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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> Ligand Preparation</TITLE></HEAD><BODY BGCOLOR="#ffffff"><H2 CLASS="Heading-3"><A NAME="pgfId=177"> </A>Ligand Preparation</H2><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=889"> </A>Single Ligand</H6><P CLASS="Body"><A NAME="pgfId=890"> </A>Before you can dock a ligand, you will need atom types and charges for every atom in the ligand. It is recommended that you use <A NAME="marker=5696"> </A><A HREF="Manual.41.html#19711" CLASS="XRef">SYBYL MOL2 format</A> for the ligand file since it contains fields for atom types and charges. For a single ligand (or several ligands), you can use <A NAME="marker=5700"> </A><A HREF="Manual.4d.html#17787" CLASS="XRef">sybyl</A> to prepare a MOL2 file for the ligand.</P></DIV><DIV><H6 CLASS="Heading-5"><A NAME="pgfId=907"> </A>Ligand Database</H6><P CLASS="Body"><A NAME="pgfId=908"> </A>Check if a database of ligands has already been prepared at your site. Again, we recommend that this database be in <A HREF="Manual.41.html#19711" CLASS="XRef">SYBYL MOL2 format</A>. If the MOL2 database does not exist, then you will need to construct it. Typically, the <A NAME="marker=5710"> </A><A HREF="Manual.4d.html#21563" CLASS="XRef">Available Chemicals Directory</A> (ACD) is used as a ligand database. This database is distributed by Molecular Design Ltd. (San Leandro, CA) for use with the <A NAME="marker=5714"> </A><A HREF="Manual.4d.html#18574" CLASS="XRef">isis</A> database package. The ACD can be output from isis in an SD-format file. Use <A NAME="marker=5728"> </A><A HREF="Manual.3c.html#32170" CLASS="XRef">sdf2mol2 & sybdb</A> to generate a MOL2 file from the SD file. This conversion requires <A NAME="marker=5727"> </A><A HREF="Manual.4d.html#17787" CLASS="XRef">sybyl</A> (from Tripos) to assign atom types and charges.</P></DIV><CENTER><P>⌨️ 快捷键说明
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