I am trying to dock a peptide to a receptor using FlexPepDock Refinement and generated 600 models,my top five models lie within sub-angstrom RMSDbb of the native structure.The lowest energy is -557.578.
Here is my flags:
Performing the command:
score.linuxgccrelease @flags > score.log
I got the total score of the native structure(-316.451).I'm confused that the total score of the native is greater than the models(-316.451>-557.578).Does it means there is something wrong with the scoring function(SCOREFUNCTION:standard SCOREFUNCTION PATCH:score12) or the default scoring function for FlexPepDock search is unfitted. My files have been attached.
Any replies is greatly appreciated.