1.
Yes, FE-Workflow creates all of the green folders, including the rbfe/CDK2/unified/run/1h1q~1h1r folders, displayed in figure 4 shown in the link you provided.
2.
State "A" refers to the first of the 2 ligands in the transformation A~B; that is, State A is the lambda=0 state. In your example, it refers to the coordinates where 1h1q are "real" and the softcore atoms of 1h1r are dummy atoms. The coordinates should be a member of the ensemble when 1h1q is a real ligand, and the dummy atoms of 1h1r are superimposed on top of it.
3.
This depends on your input settings regarding how to equilibrate the intermediate states. The relevant options are:
twostate=true
bidirection_com=false
bidirection_aq=false
In a "one-state" setup, one sequentially equilibrates each window starting from state A. In a "two-state" setup, one independently prepares states A and B; the intermediate states are sequentially equilibrated from the nearest end-state. In my understanding, a two-state equilibration implies bidirectional equilibration from the nearest end-state, whereas one can independently choose the directionality of the equilibration when using the one-state protocol. I think the FE-Workflow developers strongly encourage setting "twostate=true". I'm not convinced they run "twostate=false" enough to claim that the option is even supported (it doesn't work when I try to use it at least).
4.
Yes, unisc.parm7 merges the ligands into a single parm7.
5.
The appearance of stateA.rst7 versus stateA.rst7 and stateB.rst7 is likely because of how your equilibration options are set in the input file (see above).
6.
Each lambda has 23 input files. The TI production is performed with ${lambda}_ti.mdin. Most of the others are different parts of the sophisticated equilibration procedure, which includes coordinate minimization, heating, pressure equilibration, temperature annealing and equilibration, heavy atom restraint relaxation, etcetera.
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Received on Tue May 28 2024 - 10:00:02 PDT
