Thank you very much for this information!
Best,
Wanlei
On Sat., Apr. 17, 2021, 4:30 p.m. David A Case, <david.case.rutgers.edu>
wrote:
> 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 Sun Apr 18 2021 - 10:00:02 PDT
