Dear gmx-users,
I would like to minimize the potential energy of the active site of an enzyme.
Because I do not have too much computer power to perform a full enzyme
calculation, I need to create three different zones in which the calculation
will take place. The first one is the outer boundary of the enzyme that will
remain frozen during the calculation. The second one is a transition region
between the active site region and the outer boundary, whose atoms will receive
a parabolic potential in order to move just a little bit. The last one is the
active site itself which will be freely minimized. I would like to know how do
I implement it in practice. Does anyone has a Gromacs script for this task? The
other question is how do I freeze only the C-alpha chain?
Lacerda Jr.
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