[ WARNING ] Score term optimized with IMM1 membrane transition function, but using franklin transiton funtion!

[QuynhN2710]

Hi! I'm using the mp_symdock to model a dimer. I'm using the franklin2019 scoring function, but got this error message. Should I be concerned? Below is my command
~/rosetta.source.release-408/main/source/bin/mp_symdock.linuxgccrelease
-in:file:s VSD-VSD_noMEM_INPUT.pdb
-mp:setup:spanfiles VSD-VSD_noMEMA.span
-mp:scoring:hbond true
-score:weights franklin2019
-mp:lipids:composition POPC
-nstruct 10
-symmetry:symmetry_definition VSD-VSD.symm
-symmetry:initialize_rigid_body_dofs
-packing:pack_missing_sidechains 0
-docking:dock_lowres_filter 5.0 10.0
-overwrite

[woodsh17]

Hello,

Excellent question! Although, you are setting the score function in the command line, mp_symdock acutally ignores this and uses mpframework_symdock_fa_2015 instead because it is hard coded into the mover. This score function, mpframework_symdock_fa_2015, has score terms that were programmed and tested using the IMM1 membrane transition function not the franklin2019 transition function. The warning is essentially letting you know that the combination you are using, which is the mpframework_symdock_fa_2015 score terms with the franklin2019 transition function is un-tested, but not necessarily wrong.

To use the IMM1 membrane transition function, you can set -restore_lazaridis_imm_behavior true. I will also note that franklin2019 transition function is dependent on the lipid composition (this was one of the big advances with this score function), but IMM1 transition function is not dependent on lipid composition, so the -mp:lipids:composition POPC will have no effect if you do have -restore_lazaridis_imm_behavior true.

[QuynhN2710]

Thank you for your answer! In this case, if I want to use only franklin2019 score function, is there a way to achieve this?

[woodsh17]

As it is written now, I don't think there is a way to use franklin2019 with the mp_symdock application.

You may be able to write your own script, with PyRosetta or C++, that follows what the MPSymDockMover does except with reading in the score function as an option.

[QuynhN2710]

Thank you!