manual.41.html

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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> SYBYL MOL2 format</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=4507"> </A><A NAME="19711"> </A>SYBYL MOL2 format</H2><P CLASS="Body"><A NAME="pgfId=21580"> </A>This format is used for general molecule input and output of dock.  Although previous versions of dock supported an extended PDB format to store molecule information, the current version now uses MOL2 as the primary molecule format.  This format has the advantage of storing all the necessary information for atom features, position, and connectivity.  It is also a standardized format that other modeling programs can read.</P><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=16667"> </A>Specification</H3><P CLASS="Body"><A NAME="pgfId=16672"> </A>Please refer to sybyl documentation for format specifications.</P><P CLASS="Body"><A NAME="pgfId=21659"> </A>Of the many record types in a MOL2 file, dock recognizes the following: MOLECULE, ATOM, BOND, SUBSTRUCTURE and SET.  In the MOLECULE record, dock utilizes information about the molecule name and number of atoms, bonds, substructures and sets.  In the ATOM record dock utilizes information about the atom names, types, coordinates, and partial charges.  In the BOND record, dock utilizes the atom identifiers for the bond.  In the SUBSTRUCTURE record, dock records the fields, but does not utilize them.  The SET records are entirely optional.  They are used only in special circumstances, like when <A HREF="Manual.19.html#33669" CLASS="XRef">Ligand Flexibility</A> is considered..</P></DIV><DIV><H3 CLASS="Heading-4"><A NAME="pgfId=21574"> </A>Example</H3><P CLASS="Body"><A NAME="pgfId=21577"> </A>This example file illustrates all the elements of the MOL2 file read and written by dock.  It includes optional SET records which are used by the <A HREF="Manual.19.html#33669" CLASS="XRef">Ligand Flexibility</A> routines.</P><P CLASS="Body"><A NAME="pgfId=16679"> </A>&nbsp;</P><TABLE><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21665"> </A>@&lt;TRIPOS&gt;MOLECULE</P><P CLASS="Normal"><A NAME="pgfId=21666"> </A>Histidine</P><P CLASS="Normal"><A NAME="pgfId=21667"> </A>   20    20     1     0     2</P><P CLASS="Normal"><A NAME="pgfId=21668"> </A>SMALL</P><P CLASS="Normal"><A NAME="pgfId=21669"> </A>GASTEIGER</P><P CLASS="Normal"><A NAME="pgfId=21670"> </A>****</P><P CLASS="Normal"><A NAME="pgfId=21671"> </A>Histidine with Main Chain as Rigid Anchor</P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21673"> </A>@&lt;TRIPOS&gt;ATOM</P><P CLASS="Normal"><A NAME="pgfId=21674"> </A>      1 N1         -1.0947    0.5371    1.7186 N.4       1 &lt;1&gt;         0.2252 </P><P CLASS="Normal"><A NAME="pgfId=21675"> </A>      2 C2         -0.9885    0.9170    0.2765 C.3       1 &lt;1&gt;         0.0213 </P><P CLASS="Normal"><A NAME="pgfId=21676"> </A>      3 C3         -0.2043   -0.1565   -0.4766 C.3       1 &lt;1&gt;         0.0354 </P><P CLASS="Normal"><A NAME="pgfId=21677"> </A>      4 C4         -2.3725    1.0376   -0.3154 C.2       1 &lt;1&gt;         0.0897 </P><P CLASS="Normal"><A NAME="pgfId=21678"> </A>      5 O5         -2.7546    2.1336   -0.8057 O.co2     1 &lt;1&gt;        -0.5442 </P><P CLASS="Normal"><A NAME="pgfId=21679"> </A>      6 C6          1.1797   -0.2771    0.1153 C.2       1 &lt;1&gt;         0.0328 </P><P CLASS="Normal"><A NAME="pgfId=21680"> </A>      7 N7          2.2791    0.4215   -0.2757 N.pl3     1 &lt;1&gt;        -0.3074 </P><P CLASS="Normal"><A NAME="pgfId=21681"> </A>      8 C8          1.5387   -1.0911    1.1173 C.2       1 &lt;1&gt;         0.0462 </P><P CLASS="Normal"><A NAME="pgfId=21682"> </A>      9 C9          3.3256    0.0285    