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| Dear OpenFE users and developers. I tend to presolvate the protein using 3D-RISM before starting any simulation and it seems to work quite well for ABFE calculations. But SEPTOP calculations require the same protein to be supplied in both states. Since ligand changes are quite large in this case would it be possible to allow different solvation patterns? Is there any hack to allow it? Cheers, |
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| Hi @dkarlov thanks for opening this discussion. The nature of SepTop is that it expects everything but the ligands to be the same. Essentially the way it works is that it creates the one "environment (protein + waters + ions)" and then adds the two ligands which are alchemically interpolated. As a result, it's not really feasible to have differing waters between the endstates as you would somehow have to account for this change as part of the transformation (i.e. you would have to alchemically modify the waters as you go from state A to state B). One thing that we can look at in the future is adding something like GCMC water sampling as part of the transformation, but that isn't something we can do short term. |
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| Thanks for clarification! |
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Hi @dkarlov thanks for opening this discussion.
The nature of SepTop is that it expects everything but the ligands to be the same. Essentially the way it works is that it creates the one "environment (protein + waters + ions)" and then adds the two ligands which are alchemically interpolated.
As a result, it's not really feasible to have differing waters between the endstates as you would somehow have to account for this change as part of the transformation (i.e. you would have to alchemically modify the waters as you go from state A to state B).
One thing that we can look at in the future is adding something like GCMC water sampling as part of the transformation, but that isn't something…