Hi
> 1) I only include positions 1 and 3 into the scmask and crgmask, as
> these are the positions where the ligand changes (CH -> N and N-> CH).
> This
> works and I do get reasonable results for the Free Energy change.
> 2) I include all atoms which are connected to positions 1 and 3.
> 3) I include all atoms of the aromatic core.
in my opinion (even though I havent tried many systems like that) all
three should work but I would expect 1 to have the quickest convergence.
Changing two atoms between nitrogen and carbon is not that big a change so
I guess all should work fine. Setting the whole aromatic core to be soft
core would give it less conformational freedom than one might think if
there are real residues attached at multiple points, which would anchor
both 'copies' to the same place.
> Would there be a difference if I used a single-step procedure (ie changing
> charge and vdw parameters simultaneously) versus the "historical" 3-step
> procedure (remove charge -> change vdw -> recharge)?
Since no atoms are really disapearing in your example, you should
certainly be able to do the procedure in one step. There is an upcoming
paper of ours discussing the benefits of 1step vs. 3step transformations,
but you should be safely on the onestep side.
> Thomas, if you read this: are there any limitations/features of the code
> you
> are aware of that would strongly favor one scenario over the others?
In principle your soft core region can be as big or small as you want and
needs not to be continuous. Two softcore atoms at positions 1 and 3 of a
non-softcore ring should work as well as a complete soft core ring, at
least in my imagination :-) Let us know if you encounter any issues while
trying...
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Feb 25 2011 - 01:00:04 PST
