exprorer_msmd generates position constraints for protein heavy atoms. This is enough for equilibration, but too many atoms are constrained if we want to reduce protein flexibility in production run (in many cases). Of course, it depends on one's aim.
As a choice, I propose the position constraints is divided into two parts; main chain constraints and side chain constraints.
exprorer_msmdgenerates position constraints for protein heavy atoms. This is enough for equilibration, but too many atoms are constrained if we want to reduce protein flexibility in production run (in many cases). Of course, it depends on one's aim.As a choice, I propose the position constraints is divided into two parts; main chain constraints and side chain constraints.
Related code is https://github.com/keisuke-yanagisawa/exprorer_msmd/blob/main/script/add_posredefine2top.py