---------- Forwarded message ---------
From: Farial Tavakoli <faryal.tavakoli.gmail.com>
Date: Tue, Dec 25, 2018 at 4:35 PM
Subject: constant dieletcric
To: <amber.ambermd.org>
Dear Amber users
I am trying to calculate the binding free energy of 2 complexes including a
protein in wild type and mutant state in complex with a ligand which has 2
phosphotyrosines, using MMPBSA. There are some charged residues in the
binding pocket of both proteins: including:
mutant receptor: asp, arg, asp, arg, lys, lys
wild type receptor: asp, arg, asp, lys, lys
peptide has to phosphotyrosines and a histidine (HID)
I expected the delta total in both complexes are the same or close to each
other , but they are so different. The delta total in mutant complex is -12
kcal/mol , whereas the delta total in wild type mutant is -30 kcal/mol.
The experimental binding energy was calculated and it was -10 kcal/mol.
I dont know why the calculated binding free energy using mmpbsa in both
proteins are not the same.
I need to know whether the solute dielectric constant definition for
binding pocket or whole the protein?
Would you please advice me which number I should put for the internal
dielectric?
Best regard
Farial
my input file is :
&general
startframe=1, endframe=1000, interval=10,
verbose=2, keep_files=0,
/
&pb
istrng=0.15, fillratio=4.0, indi=4, exdi=80,
/
and this is mmpbsa command:
mpirun -np 16 MMPBSA.py.MPI -O -i mp.in -o final.dat -sp
complex_solvated.top -cp complex.top -rp receptor.top -lp ligand.top -y
.mdcrd
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Received on Thu Dec 27 2018 - 22:30:03 PST