0.4990 C.2       1 &lt;1&gt;         0.0853 </P><P CLASS="Normal"><A NAME="pgfId=21683"> </A>     10 N10         2.9039   -0.8872    1.3511 N.2       1 &lt;1&gt;        -0.2465 </P><P CLASS="Normal"><A NAME="pgfId=21684"> </A>     11 H11        -1.6259    1.2643    2.2287 H         1 &lt;1&gt;         0.2001 </P><P CLASS="Normal"><A NAME="pgfId=21685"> </A>     12 O12        -3.1452    0.0423   -0.3188 O.co2     1 &lt;1&gt;        -0.5442 </P><P CLASS="Normal"><A NAME="pgfId=21686"> </A>     13 H13        -0.1461    0.4545    2.1242 H         1 &lt;1&gt;         0.2001 </P><P CLASS="Normal"><A NAME="pgfId=21687"> </A>     14 H14        -0.4726    1.8710    0.1898 H         1 &lt;1&gt;         0.0918 </P><P CLASS="Normal"><A NAME="pgfId=21688"> </A>     15 H15        -0.7202   -1.1105   -0.3899 H         1 &lt;1&gt;         0.0385 </P><P CLASS="Normal"><A NAME="pgfId=21689"> </A>     16 H16        -0.1270    0.1200   -1.5261 H         1 &lt;1&gt;         0.0385 </P><P CLASS="Normal"><A NAME="pgfId=21690"> </A>     17 H17         2.3126    1.1114   -1.0125 H         1 &lt;1&gt;         0.1528 </P><P CLASS="Normal"><A NAME="pgfId=21691"> </A>     18 H18         0.8943   -1.7774    1.6466 H         1 &lt;1&gt;         0.0845 </P><P CLASS="Normal"><A NAME="pgfId=21692"> </A>     19 H19         4.3357    0.4040    0.4286 H         1 &lt;1&gt;         0.1000 </P><P CLASS="Normal"><A NAME="pgfId=21693"> </A>     20 H20        -1.5855   -0.3703    1.8010 H         1 &lt;1&gt;         0.2001 </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21695"> </A>@&lt;TRIPOS&gt;BOND</P><P CLASS="Normal"><A NAME="pgfId=21696"> </A>     1    1    2 1    </P><P CLASS="Normal"><A NAME="pgfId=21697"> </A>     2    2    3 1    </P><P CLASS="Normal"><A NAME="pgfId=21698"> </A>     3    2    4 1    </P><P CLASS="Normal"><A NAME="pgfId=21699"> </A>     4    3    6 1    </P><P CLASS="Normal"><A NAME="pgfId=21700"> </A>     5    4    5 ar   </P><P CLASS="Normal"><A NAME="pgfId=21701"> </A>     6    6    7 1    </P><P CLASS="Normal"><A NAME="pgfId=21702"> </A>     7    6    8 2    </P><P CLASS="Normal"><A NAME="pgfId=21703"> </A>     8    7    9 1    </P><P CLASS="Normal"><A NAME="pgfId=21704"> </A>     9    8   10 1    </P><P CLASS="Normal"><A NAME="pgfId=21705"> </A>    10    9   10 2    </P><P CLASS="Normal"><A NAME="pgfId=21706"> </A>    11    1   11 1    </P><P CLASS="Normal"><A NAME="pgfId=21707"> </A>    12    4   12 ar   </P><P CLASS="Normal"><A NAME="pgfId=21708"> </A>    13    1   13 1    </P><P CLASS="Normal"><A NAME="pgfId=21709"> </A>    14    2   14 1    </P><P CLASS="Normal"><A NAME="pgfId=21710"> </A>    15    3   15 1    </P><P CLASS="Normal"><A NAME="pgfId=21711"> </A>    16    3   16 1    </P><P CLASS="Normal"><A NAME="pgfId=21712"> </A>    17    7   17 1    </P><P CLASS="Normal"><A NAME="pgfId=21713"> </A>    18    8   18 1    </P><P CLASS="Normal"><A NAME="pgfId=21714"> </A>    19    9   19 1    </P><P CLASS="Normal"><A NAME="pgfId=21715"> </A>    20    1   20 1    </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21717"> </A>@&lt;TRIPOS&gt;SUBSTRUCTURE</P><P CLASS="Normal"><A NAME="pgfId=21718"> </A>     1 ****        1 TEMP              0 ****  ****    0 ROOT </P></TD></TR><TR><TD ROWSPAN="1" COLSPAN="1"><P CLASS="Normal"><A NAME="pgfId=21720"> </A>@&lt;TRIPOS&gt;SET</P><P CLASS="Normal"><A NAME="pgfId=21721"> </A>ANCHOR          STATIC     ATOMS    &lt;user&gt;   **** Anchor Atom Set</P><P CLASS="Normal"><A NAME="pgfId=21722"> </A>1 2</P><P CLASS="Normal"><A NAME="pgfId=21723"> </A>RIGID           STATIC     BONDS    &lt;user&gt;   **** Rigid Bond Set</P><P CLASS="Normal"><A NAME="pgfId=21724"> </A>2 1 3</P></TD></TR></TABLE></DIV><CENTER><P>

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