Mercurial > repos > chemteam > gmx_solvate
comparison solvate.xml @ 14:2c8ed1b52bf7 draft
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit 773a59c78e148b770d1a8b0dc6ee2546bae87c3e"
author | chemteam |
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date | Wed, 13 Jan 2021 10:26:35 +0000 |
parents | ae87e7b2454c |
children | 97b2c06ae168 |
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13:ae87e7b2454c | 14:2c8ed1b52bf7 |
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1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> | 1 <tool id="gmx_solvate" name="GROMACS solvation and adding ions" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> |
2 <description>to structure and topology files</description> | 2 <description>to structure and topology files</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 <token name="@GALAXY_VERSION@">0</token> | 5 <token name="@GALAXY_VERSION@">1</token> |
6 </macros> | 6 </macros> |
7 | 7 |
8 <expand macro="requirements" /> | 8 <expand macro="requirements" /> |
9 | 9 |
10 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
13 ln -s '$gro_input' ./gro_input.gro && | 13 ln -s '$gro_input' ./gro_input.gro && |
14 ln -s '$top_input' ./top_input.top && | 14 ln -s '$top_input' ./top_input.top && |
15 | 15 |
16 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && | 16 gmx solvate -cp ./gro_input.gro -cs ${water_model}.gro -o solv.gro -p ./top_input.top &>> verbose.txt && |
17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt | 17 gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr &>> verbose.txt |
18 #if $neutralise and $conc: ## else this step would do nothing | 18 #if $neutralise or $conc: ## else this step would do nothing |
19 && | 19 && |
20 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc &>> verbose.txt && | 20 echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL $neutralise -conc $conc &>> verbose.txt && |
21 mv solv_ions.gro solv.gro | 21 mv solv_ions.gro solv.gro |
22 #end if | 22 #end if |
23 | 23 |