All scorers (SFs) should be inside the ['paths']['scorers'] (see input config yaml) directory. Their folder names should match the exact names of the scorers used in the config file and their binaries should be on the top level of their folders and also be named with the exact scorer’s name. Some scorers have additional requirements, like parameter files, or the case of gmxmmpbsa which is included with the protocol and only needs an input text file.

Additional requirements for specific SFs

Assuming a scorers folder set to: ['paths']['scorers']=home/user/my_SFs.


gmxmmpbsa directory: home/user/my_SFs/gmxmmpbsa

This is the only scorer that comes bundled with the protocol. Inside the gmxmmpbsa folder, a gmxmmpbsa input text file is needed. The contents are up to the user. For example, for a simple MM-GBSA:

igb=2, saltcon=0.150,

We advise igb=2 since igb=5 requires a modification of the topology that is not available in the protocol. From the Amber manual:

With this option (igb=5), you should use the command “set default PBradii mbondi2” in setting up the prmtop file, although “set default PBradii bondi” is also OK

And if residue decomposition is needed (for a mmpbsa generator):

igb=2, saltcon=0.150,
idecomp=2, dec_verbose=0,
print_res="within 4"

Though locuaz, as a rule, avoids stepping over other external tools, you’ll notice that the input script has 1-indexed startframe and endframe options that conflict with the 0-indexed start and end options from the input config file. This means that they have to be manually checked. If, for example, you are writing 250 frames during your NPT run and you set your start option to 50, then your gmxmmpbsa input file would look like the one above. Check YAML configuration file for more info.


pisa directory: home/user/my_SFs/pisa
pisa binary: home/user/my_SFs/pisa/pisa
pisa parameters: home/user/my_SFs/pisa/pisa.params


rosetta directory: home/user/my_SFs/rosetta

Symbolic links on the top rosetta folder should be added, pointing to files in the rosetta installation Eg: inside the main rosetta folder, with the rosetta directory called sources:

ln -s sources/rosetta_source/bin/InterfaceAnalyzer.linuxgccrelease rosetta
ln -s sources/rosetta_database/ rosetta_database
ln -s sources/rosetta_source/build/src/release/linux/4.14/64/ppc64le/gcc/8.4/ parameters
ln -s sources/rosetta_source/build/external/release/linux/4.14/64/ppc64le/gcc/8.4/ external_parameters


haddock directory: home/user/my_SFs/haddock

As with all the scorers, all the necessary files have to be at the top level. The template_scoring.inp file has to be at the top level of the haddock, as the rescoring-scripts folder (included with the protocol insed the sample_bin folder). Then, the following smybolic links have to be created. Version number and specific folder names and locations may change:

ln -s ./cns_solve_1.3/ibm-ppc64le-linux/bin/cns haddock
ln -s haddock/protocols/ protocols
ln -s haddock/toppar/ toppar
ln -s cns_solve_1.3/cns_solve_env cns_solve_env
ln -s haddock/haddock_configure.csh haddock_configure.csh


piepisa directory: home/user/my_SFs/piepisa

Download pie. If you can run the binary, good, if you can’t, then you probably won’t be able to run it, since compiling and running it in a modern PC is quite cumbersome. Then, normalize the directory to the scorers standard:

  • rename the pie folder to piepisa

  • be sure to also have the pisa scorer

  • Inside the piepisa folder, make symbolic links to the binaries and parameters so they have proper names:

    ln -s bin/pie_score pie
    ln -s bin/pie.params pie.params
    ln -s ../pisa/pisaEnergy_linux pisa
    ln -s ../pisa/pisa.params pisa.params


evoef2 directory: home/user/my_SFs/evoef2

Download and compile evoef2.

  • rename the EvoEF2 folder to evoef2

  • Inside the evoef2 folder, make a symbolic link to the binary so it has a proper name:

    ln -s bin/evoef2 evoef2


bluues directory: home/user/my_SFs/bluues
  • Inside the bluues folder, make symbolic links to the binaries so it has a proper name:

    ln -s bin/bluues_new_2 bluues


bluuesbmf directory: home/user/my_SFs/bluuesbmf
  • Inside the bluuesbmf folder, make symbolic links to the binary so it has a proper name:

    ln -s bin/bluues_new_2 bluues
    ln -s bin/score_bmf_3 bmf


autodockvina directory: home/user/my_SFs/autodockvina

Download autodockvina. Then, normalize the directory to the scorers standard: * create a folder named autodockvina with the downloaded binary * Inside the autodockvina folder, make symbolic links to the binary so it has a proper name:

ln -s vina_1.2.3_linux_x86_64 autodockvina

locuaz.scorers module

locuaz.abstractscorer module











locuaz.scoring module

locuaz.utils_scoring module