Dear All,
I have a question regarding mm-pbsa calculations.
I'm little confused by the way mm-pbsa calculates MM energies. I've
enzyme-ligand complex for which I have tried to calculate binding
energies selecting different dielectric constant for complex, from 1
to 20.
When I choose to calculate both GB (GB=1) and PB (PB=1) in
mm_pbsa_Binding.in script, MM energies, more precisely ELE term, seems
not to depend on dielectric constant, i.e. I always get the same value
for ELE. On the other hand, when I switch off GB calculations (using
GB 0 in mm_pbsa_Binding.in script) values for ELE are scaled according
to selected dielectric constant.
Why is this happening?
Meanwhile I have also tried to compare these results with those
obtained using APBS program, to be more precise PBCAL value, using the
same parameters as in mm-pbsa. PQR files for APBS were derived using
ambpdb option. The values I get with APBS differ significantly with
those obtained with mm_pbsa. Does anyone has experience with this?
Kind regards,
Antonija
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Received on Fri Oct 15 2010 - 08:30:03 PDT
