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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> Parameter Files</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-2"><A NAME="pgfId=4869"> </A>Parameter Files</H2><DIV><H4 CLASS="Heading-4"><A NAME="pgfId=4871"> </A>Introduction</H4><P CLASS="Body"><A NAME="pgfId=20030"> </A>The parameter files contain atom and bond data needed during dock calculations. The definition (*.defn) files contain atom and bond labeling data. The table (*.tbl) files contain additional data for chemical interactions and flexible bond torsion positions. They may be edited by the user. </P></DIV><DIV><H4 CLASS="Heading-4"><A NAME="pgfId=19655"> </A><A NAME="43103"> </A>Atom definition rules</H4><P CLASS="Body"><A NAME="pgfId=19656"> </A>The definition files use a consistent atom labeling convention for which an atom in virtually any chemical environment can be identified. The specification of adjacent atoms is nested using the elements listed in <A HREF="Manual.45.html#12342" CLASS="XRef">Table 7.</A> Some sample definitions are provided in <A HREF="Manual.45.html#22276" CLASS="XRef">Table 8.</A></P><UL><LI CLASS="Body-Bullet"><A NAME="pgfId=20253"> </A>Each element must be separated by a space.</LI><LI CLASS="Body-Bullet"><A NAME="pgfId=20254"> </A>If more than one adjacent atom is specified, then ALL must be present (i.e. a boolean AND for rules within a line).</LI><LI CLASS="Body-Bullet"><A NAME="pgfId=20255"> </A>If a label can have multiple definition lines, then any ONE of them must be satisfied for inclusion (i.e. a boolean OR for rules on different lines).</LI></UL><H3 CLASS="Table"><A NAME="pgfId=19660"> </A>Table 7. <A NAME="12342"> </A>Atom definition elements</H3><TABLE><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19663"> </A>element</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19665"> </A>function</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19689"> </A>atom type</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19669"> </A>Specifies partial or complete atom type. A partial specification is more general (i.e. "C" versus "C.3"). An asterisk (*) specifies ANY atom type.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19704"> </A>( )</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19695"> </A>Specifies atoms that must be bonded to parent atom.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19682"> </A>[ ]</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19673"> </A>Specifies atoms that must NOT be bonded to parent atom.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19697"> </A>integer</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19699"> </A>Specifies the number of an atom that must be bonded.</P></TD></TR></TABLE><H3 CLASS="Table"><A NAME="pgfId=19970"> </A>Table 8. <A NAME="22276"> </A>Example definitions</H3><TABLE><TR><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19974"> </A>example</P></TH><TH ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19976"> </A>explanation</P></TH></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19982"> </A>C.2 ( 2 O.co2 )</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19984"> </A>A carboxylate carbon.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19986"> </A>.3 [ 3 H ]</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=19988"> </A>Any sp3 hybridized atom that is not attached to three hydrogens.</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=20027"> </A>C. [ O. ] [ N. [ 2 O.2 ] [ 2 C. ] ]</P></TD><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=20029"> </A>Any carbon not attached to an oxygen or a nitrogen (unless the nitrogen is a nitro or tertiary nitrogen).</P></TD></TR></TABLE></DIV><H3 CLASS="Heading-3TOC"><A HREF="Manual.46.html#pgfId=5015" CLASS="Hypertext">vdw.defn</A></H3><H3 CLASS="Heading-3TOC"><A HREF="Manual.47.html#pgfId=20180" CLASS="Hypertext">chem.defn</A></H3><H3 CLASS="Heading-3TOC"><A HREF="Manual.48.html#pgfId=20215" CLASS="Hypertext">chem_match.tbl</A></H3><H3 CLASS="Heading-3TOC"><A HREF="Manual.49.html#pgfId=19482" CLASS="Hypertext">chem_score.tbl</A></H3><H3 CLASS="Heading-3TOC"><A HREF="Manual.4a.html#pgfId=19483" CLASS="Hypertext">chem_screen.tbl</A></H3><H3 CLASS="Heading-3TOC"><A HREF="Manual.4b.html#pgfId=19484" CLASS="Hypertext">flex.defn</A></H3><H3 CLASS="Heading-3TOC"><A HREF="Manual.4c.html#pgfId=19485" CLASS="Hypertext">flex_drive.tbl</A></H3><CENTER><P>?? 快捷鍵說明
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