Mercurial > repos > chemteam > gmx_solvate
comparison solvate.xml @ 0:77aaf9a68166 draft
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 4546df85653df59e357c5865ac4e538ea71a3048
| author | chemteam |
|---|---|
| date | Thu, 04 Oct 2018 18:22:34 -0400 |
| parents | |
| children | 7161b230adad |
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| -1:000000000000 | 0:77aaf9a68166 |
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| 1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@VERSION@"> | |
| 2 <description>to structure and topology files</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 | |
| 7 <expand macro="requirements" /> | |
| 8 | |
| 9 <command detect_errors="exit_code"><![CDATA[ | |
| 10 | |
| 11 ln -s '$ions' ./ions.mdp && | |
| 12 ln -s '$gro_input' ./gro_input.gro && | |
| 13 ln -s '$top_input' ./top_input.top && | |
| 14 | |
| 15 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && | |
| 16 | |
| 17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr -maxwarn 1 &>> verbose.txt && | |
| 18 | |
| 19 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt | |
| 20 | |
| 21 ]]></command> | |
| 22 <configfiles> | |
| 23 <!-- .mdp file for the gromacs simulation --> | |
| 24 <configfile name="ions"> | |
| 25 : Parameters are not so important here as no simulation is run | |
| 26 integrator = steep | |
| 27 emtol = 1000.0 | |
| 28 emstep = 0.01 | |
| 29 nsteps = 1 | |
| 30 nstlist = 1 | |
| 31 cutoff-scheme = Verlet | |
| 32 ns_type = grid | |
| 33 coulombtype = PME | |
| 34 rcoulomb = 1.0 | |
| 35 rvdw = 1.0 | |
| 36 pbc = xyz | |
| 37 </configfile> | |
| 38 </configfiles> | |
| 39 <inputs> | |
| 40 <param argument="gro_input" type="data" format='gro' label="GRO structure file."/> | |
| 41 <param argument="top_input" type="data" format='top' label="Topology (TOP) file."/> | |
| 42 <param name="water_model" type="select" label="Water model for solvation."> | |
| 43 <option value="tip3p">TIP3P</option> | |
| 44 <option value="tip4p">TIP4P</option> | |
| 45 <option value="spc216">SPC</option> | |
| 46 </param> | |
| 47 <param name="capture_log" type="boolean" value="false" label="Generate Detailed Log" help="Generate detailed log information that can be summarized with ParseLog."/> | |
| 48 | |
| 49 </inputs> | |
| 50 <outputs> | |
| 51 <data name="output1" format="gro" from_work_dir="solv_ions.gro"/> | |
| 52 <data name="output2" format="top" from_work_dir="./top_input.top"/> | |
| 53 <data name="report" format="txt" from_work_dir="verbose.txt"> | |
| 54 <filter>capture_log</filter> | |
| 55 </data> | |
| 56 </outputs> | |
| 57 <tests> | |
| 58 <test> | |
| 59 <param name="gro_input" value="newbox.gro" /> | |
| 60 <param name="top_input" value="topol.top" /> | |
| 61 <param name="water_model" value="spc216" /> | |
| 62 <output name="output1" file="solv_ions.gro" ftype="gro" compare="sim_size"/> | |
| 63 <output name="output2" file="topol_solv.top" ftype="top"/> | |
| 64 </test> | |
| 65 </tests> | |
| 66 <help><![CDATA[ | |
| 67 | |
| 68 Select a water model - consistent with the one selected in system set-up and provide GRO and TOP files to be updated with the added water molecules. In addition, sodium or chloride ions are added if necessary to ensure the system is charge-neutral. | |
| 69 | |
| 70 ]]></help> | |
| 71 | |
| 72 <expand macro="citations" /> | |
| 73 </tool> |