Mercurial > repos > chemteam > gmx_solvate
changeset 12:e205c82e9959 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 98e34b799346c6bbe5d28d4659d93d92cc7827cc"
| author | chemteam |
|---|---|
| date | Tue, 20 Oct 2020 10:43:39 +0000 |
| parents | 27ea4e1a3f95 |
| children | ae87e7b2454c |
| files | solvate.xml |
| diffstat | 1 files changed, 9 insertions(+), 11 deletions(-) [+] |
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--- a/solvate.xml Wed May 20 12:57:49 2020 -0400 +++ b/solvate.xml Tue Oct 20 10:43:39 2020 +0000 @@ -2,7 +2,7 @@ <description>to structure and topology files</description> <macros> <import>macros.xml</import> - <token name="@GALAXY_VERSION@">0</token> + <token name="@GALAXY_VERSION@">1</token> </macros> <expand macro="requirements" /> @@ -13,16 +13,14 @@ ln -s '$gro_input' ./gro_input.gro && ln -s '$top_input' ./top_input.top && - gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt - - #if $neutralise == "true": + gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && + gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt + #if $neutralise and $conc: ## else this step would do nothing && - gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt && - echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc $conc &>> verbose.txt && + echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc &>> verbose.txt && mv solv_ions.gro solv.gro #end if - ]]></command> <configfiles> <!-- .mdp file for the gromacs simulation --> @@ -51,8 +49,8 @@ <option value="tip5p">TIP5P (five-point model)</option> </param> <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."> - <option value="true">Yes, add ions</option> - <option value="false">No</option> + <option value="-neutral">Yes, add ions</option> + <option value="">No</option> </param> <param argument="conc" type="float" value="0" min="0" max="6" label="Specify salt concentration (sodium chloride) to add, in mol/liter" help="Note existing ions in the system are not taken into account - including those added if the neutralise option is selected. Ions are added by randomly replacing water molecules." /> @@ -68,7 +66,7 @@ <tests> <test> <param name="gro_input" value="newbox.gro" /> - <param name="neutralise" value="true" /> + <param name="neutralise" value="-neutral" /> <param name="top_input" value="topol.top" /> <param name="water_model" value="spc216" /> <param name="conc" value="1" /> @@ -92,7 +90,7 @@ </test> <test> <param name="gro_input" value="newbox.gro" /> - <param name="neutralise" value="false" /> + <param name="neutralise" value="" /> <param name="top_input" value="topol.top"/> <param name="water_model" value="spc216" /> <param name="conc" value="0" />