Mercurial > repos > chemteam > ambertools_acpype
view acpype.xml @ 4:f4230f116196 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3664d8011044773cc3250ce15d712d97b0b91373"
author | chemteam |
---|---|
date | Tue, 07 Apr 2020 08:10:40 -0400 |
parents | 0d640d752e8a |
children | 27ee142314a9 |
line wrap: on
line source
<tool id="ambertools_acpype" name="Generate MD topologies for small molecules" version="@VERSION@"> <description>using acpype</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="2019.10.05.12.26">acpype</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ ln -s '$input1' ./input1.${input1.ext} && acpype -i './input1.${input1.ext}' -n '$charge' -b base -m '$multiplicity' -a '$atomtype' -o gmx ]]></command> <inputs> <param name="input1" type="data" format="pdb,mol2" label="Input file" help="Structure of the compound in pdb or mol2 format"/> <param name="charge" type="integer" value="0" label="Charge of the molecule"/> <param name="multiplicity" type="integer" value="1" label="Multiplicity" help="Default value is 1, which is correct for almost all organic molecules."/> <param name="atomtype" type="select" value="gaff" label="Force field to use for parameterization"> <option value="gaff">gaff</option> <option value="amber">AMBER14SB</option> <option value="gaff2">gaff2</option> <option value="amber2">AMBER14SB + gaff2</option> </param> <param name="save_gro" type="boolean" value="false" label="Save GRO file?" help="Save atomic coordinates of ligand in GRO format."/> </inputs> <outputs> <data format="itp" name="output" label="Topology" from_work_dir='base.acpype/base_GMX.itp'/> <data format="gro" name="gro_output" label="Structure file (GRO format, optional)" from_work_dir="base.acpype/base_GMX.gro"> <filter>save_gro</filter> </data> </outputs> <tests> <test> <param name="input1" value="JZ4.mol2"/> <param name="save_gro" value="True"/> <output name="output"> <assert_contents> <has_line line="[ atoms ]"/> <has_text text=" 15 ha 1 JZ4 H4 15 0.13"/> <has_text text=" 18 hc 1 JZ4 H7 18 0.05"/> </assert_contents> </output> <output name="gro_output" file="base_GMX.gro" lines_diff="2"/> </test> </tests> <help><![CDATA[ Tool to produce GROMACS topologies for small molecules using the acpype interface to AmberTools. .. class:: infomark **Input** Either a mol2 file (more appropriate for small structures) or a pdb file. If you want to parameterize a large macromolecule (which is more likely to be stored in PDB format, e.g. a protein) consider using a tool such as 'GROMACS initial setup' instead. .. class:: infomark **Outputs** GROMACS topology for the ligand, in itp format. Optional: structure file, in gro format. ]]></help> <expand macro="citations"> <citation type="doi">doi:10.1186/1756-0500-5-367</citation> </expand> </tool>