On 14/06/2012 12:04 PM, bharat gupta wrote:
Thanks for the reply . Is it possible to calculate the dihedral energy
of certain residues, like in my case for turn residues ??.. How can
that be done
First, seek to define "dihedral energy"... Force fields are not
parametrized such that parts of them are expected to correlate with
observables.
This another question is regarding energy minimization. Suppose, I
minimize the the protein solvated in water, the energy value that I
get is for the whole system or for the protein alone. If it's for the
system then how can I get the energy for the protein alone.
You can define energy groups (see manual) to do this for the nonbonded
contributions. Bonded contributions are easy to do in your case. Whether
this energy is useful for anything is quite another matter.
Mark
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