Mercurial > repos > chemteam > gmx_solvate
changeset 17:9a1e472aa515 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/gromacs commit 04ccbbe525c43164b061fe738500a84d73f89afa"
| author | chemteam |
|---|---|
| date | Mon, 08 Nov 2021 18:40:42 +0000 |
| parents | 61094e01eff9 |
| children | ebcef04f4a78 |
| files | solvate.xml |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
line wrap: on
line diff
--- a/solvate.xml Wed Oct 27 08:00:42 2021 +0000 +++ b/solvate.xml Mon Nov 08 18:40:42 2021 +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" /> @@ -14,7 +14,7 @@ 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 && - gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt + gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr @MAXWARN_CMD@ &>> verbose.txt #if $neutralise or $conc: ## else this step would do nothing && echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc -seed $seed &>> verbose.txt && @@ -56,6 +56,7 @@ <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." /> <param argument="seed" type="integer" value="1" min="0" label="Random seed for adding ions" help="Select a random seed for replacing solvent with ions. Set to 0 to generate a seed." /> + <expand macro="maxwarn" /> <expand macro="log" /> </inputs>