Mercurial > repos > chemteam > gmx_solvate

annotate solvate.xml @ 6:d0fefb855be6 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 16:03:33 +0000
parents a1255ccf44f2
children ab47c1342cb5
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e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@VERSION@">
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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2 <description>to structure and topology files</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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e85ae7bff197 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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e85ae7bff197 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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e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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11 ln -s '$ions' ./ions.mdp &&
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12 ln -s '$gro_input' ./gro_input.gro &&
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13 ln -s '$top_input' ./top_input.top &&
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d0fefb855be6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt
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17 #if $neutralise == "true":
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18 &&
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19 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt &&
d0fefb855be6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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20 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt &&
d0fefb855be6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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21 mv solv_ions.gro solv.gro
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22 #end if
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23
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0
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25 ]]></command>
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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26 <configfiles>
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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27 <!-- .mdp file for the gromacs simulation -->
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28 <configfile name="ions">
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29 : Parameters are not so important here as no simulation is run
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30 integrator = steep
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31 emtol = 1000.0
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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32 emstep = 0.01
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33 nsteps = 1
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34 nstlist = 1
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35 cutoff-scheme = Verlet
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36 ns_type = grid
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37 coulombtype = cutoff
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38 rcoulomb = 1.0
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39 rvdw = 1.0
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40 pbc = xyz
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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41 </configfile>
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42 </configfiles>
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43 <inputs>
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44 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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45 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
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46 <param name="water_model" type="select" label="Water model for solvation" help="Note SPC is a generic equilibrated 3-point solvent model and can be used as the solvent configuration for any of SPC, SPC/E, or TIP3P water.">
a1255ccf44f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30"
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47 <option value="spc216" selected="true">SPC (generic three-point model)</option>
a1255ccf44f2 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 10f45d117e34624bceb32442742ae0b8eb2dae30"
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48 <option value="tip4p">TIP4P (four-point model)</option>
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49 <option value="tip5p">TIP5P (five-point model)</option>
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50 </param>
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51 <param name="neutralise" label="Add ions to neutralise system?" type="select" help="If system is charged, replace an appropriate number of randomly selected solvent molecules with sodium or chloride ions to neutralise it.">
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52 <option value="true">Yes, add ions</option>
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53 <option value="false">No</option>
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54 </param>
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55
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56 <expand macro="log" />
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57
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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58 </inputs>
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59 <outputs>
6
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60 <data name="output1" format="gro" from_work_dir="solv.gro"/>
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61 <data name="output2" format="top" from_work_dir="./top_input.top"/>
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62 <expand macro="log_outputs" />
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="gro_input" value="newbox.gro" />
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67 <param name="neutralise" value="true" />
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68 <param name="top_input" value="topol.top" />
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69 <param name="water_model" value="spc216" />
6
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70 <output name="output1" ftype="gro">
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71 <!-- replacement of water with ions is random, thus we cannot compare the whole file -->
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72 <assert_contents>
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73 <has_text text="1.014 5.822 2.833"/>
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74 <has_text text="6.831 5.961 6.119"/>
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75 <has_text text="3.592 6.520 5.241"/>
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76 </assert_contents>
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77 </output>
0
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78 <output name="output2" file="topol_solv.top" ftype="top"/>
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79 </test>
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80 <test>
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81 <param name="gro_input" value="newbox.gro" />
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82 <param name="neutralise" value="false" />
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83 <param name="top_input" value="topol.top" />
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84 <param name="water_model" value="spc216" />
d0fefb855be6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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85 <output name="output1" file="solv.gro" ftype="gro"/>
d0fefb855be6 "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa"
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86 </test>
0
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87 </tests>
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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88 <help><![CDATA[
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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89
4
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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90 .. class:: infomark
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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91
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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92 **What it does**
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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93
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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94 This tool solvates a system prior to a GROMACS simulation. In addition, sodium or chloride ions will be added if necessary to ensure the system is charge-neutral.
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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95
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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96 _____
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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97
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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98 .. class:: infomark
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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99
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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100 **Input**
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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101
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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102 - GRO structure file.
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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103 - Topology (TOP) file.
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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104
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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105 In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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106
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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107 _____
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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108
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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109
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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110 .. class:: infomark
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111
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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112 **Output**
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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113
ed5f2bc9db4b "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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114 - GRO structure file.
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115
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116 ]]></help>
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117
e85ae7bff197 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 177cab098ac548bfdecba9d9f04614aec5f6c618
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118 <expand macro="citations" />
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119 </tool>