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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> hbdata</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=15652"> </A><A NAME="marker=15651"> </A>hbdata</H2><P CLASS="Body"><A NAME="pgfId=3657"> </A>Author: Andy Good</P><P CLASS="Body"><A NAME="pgfId=3665"> </A>This program automatically runs <A HREF="Manual.4d.html#30334" CLASS="XRef">Goodford's grid</A> program (version 11.01, distributed independently; Goodford, 1985) for a variety of probes, creating sybyl contour files and files containing centers of favorable interaction energy for <A HREF="Manual.20.html#17338" CLASS="XRef">sphgen</A> file creation. It also runs grin and will stop if grin encounters a problem with the pdb file. The program requires an input file called hbin which should follow this example:</P><P CLASS="Body"><A NAME="pgfId=3667"> </A> </P><P CLASS="Body"><A NAME="pgfId=3669"> </A>3dfr name of parent protein (pdb file name - used for file naming)</P><P CLASS="Body"><A NAME="pgfId=3671"> </A>/bert/grid11.01 root directory for GRID</P><P CLASS="Body"><A NAME="pgfId=3673"> </A>-12.0 minimum x coordinate</P><P CLASS="Body"><A NAME="pgfId=3675"> </A>26.0 minimum y coordinate</P><P CLASS="Body"><A NAME="pgfId=3677"> </A>4.0 minimum z coordinate</P><P CLASS="Body"><A NAME="pgfId=3679"> </A>9.0 maximum x coordinate</P><P CLASS="Body"><A NAME="pgfId=3681"> </A>48.0 maximum y coordinate</P><P CLASS="Body"><A NAME="pgfId=3683"> </A>33.0 maximum z coordinate</P><P CLASS="Body"><A NAME="pgfId=3685"> </A>1.0 grid density - # of planes per Angstrom of grid map</P><P CLASS="Body"><A NAME="pgfId=3687"> </A>-7.0 highest permitted interaction energy included in site point creation</P><P CLASS="Body"><A NAME="pgfId=3691"> </A>1.0 exclusion sphere to remove local low energy pts. near each local minimum</P><P CLASS="Body"><A NAME="pgfId=3695"> </A>2 # of probes in probe list that will be used - first two are N3+, O::</P><P CLASS="Body"><A NAME="pgfId=3697"> </A> </P><P CLASS="Body"><A NAME="pgfId=3703"> </A>Notes for use in conjunction with <A HREF="Manual.30.html#10859" CLASS="XRef">mol2sph</A>: The grid energy of each point is assigned to the charge field for reference purposes and atom types are set to dummy. Both of these fields must be corrected, the sphgen file converted into pdb format using <A HREF="Manual.3e.html#17130" CLASS="XRef">showsphere</A>, the resulting atom types modified and combined within sybyl before they can be written to MOL2 format in preparation for <A HREF="Manual.30.html#10859" CLASS="XRef">mol2sph</A> conversion. </P><CENTER><P>⌨️ 快捷键说明
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