=14761"> </A>CHARGED RESIDUE HIP153 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14762"> </A>CHARGED RESIDUE GLU156 : -1.000</P><P CLASS="Normal"><A NAME="pgfId=14764"> </A>CHARGED RESIDUE LYS161 : 1.000</P><P CLASS="Normal"><A NAME="pgfId=14765"> </A>CHARGED RESIDUE ALA162 : -1.000</P><P CLASS="Normal"><A NAME="pgfId=14766"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14767"> </A>Total charge on UNNAMED : 4.000</P><P CLASS="Normal"><A NAME="pgfId=14663"> </A> </P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=14784"> </A>This portion of the output lists any merged cap residues. The cap residues are introduced by sybyl. Charged residues are also listed. If any residues have a non-integer charge, then either the charges were not properly loaded into the receptor input file, or some atoms are missing from the input file. These problems should be resolved before continuing with the grid calculation.</P><P CLASS="Body"><A NAME="pgfId=14787"> </A>To display more information about parameters that grid assigns to the receptor, use the -v option (see <A HREF="Manual.1d.html#42263" CLASS="XRef">Command-line Arguments on page 79</A>).</P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=14798"> </A>Grid Information</H3><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=14825"> </A>Reading in grid box information.</P><P CLASS="Normal"><A NAME="pgfId=14826"> </A>Box center of mass : -1.315 36.145 21.153</P><P CLASS="Normal"><A NAME="pgfId=14827"> </A>Box dimensions : 27.525 26.519 26.686</P><P CLASS="Normal"><A NAME="pgfId=14828"> </A>Number of grid points per side [x y z] : 93 90 90</P><P CLASS="Normal"><A NAME="pgfId=14829"> </A>Total number of grid points : 753300</P><P CLASS="Normal"><A NAME="pgfId=14830"> </A> </P><P CLASS="Normal"><A NAME="pgfId=14831"> </A>Generating scoring grids.</P><P CLASS="Normal"><A NAME="pgfId=14834"> </A>Percent of protein atoms processed : 0</P><P CLASS="Normal"><A NAME="pgfId=14836"> </A>Percent of protein atoms processed : 10</P><P CLASS="Normal"><A NAME="pgfId=14838"> </A>Percent of protein atoms processed : 20</P><P CLASS="Normal"><A NAME="pgfId=14822"> </A>...etc...</P><P CLASS="Normal"><A NAME="pgfId=14839"> </A> </P></TD></TR></TABLE><P CLASS="Body"><A NAME="pgfId=14799"> </A>Information about the grid geometry is reported. The total number of grid points can be adjusted by changing the input box dimensions or changing the grid spacing. Generally a value under 1 million is appropriate, but this depends on system resources.</P><P CLASS="Body"><A NAME="pgfId=14842"> </A>The progress of the calculation is reported as the percent of protein atoms processed. This calculation usually takes up to 30 minutes depending on the grid geometry and the receptor size.</P><DIV><H6 CLASS="New-Page"><A NAME="pgfId=2947"> </A> </H6></DIV></DIV><CENTER><P>⌨️ 快捷键说明
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