Scorers
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
home/user/my_SFs/gmxmmpbsaThis 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:
&general
sys_name="Prot-Prot",
startframe=51,
endframe=250,
/
&gb
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):
&general
sys_name="Prot-Prot",
startframe=51,
endframe=250,
/
&gb
igb=2, saltcon=0.150,
/
&decomp
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
home/user/my_SFs/pisahome/user/my_SFs/pisa/pisahome/user/my_SFs/pisa/pisa.paramsrosetta
home/user/my_SFs/rosettaSymbolic 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
home/user/my_SFs/haddockAs 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
home/user/my_SFs/piepisaDownload 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
home/user/my_SFs/evoef2Download 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
home/user/my_SFs/bluuesInside the bluues folder, make symbolic links to the binaries so it has a proper name:
ln -s bin/bluues_new_2 bluues
bluuesbmf
home/user/my_SFs/bluuesbmfInside 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
home/user/my_SFs/autodockvinaDownload 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