Dear Amber Users
I used MMPBSA.py to calculate the binding free energy of different single
position mutants protein-protein complexes. Here is pbsa name list i used
startframe=1, endframe=1000, interval=2,
verbose=1, keep_files=0,
/
&gb
igb=5,
/
&pb
inp=1,
indi=1,
radiopt=0
/
But the results are not comparable with the experimental energies. I use
the default dielectric constant and I ran the protein-protein mutant
complex from 2 ns and then consider every 2nd frame to calculate MMPBSA.
Please guide me, I am doing something wrong due to which energies are not
comparable with experimental. Some studies showed that increasing the
dielectric helps to get better results. please also guide what dielectric
constant should use for mutants protein complexes. I am using amber2020,
what name list/ keyword should I need to change the dielectric constant in
PB namlist.
Best
Ray
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Received on Thu Oct 14 2021 - 16:00:03 PDT
