Mercurial > repos > chemteam > gmx_setup

annotate setup.xml @ 4:b4a5cd662f89 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
author chemteam
date Mon, 07 Oct 2019 12:38:50 -0400
parents a0864cc9ac24
children 811e12c235e1
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1 <tool id="gmx_setup" name="GROMACS initial setup" version="@VERSION@">
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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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a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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7 <expand macro="requirements" />
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9 <command detect_errors="exit_code"><![CDATA[
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11 ln -s '$pdb_input' ./pdb_input.pdb &&
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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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 &>> verbose.txt &&
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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13 gmx editconf -f processed.gro -o newbox.gro -c -d $box_d -bt $box_type &>> verbose.txt
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15 ]]></command>
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17 <inputs>
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18 <!-- PDB2GMX VARS -->
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19 <param argument="pdb_input" type="data" format='pdb' label="PDB input file" help="Input structure"/>
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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20 <param argument="water" type="select" label="Water model" help="Model for simulating water molecules in the solvent">
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21 <option value="tip3p" selected="true">TIP3P</option>
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22 <option value="tip4p">TIP4P</option>
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23 <option value="tips3p">TIPS3P</option>
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24 <option value="tip5p">TIP5P</option>
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25 <option value="spc">SPC</option>
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26 <option value="spce">SPC/E</option>
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27 <option value="none">None</option>
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28 </param>
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29
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30 <param argument="ff" type="select" label="Force field" help="Specify a molecular force field">
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31 <option value="oplsaa" selected="true">OPLS/AA</option>
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32 <option value="gromos43a1">GROMOS43A1</option>
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33 <option value="amber96">AMBER96</option>
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34 <option value="gromos53a6">GROMOS53A6</option>
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35 <option value="amber99sb-ildn">AMBER99SB-ILDN</option>
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36 <option value="amber99sb">AMBER99SB</option>
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37 <option value="gromos53a5">GROMOS53A5</option>
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38 <option value="gromos43a2">GROMOS43A2</option>
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39 <option value="amberGS">AMBERGS</option>
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40 <option value="charmm27">CHARMM27</option>
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41 <option value="amber03">AMBER03</option>
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42 <option value="gromos54a7">GROMOS54A7</option>
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43 <option value="gromos45a3">GROMOS45A3</option>
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44 <option value="amber99">AMBER99</option>
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45 <option value="amber94">AMBER94</option>
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46 </param>
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47
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48 <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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49
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50 <!-- EDITCONF VARS -->
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51 <param argument="box_d" type="float" label="Box dimensions in nanometers" value="0.0" min="0.0" max="10.0" help="Dimensions of the box in which simulation will take place" />
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52 <param argument="box_type" type="select" label="Box type"
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53 help="triclinic is a triclinic box, cubic is a rectangular box with all sides equal dodecahedron represents a rhombic dodecahedron and octahedron is a truncated octahedron. The last two are special cases of a triclinic box. The length of the three box vectors of the truncated octahedron is the shortest distance between two opposite hexagons. Relative to a cubic box with some periodic image distance, the volume of a dodecahedron with this same periodic distance is 0.71 times that of the cube, and that of a truncated octahedron is 0.77 times.">
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54 <option value="cubic">Rectangular box with all sides equal</option>
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55 <option value="triclinic">Triclinic</option>
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56 <option value="dodecahedron">represents a rhombic dodecahedron</option>
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57 <option value="octahedron">truncated octahedron</option>
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58 </param>
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59
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60 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
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61
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62 </inputs>
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63 <outputs>
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64 <data name="output1" format="top" from_work_dir="topol.top"/>
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65 <data name="output2" format="gro" from_work_dir="newbox.gro"/>
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66 <data name="output3" format="itp" from_work_dir="posres.itp"/>
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67 <data name="report" format="txt" from_work_dir="verbose.txt">
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68 <filter>capture_log</filter>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <test>
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73 <param name="pdb_input" value="1AKI.pdb" />
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74 <param name="water" value="spce" />
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75 <param name="ff" value="oplsaa" />
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76 <param name="ignore_h" value="no" />
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77 <param name="box_d" value="1.0" />
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78 <param name="box_type" value="cubic" />
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79 <output name="output1" file="topol.top" ftype="top" compare="diff" lines_diff="20"/>
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80 <output name="output2" file="newbox.gro" ftype="gro"/>
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81 <output name="output3" file="posres.itp" ftype="itp"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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85
4
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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86 .. class:: infomark
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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87
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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88 **What it does**
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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89
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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90 This tool performs the initial setup prior to a GROMACS simulation. This entails producing a topology from an input structure using the pdb2gmx command and also defining a simulation box with editconf.
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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91
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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92 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.
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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93
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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94 _____
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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95
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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96 .. class:: infomark
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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97
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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98 **Input**
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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99
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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100 - PDB file.
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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101 - Water model and forcefield must be specified.
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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102 - Parameters for the simulation box (dimensions and shape).
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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103
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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104 _____
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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105
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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106
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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107 .. class:: infomark
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108
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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109 **Output**
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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110
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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111 - GROMACS topology (TOP) file.
b4a5cd662f89 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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112 - Position restraint (itp) file, which may be useful for system equilibration.
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113 - GRO structure file.
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114
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115 ]]></help>
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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116
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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117 <expand macro="citations" />
a0864cc9ac24 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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118 </tool>