On Sat, Apr 10, 2021, WW wrote:
>
>I just have one more question regarding running TI on estimating relative
>P-P binding free energy. Near small (ie. 0.00922) values of lambda (I'm
>using a 12-point lambda transformation), there are geometries where the
>almost "ghost"-like softcore atoms are sterically clashing and actually
>goes through the rest of the protein, and give exceptionally high VDW
>energies. I was just wondering if this behavior is normal in TI. Another
>one of my concerns is that if I were to start the next lambda simulation
>from the end of the current, clashing state, I am fearful that this would
>lead the system to crash. Sorry for these naive questions, and thanks for
>your time.
If you are making an entire ligand "disappear" (i.e. become uncoupled from
interaction with its environment), then you will generally need to add
positional restraints to keep it from moving far away from its starting
points. The TI gurus on the list can probably point to reference or
examples about how to accomplish this.
....dac
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Received on Sat Apr 17 2021 - 14:00:02 PDT
