test.sh

Testset for martinize script. May 2012, DdJ

Run using: ./test.sh 2>&1 >&log&

Maybe we need to add 'failing' tests?

SCRIPT='../../../GIT/martinize-2.5.py' PDBGMX=pdb2gmx

function pdbgett { wget http://www.rcsb.org/pdb/files/$1.pdb.gz gzip -d $1.pdb.gz }

VERSION=Vecho ${SCRIPT:0:${#SCRIPT}-3} |cut -d '-' -f 2 mkdir ${VERSION} cd ${VERSION}

Most standard function, of course with ubiquitin

block=standard21 echo ''${block}'**' mkdir $block cd $block pdbgett 1UBQ echo 12|${PDBGMX} -f 1UBQ.pdb -o 1UBQ.gro -water spc $SCRIPT -f 1UBQ.gro -o 1UBQ_cg.top -x 1UBQ_cg.pdb -dssp $DSSP -ff martini21 cd ..

Most standard function for M2.2, of course with ubiquitin

block=standard22 echo ''${block}'**' mkdir $block cd $block pdbgett 1UBQ $SCRIPT -f 1UBQ.pdb -o 1UBQ_cg.top -x 1UBQ_cg.pdb -dssp $DSSP -ff martini22 cd ..

Most standard functions for polarizable martini, of course with ubiquitin

block=standard22p echo ''${block}'**' mkdir $block cd $block pdbgett 1UBQ $SCRIPT -f 1UBQ.pdb -o 1UBQ_cg.top -x 1UBQ_cg.pdb -dssp $DSSP -ff martini22p cd ..

Elnedyn (1) with a protein that does contain TRP's

block=elnedyn_TRP echo ''${block}'**' mkdir $block cd $block pdbgett 1L35 $SCRIPT -f 1L35.pdb -o 1L35_cg.top -x 1L35_cg.pdb -dssp $DSSP -ff elnedyn cd ..

Elnedyn (1) and giving secondary sturcture as string. Use custom elastic force.

block=elnedyn1 echo ''${block}'**' mkdir $block cd $block pdbgett 1UBQ $SCRIPT -f 1UBQ.pdb -o 1UBQ_cg.top -x 1UBQ_cg.pdb -ss EEEEEETTSEEEEETTSBHHHHHHHHHHHH~~~GGGEEEEETTEETTSBTGGGTTT~EEEEEES~~ -ff elnedyn -ef 700 cd ..

Elnedyn (2) and giving secondary sturcture as string. Use custom elastic force.

block=elnedyn2 echo ''${block}'**' mkdir $block cd $block pdbgett 1UBQ $SCRIPT -f 1UBQ.pdb -o 1UBQ_cg.top -x 1UBQ_cg.pdb -ss EEEEEETTSEEEEETTSBHHHHHHHHHHHH~~~GGGEEEEETTEETTSBTGGGTTT~EEEEEES~~ -ff elnedyn22p cd ..

Test the seperate writing of chains, position restraints, neutral termini. Use Mscl.

block=chain21 echo ''${block}'**' mkdir $block cd $block pdbgett 2OAR $SCRIPT -f 2OAR.pdb -o 2OAR_cg.top -x 2OAR_cg.pdb -sep -nt -p All -pf 500 -dssp $DSSP -ff martini21 cd ..

Test the seperate writing of chains, position restraints, neutral termini. Use Mscl.

block=chains22 echo ''${block}'**' mkdir $block cd $block pdbgett 2OAR $SCRIPT -f 2OAR.pdb -o 2OAR_cg.top -x 2OAR_cg.pdb -sep -nt -p All -pf 500 -dssp $DSSP -ff martini22 cd ..

Test cysteine bridge (between cys 9 and cys 164), naming protein and use dihedrals for extended regions. Use mutated lysozyme.

block=Sbonds21 echo ''${block}'**' mkdir $block cd $block pdbgett 1L35 $SCRIPT -f 1L35.pdb -o 1L35_cg.top -x 1l35_cg.pdb -cys auto -name lysozyme -dssp $DSSP -ed -ff martini21 cd ..

Test cysteine bridge (between cys 9 and cys 164), naming protein and use dihedrals for extended regions. Use mutated lysozyme.

block=Sbonds22 echo ''${block}'**' mkdir $block cd $block pdbgett 1L35 $SCRIPT -f 1L35.pdb -o 1L35_cg.top -x 1l35_cg.pdb -cys auto -name lysozyme -dssp $DSSP -ed -ff martini22 cd ..

Test collagen paramters on of the six collagen parameters.

block=collagen21 echo ''${block}'**' mkdir $block cd $block pdbgett 1CAG $SCRIPT -f 1CAG.pdb -o 1CAG_cg.top -x 1CAG_cg.pdb -collagen -ff martini21 cd ..

Test collagen paramters on of the six collagen parameters.

block=collagen22 echo ''${block}'**' mkdir $block cd $block pdbgett 1CAG $SCRIPT -f 1CAG.pdb -o 1CAG_cg.top -x 1CAG_cg.pdb -collagen -ff martini22 cd ..

Test mixed DNA-protein.

block=DNAprotein echo ''${block}'**' mkdir $block cd $block pdbgett 3SJM $SCRIPT -f 3SJM.pdb -o 3SJM_cg.top -x 3SJM_cg.pdb -collagen -ff martini22dna cd ..

cd ..