Mercurial > repos > chemteam > gmx_setup

annotate setup.xml @ 6:c7bcae9fe040 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
author chemteam
date Wed, 20 Nov 2019 11:16:14 -0500
parents b43abebffad6
children 4da9ee404eab
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1 <tool id="gmx_setup" name="GROMACS initial setup" version="@VERSION@">
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2 <description>of topology and GRO structure file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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7 <expand macro="requirements" />
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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9 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$pdb_input' ./pdb_input.pdb &&
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12 gmx pdb2gmx -f ./pdb_input.pdb -o processed.gro -p topol.top -i posres.itp -water $water -ff $ff -${ignore_h}ignh -merge all &>> verbose.txt
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644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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14 ]]></command>
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16 <inputs>
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17 <param argument="pdb_input" type="data" format='pdb' label="PDB input file" help="Input structure"/>
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18 <param argument="water" type="select" label="Water model" help="Model for simulating water molecules in the solvent">
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19 <option value="tip3p" selected="true">TIP3P</option>
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20 <option value="tip4p">TIP4P</option>
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21 <option value="tips3p">TIPS3P</option>
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22 <option value="tip5p">TIP5P</option>
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23 <option value="spc">SPC</option>
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24 <option value="spce">SPC/E</option>
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25 <option value="none">None</option>
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26 </param>
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28 <param argument="ff" type="select" label="Force field" help="Specify a molecular force field">
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29 <option value="oplsaa" selected="true">OPLS/AA</option>
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30 <option value="gromos43a1">GROMOS43A1</option>
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31 <option value="amber96">AMBER96</option>
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32 <option value="gromos53a6">GROMOS53A6</option>
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33 <option value="amber99sb-ildn">AMBER99SB-ILDN</option>
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34 <option value="amber99sb">AMBER99SB</option>
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35 <option value="gromos53a5">GROMOS53A5</option>
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36 <option value="gromos43a2">GROMOS43A2</option>
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37 <option value="amberGS">AMBERGS</option>
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38 <option value="charmm27">CHARMM27</option>
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39 <option value="amber03">AMBER03</option>
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40 <option value="gromos54a7">GROMOS54A7</option>
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41 <option value="gromos45a3">GROMOS45A3</option>
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42 <option value="amber99">AMBER99</option>
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43 <option value="amber94">AMBER94</option>
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44 </param>
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45
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46 <param argument="ignore_h" type="boolean" label="Ignore hydrogens" truevalue="" falsevalue="no" help="Ignore hydrogen atoms that are in the coordinate file." />
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47
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48 <expand macro="log" />
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50 </inputs>
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51 <outputs>
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52 <data name="output1" format="top" from_work_dir="topol.top"/>
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53 <data name="output2" format="gro" from_work_dir="processed.gro"/>
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54 <data name="output3" format="itp" from_work_dir="posres.itp"/>
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55 <expand macro="log_outputs" />
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56 </outputs>
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57 <tests>
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58 <test>
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59 <param name="pdb_input" value="1AKI.pdb" />
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60 <param name="water" value="spce" />
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61 <param name="ff" value="oplsaa" />
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62 <param name="ignore_h" value="no" />
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63 <param name="box_d" value="1.0" />
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64 <param name="box_type" value="cubic" />
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65 <output name="output1" file="topol.top" ftype="top" compare="diff" lines_diff="20"/>
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66 <output name="output2" file="processed.gro" ftype="gro"/>
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67 <output name="output3" file="posres.itp" ftype="itp"/>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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72 .. class:: infomark
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74 **What it does**
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75
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76 This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command.
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78 Please note that the tool will only successfully generate a topology for residues it recognizes (i.e. standard amino acids). If the structure contains other components such as ligands, these should be separately parameterized with the AmberTools or ACPYPE tools. In this case, make sure to also use an AMBER forcefield for this tool to ensure compatability with the ligand topology.
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80 _____
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82 .. class:: infomark
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84 **Input**
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85
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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86 - PDB file.
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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87 - Water model and forcefield must be specified.
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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88
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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89 _____
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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90
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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91
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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92 .. class:: infomark
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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93
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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94 **Output**
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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95
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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96 - GROMACS topology (TOP) file.
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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97 - Position restraint (itp) file, which may be useful for system equilibration.
b43abebffad6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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98 - GRO structure file.
0
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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99
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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100 ]]></help>
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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101
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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102 <expand macro="citations" />
644ca8dfdf28 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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103 </tool>