Mercurial > repos > chemteam > gmx_solvate

annotate solvate.xml @ 3:7161b230adad 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 12:47:31 -0400
parents 77aaf9a68166
children cdacad684da1
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77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@VERSION@">
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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2 <description>to structure and topology files</description>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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3 <macros>
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4 <import>macros.xml</import>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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5 </macros>
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6
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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7 <expand macro="requirements" />
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8
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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9 <command detect_errors="exit_code"><![CDATA[
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10
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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11 ln -s '$ions' ./ions.mdp &&
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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12 ln -s '$gro_input' ./gro_input.gro &&
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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13 ln -s '$top_input' ./top_input.top &&
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14
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt &&
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn 1 &>> verbose.txt &&
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18
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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19 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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21 ]]></command>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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22 <configfiles>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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23 <!-- .mdp file for the gromacs simulation -->
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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24 <configfile name="ions">
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25 : Parameters are not so important here as no simulation is run
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26 integrator = steep
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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27 emtol = 1000.0
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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28 emstep = 0.01
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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29 nsteps = 1
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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30 nstlist = 1
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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31 cutoff-scheme = Verlet
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32 ns_type = grid
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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33 coulombtype = PME
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34 rcoulomb = 1.0
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35 rvdw = 1.0
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36 pbc = xyz
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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37 </configfile>
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38 </configfiles>
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39 <inputs>
3
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40 <param argument="gro_input" type="data" format='gro' label="GRO structure file"/>
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41 <param argument="top_input" type="data" format='top' label="Topology (TOP) file"/>
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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42 <param name="water_model" type="select" label="Water model for solvation">
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43 <option value="tip3p">TIP3P</option>
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44 <option value="tip4p">TIP4P</option>
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45 <option value="spc216">SPC</option>
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46 </param>
3
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47 <param name="capture_log" type="boolean" value="false" label="Generate detailed log" help="Generate detailed log information that can be summarized with ParseLog."/>
0
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48
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49 </inputs>
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50 <outputs>
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51 <data name="output1" format="gro" from_work_dir="solv_ions.gro"/>
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52 <data name="output2" format="top" from_work_dir="./top_input.top"/>
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53 <data name="report" format="txt" from_work_dir="verbose.txt">
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54 <filter>capture_log</filter>
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55 </data>
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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="gro_input" value="newbox.gro" />
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60 <param name="top_input" value="topol.top" />
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61 <param name="water_model" value="spc216" />
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62 <output name="output1" file="solv_ions.gro" ftype="gro" compare="sim_size"/>
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63 <output name="output2" file="topol_solv.top" ftype="top"/>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67
3
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68 .. class:: infomark
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69
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70 **What it does**
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71
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72 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.
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73
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74 _____
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75
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76 .. class:: infomark
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78 **Input**
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80 - GRO structure file.
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81 - Topology (TOP) file.
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82
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83 In addition, a water model must be selected - this should be consistent with the one selected previously in the system setup.
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84
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85 _____
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86
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87
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88 .. class:: infomark
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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89
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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90 **Output**
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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91
7161b230adad "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 3b99f08f22b9e0c16c0a0adc82f8c16c1a25cedf"
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92 - GRO structure file.
0
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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93
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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94 ]]></help>
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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95
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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96 <expand macro="citations" />
77aaf9a68166 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
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97 </tool>