Dear Dr. Steinbrecher,
Thank you so much for this very helpful discussion. I think this question would be occured in many others free energy study.
Now let me make my question clear.
You told me in last email:
>Amber's softcore TI
>implementation requires a setup e.g. like this:
>
>pmrtop V0: Protein+Ligand+Solvent
>prmtop V1: Protein+Solvent
>
>so the end state system prmtop does not contain the ligand. Since you run
>the calculation using groupsander on both prmtops, your ligand will still
>be 'there' at lambda=1, but it will not interact with anything else (but
>maintains its internal potentials).
>
So this set up still no ligand in V1 state. Can you kindly explain why you think still maintains ligand internal potentials? I thought this ligand internal potential was perturbated to none. Am I wrong?
Another question is about dvdl_norest, in this kind free energy calculation, we usually need restraint the ligand around origin position ( in protein binding site). So I thought we need set this parameter to no. But how to correct this restraint later on?
Thank you very very much for this helpful discussion!
Best wishes,
Bing
>
>Kind Regards,
>
>Thomas
>
>Dr. Thomas Steinbrecher
>formerly at the
>BioMaps Institute
>Rutgers University
>610 Taylor Rd.
>Piscataway, NJ 08854
>
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Received on Wed Jan 04 2012 - 17:00:02 PST
