Hello,
I am trying to do an umbrella sampling simulation with amber to calculate
the dimerization free energy of protein with more than 200 residues. The
major part of this calculation is to apply a harmonic restraint to the
distance between two proteins chain. The harmonic restraint will keep the
distance fluctuating around a target distance with tunable amplitude. I
searched for applying harmonic potential and umbrella sampling in amber and
found one helpful tutorial
<
https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial>.
According to this tutorial, to apply the harmonic restraint to the distance
we need to define the center of mass of two groups of atoms via "igr1 and
igr2". The problem with this method is that we cannot group more than 200
atoms. I was wondering if you know a method in amber that I can apply the
harmonic restraint to the distance between two groups with more than 200
atoms. I am asking this because each protein chain in my study has more
than 200 atoms. Please let me know if my explanation was not clear enough.
Thanks,
Ramin
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 22 2020 - 07:30:02 PDT
