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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ForceFields]-->
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4 <tool id="CalculateSolvationFreeEnergy" name="CalculateSolvationFreeEnergy" version="1.1.0">
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5 <description>calculate solvation free energy of a protein using AMBER </description>
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6 <macros>
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7 <token name="@EXECUTABLE@">CalculateSolvationFreeEnergy</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>CalculateSolvationFreeEnergy
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13
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14 #if $param_pdb:
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15 -pdb $param_pdb
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16 #end if
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17 #if $param_epsilon_medium:
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18 -epsilon_medium $param_epsilon_medium
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19 #end if
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20 #if $param_epsilon_vacuum:
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21 -epsilon_vacuum $param_epsilon_vacuum
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22 #end if
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23 </command>
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24 <inputs>
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25 <param name="param_pdb" type="data" format="pdb" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input pdb file" help="(-pdb) "/>
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26 <param name="param_epsilon_medium" type="float" value="0.0" label="dielectric constant in medium" help="(-epsilon_medium) "/>
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27 <param name="param_epsilon_vacuum" type="float" value="1.0" label="dielectric constant in vacuum" help="(-epsilon_vacuum) "/>
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28 </inputs>
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29 <expand macro="advanced_options"/>
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30 <outputs>
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31 <data name="param_stdout" format="text" label="Output from stdout"/>
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32 </outputs>
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33 <help>This tool computes the solvation free energy of a pdb file using the Jackson-Sternberg approach (bonded energy using a force field and a non bonded energy (electrostatics only) by solving the Poisson-Boltzmann equation. Parameters are the dielectric constants for the medium (-epsilon_medium) and the vacuum (-epsilon_vacuum).
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34
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35 </help>
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36 </tool>
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