[gmx-users] How to create three different zones to minimize energy of a enzyme?

[Evanildo Júnior]

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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