Repository revision
10:608098b3668d

Repository 'mmpbsa_mmgbsa'
hg clone https://toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa

MMPBSA/MMGBSA tool metadata
Miscellaneous
tool for estimating ligand binding affinities
mmpbsa_mmgbsa
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.10+galaxy0
21.10+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.10+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.7+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.3+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.0+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/20.15+galaxy0
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/19.11.1
toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/19.11
mmpbsa_mmgbsa
Requirements (dependencies defined in the <requirements> tag set)
name version type
ambertools 21.10 package
jinja2 3.0.1 package
Additional information about this tool
python '$mmpbsa_script' '$inputs' &&
        PATH_TO_MMPBSA=\$(dirname `which MMPBSA.py`) &&
        export AMBERHOME=\$(dirname \$PATH_TO_MMPBSA) &&
        #if $input.simulation.solvatedcomplex:
            MMPBSA.py -O -i '$parameteroutfile' -sp '$input.simulation.solvatedcomplex' -cp '$input.simulation.complex' -rp '$input.simulation.receptor' -lp '$input.simulation.ligand' -y '$input.simulation.trajcomplex' -o '$resultoutfile' -do '$decompoutfile'
        #else:
            MMPBSA.py -O -i '$parameteroutfile' -cp '$input.simulation.complex' -rp '$input.simulation.receptor' -lp '$input.simulation.ligand' -y '$input.simulation.trajcomplex' -o '$resultoutfile' -do '$decompoutfile'
        #end if
    
None
False
Functional tests
name inputs outputs required files
Test-1 input|simulation|ligand: ligand.prmtop
input|simulation|receptor: receptor.prmtop
input|simulation|complex: complex.prmtop
input|simulation|trajcomplex: 1err_desolvated_mini.nc
allparams|entropy: False
allparams|keep_files: True
calcdetails|gb_pb_calc|igb: 2
calcdetails|gb_pb_calc|saltcon: 0.100
calcdetails|gb_pb_calc|calctype: gb
calcdetails|decomposition|decomposition: no
name: value
ligand.prmtop
receptor.prmtop
complex.prmtop
1err_desolvated_mini.nc
value
Test-2 input|simulation|ligand: ligand.prmtop
input|simulation|receptor: receptor.prmtop
input|simulation|complex: complex.prmtop
input|simulation|trajcomplex: 1err_desolvated_mini.nc
allparams|startframe: 1
allparams|endframe: 1
allparams|entropy: False
calcdetails|gb_pb_calc|istrng: 0.100
calcdetails|gb_pb_calc|calctype: pb
calcdetails|decomposition|decomposition: yes
name: value
name: value
ligand.prmtop
receptor.prmtop
complex.prmtop
1err_desolvated_mini.nc
value