Because you are quite greedy with parameters, one can just rougly assume
that,e.g. your distance restraints are too short and therefore just kind
of bend your ligand. Therefore it seems to find an energy minimum in
modifiying some internal degrees of freedom to your restraint potential.
Maybe
Hi,
I just have a couple of things i want to clarify about the constrain
distances i used. The distance I used to pull the ligand and receptor
apart was a non-bonded distance between the amide nitrogen of the ligand
and the oxygen carbonyl of the receptor (on both ends). looking at the
Thank you David and Arneh for the comments.
I just have a couple of things i want to clarify about the constrain
distances i used. The distance I used to pull the ligand and receptor
apart was a non-bonded distance between the amide nitrogen of the ligand
and the oxygen carbonyl of the receptor
Hi,
I have been reading your work about free energy calculations and it is
impressive. I want to estimate binding free energy for a ligand/receptor
complex and I would appreciate your valuable input on how to approach the
system I am using. It is the first time I attempt free energy
Maybe it should be obvious, but (a) why are you constraining two
distances, and (b) are you sure your constraints aren't going to muck
with the internal degrees of freedom for the ligand? I would think one
would like to pull the ligand out of the receptor along some
particular direction,
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