File: apbs-input.xml

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apbs 1.0.0-2
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<sect1 id="apbs-input"> <title>Input files</title>
	<para> APBS input files are loosely-formatted files which contain
		information about the input, parameters, and output for each calculation.
		These files are whitespace- or linefeed-delimited.  Comments can be added
		to the input files via the <literal>#</literal> character; all text
		between the <literal>#</literal> and the end of the line is not parsed by
		APBS.  Specific examples of APBS input are described in the 
		<link linkend="examples-sect">Examples section</link>.</para>
	<tip>
		<para>Please note that there are several tools which help
			prepare APBS input files based on molecular structures,
			memory constraints, etc.  These tools are described in
			more detail in <xref linkend="problem-setup"/>.</para>
	</tip>

	<para> APBS input files contain three basic sections which can be repeated
		any number of times:
		<itemizedlist>
			<listitem>
				<para>
					<link linkend="read"><command>READ</command></link>:  
					section for specifying input.</para>
			</listitem>
			<listitem>
				<para>
					<link linkend="elec"><command>ELEC</command></link>:  
					section for specifying polar solvation
					(electrostatics) calculation parameters.</para>
			</listitem>
			<listitem>
				<para>
					<link linkend="apolar"><command>APOLAR</command></link>:
					section for specifying apolar solvation
					calculation parameters.</para>

			</listitem>
			<listitem>
				<para>
					<link linkend="print"><command>PRINT</command></link>:  
					section for specifying summary output.</para>
			</listitem>
		</itemizedlist>
		The APBS input file is constructed from these sections in the following
		format:
		<example> <title>Template for APBS input file</title>
			<programlisting>
				READ
				...
				END
				ELEC
				...
				END
				APOLAR
				...
				END
				ELEC
				...
				END
				APOLAR
				...
				END
				PRINT
				...
				END
				QUIT
			</programlisting>
		</example>
	</para>
	<para>These sections can occur in any order, however, they are clearly
		interdependent. For example, <command>PRINT</command> requires
		<command>ELEC</command> and/or <command>APOLAR</command> while
		<command>ELEC</command> requires one or more
		<command>READ</command> sections. Sections can also be
		repeated; several <command>READ</command> statements may be
		used to load molecules and multiple <command>ELEC</command> or
		<command>APOLAR</command> sections would specify various
		electrostatics calculations on one or more molecules.</para>


	<sect2 id="read"> <title>READ statements</title>
		&read-sect;
	</sect2>

	<sect2 id="elec"> <title>ELEC statements</title>
		&elec-sect;
	</sect2>

	<sect2 id="apolar"> <title>APOLAR statements</title>
		&apolar-sect;
	</sect2>

	<sect2 id="print"> <title>PRINT statements</title>
		&print-sect;
	</sect2>

</sect1>