Evanildo Júnior wrote:
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.
Look for "freeze groups" in the manual. They work with MD and I'm
guessing they also work with EM.
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.
Use position restraints.
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?
Apply a freeze group only to the C-alpha atoms. You'll need to use
make_ndx to make the group and give that index file to grompp as well as
the usual stuff.
If you're as new to GROMACS as you sound like you might be, you should
do some tutorial material and read the first few chapters of the manual
thoroughly. Doing the above would not be a good way to get your first
exposure to using GROMACS.
Mark
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