radhika jaswal wrote:
Respected Sir,
As u suggested I did the same, but I was unable to calculate it. I
used make_ndx in which I selected protein and then I used with
grompp with -n option but the energy it is showing is of the whole
system not of the protein only.
To mke it clear suppose if I have a protein A and solvent system B.
I want to simulate the system A + B but I want the energy of A
separately with the co-ordinates of A as in A + B and then energy of
B with its original co-ordinates in A + B as I want to compare the
different conformational states of a protein because editconf or
genbox adds unequal number of water molecules. OR I have a method to
add same number of water molecules to every state as water molecules
which are not interacting also contribute towards energy parameter.
THANKS SIR
Radhika
how do you define the energy of just the protein if it is in solvent?
genbox -maxsol XX gives you at most XX waters.
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