# HG changeset patch # User chemteam # Date 1574266225 18000 # Node ID 645139abefae90b1491b434a28496725355f705f # Parent cdacad684da132aba4936857b5d97918c5db4e2a "planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/gromacs commit a71d03531d57b87b5e3ce40ee7d974fbe53a1dfa" diff -r cdacad684da1 -r 645139abefae macros.xml --- a/macros.xml Wed Oct 30 13:32:37 2019 -0400 +++ b/macros.xml Wed Nov 20 11:10:25 2019 -0500 @@ -1,5 +1,5 @@ - 2019.1.2 + 2019.1.3 gromacs @@ -11,19 +11,6 @@ - - - - - - - - - - - - - @@ -73,6 +60,15 @@ + + + + + + + capture_log + + diff -r cdacad684da1 -r 645139abefae solvate.xml --- a/solvate.xml Wed Oct 30 13:32:37 2019 -0400 +++ b/solvate.xml Wed Nov 20 11:10:25 2019 -0500 @@ -12,12 +12,16 @@ 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 && + 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 == "true": + && + 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 &>> verbose.txt && + mv solv_ions.gro solv.gro + #end if - echo 'SOL' | gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral &>> verbose.txt - + ]]> @@ -44,24 +48,42 @@ - + + + + + + - + - - capture_log - + + - + + + + + + + + + + + + + + +