Many thanks, inp=1 does match well with GBSA. I will try both approaches, I
was just cautious and tried to understand why the numbers could be so
different. Thanks again.
Mish
On Sat, Feb 13, 2021 at 4:22 PM Ray Luo <rluo.uci.edu> wrote:
> Mish,
>
> If you want to compare MMPBSA and MMGBSA, you'll have to use radiopt=0
> and inp=1.
>
> You are using inp=2, which is a new approach to compute the nonpolar
> solvation free energies. It can't be compared with inp=1 or the SA
> part in GBSA directly. Instead, you may want to compare computed delta
> delta G from all approaches with experimental values to see which
> approaches give you lower RMSD's.
>
> All the best,
> Ray
>
> All the best,
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
> Biomedical Engineering, and Materials Science and Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
>
> On Sat, Feb 13, 2021 at 1:56 PM mish <smncbr.gmail.com> wrote:
> >
> > Dear all,
> >
> > I am trying to calculate the binding free-energy of hydrophobic molecules
> > with a protein using MM/GBSA, and MM/PBSA approaches. I did enthalpy
> > calculations using igb 1, 2, 5, 7, and 8 separately with appropriate VDW
> > radii sets mentioned in the Amber20 manual. This all looked fine
> (obtained
> > binding energies in the range of -50 to -70 kcal/mol) until I did MM/PBSA
> > calculations on the same system. While doing MM/PBSA, I get +ve binding
> > free energy, and a difference of about +70 kcal/mol is caused by large
> > positive dE_SA (ENPLOAR + EDISPER) values in MM/PBSA (~ +40 kcal/mol). I
> > used radiopt=0, cavity_surften-0.378, cavity_offset=-0.5692 with all four
> > vdW radii sets (bondi, mbondi, mbondi2, mbondi3) and I am getting
> exactly
> > same dE_SA values.
> >
> > I wonder what could be the source of such a different discrepancy between
> > MM/GBSA and MM/PBSA entropy values. I am worried that something might be
> > technically wrong as the MD simulations were run using CHARMM forcefield,
> > and I am convertingCHARMM topology file into Amber topology using
> parmed. I
> > believe it is still using CHARMM forcefield parameters in the
> calculations
> > (other than vdW radii sets that I changed using --radii option in the
> > ante-MMPBSA.py script. Can someone help understand why dE_SA (ENPLOAR +
> > EDISPER) is positive and different from dE_SA (ESURF) from MM/GBSA?
> >
> > Thanks,
> > Mish
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Received on Sat Feb 13 2021 - 15:30:02 PST
