Ok. overall change in binding free energy is matching close with paper when
SASA parameters are taking from the amber22 default values. But, energetic
contributions is not matching well. Like, nonpolar solvation free energy
change for my calculation is -31.3532 kcal/mol, whereas the value is -3.67
kcal/mol, DelE_electrostatics for my calculation is -1.4430 kcal/mol,
whereas the paper is having -26.99 kcal/mol.
So, in amber22 version, I have to only include "inp=2" and SASA parameters
would be taking from the amber22 default values ?
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08/28/23,
10:00:13 PM
On Mon, Aug 28, 2023, 21:17 Ray Luo <rluo.uci.edu> wrote:
> The default inp was changed from 1 to 2 by developers. So you are
> using two different nonpolar solvent models between amber12 and
> amber22, leading to your observation. This has been raised many times
> in the past.
>
> Please read the following paper to gain some background information on
> nonpolar solvation modeling:
>
> Tan et al, Implicit Nonpolar Solvent Models,
> https://doi.org/10.1021/jp073399n
>
> 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
>
> --
> 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 Mon, Aug 28, 2023 at 5:09 AM Kankana Bhattacharjee
> <kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
> >
> > Ok. When I explicitly mentioned the cavity surften, cavity offset values
> based on the paper (amber 12 version) in my input file (amber 22 version),
> then non-polar solvation free energy change is decreasing and matching with
> the paper. But, total bonding free energy change is zero. How is it
> possible ?
> > While I took the default SASA parameters according to amber22 version,
> then total binding free energy change is matching close. Is it because of
> SASA parameters in different amber versions (amber 12, amber 22) ya "inp"
> model ?
> >
> >
> >
> >
> > Sender notified by
> > Mailtrack 08/28/23, 05:36:07 PM
> >
> > On Mon, Aug 28, 2023 at 10:43 AM Ray Luo <rluo.uci.edu> wrote:
> >>
> >> No. It's the nonpolar solvent model option.
> >>
> >> Ray
> >>
> >> On Sun, Aug 27, 2023, 20:25 Kankana Bhattacharjee <
> kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
> >>>
> >>> Are you talking about internal dielectric constant?
> >>>
> >>> On Mon, Aug 28, 2023, 04:43 Ray Luo <rluo.uci.edu> wrote:
> >>>>
> >>>> The final output shows that you are using the default inp=2 option.
> Please set inp=1 in your pb section if you want to seek agreement with the
> tutorial setting.
> >>>>
> >>>> 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 Sun, Aug 27, 2023 at 12:15 PM Kankana Bhattacharjee <
> kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
> >>>>>
> >>>>> Hello,
> >>>>>
> >>>>> I am sharing the "mmpbsa.in" and "Final-mmpbsa.dat", "energy.dat"
> files herewith.
> >>>>>
> >>>>> Thanks & Regards
> >>>>> Kankana Bhattacharjee
> >>>>>
> >>>>> ---------- Forwarded message ---------
> >>>>> From: Ray Luo <rluo.uci.edu>
> >>>>> Date: Sun, Aug 27, 2023 at 11:13 AM
> >>>>> Subject: Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:
> >>>>> To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>,
> AMBER Mailing List <amber.ambermd.org>
> >>>>>
> >>>>>
> >>>>> Dear Bhattacharjee,
> >>>>>
> >>>>> Can you share your "mmpbsa.in" and also the result output files?
> >>>>>
> >>>>> 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 Fri, Aug 25, 2023 at 12:48 PM Kankana Bhattacharjee via AMBER
> >>>>> <amber.ambermd.org> wrote:
> >>>>> >
> >>>>> > Dear AMBER users,
> >>>>> >
> >>>>> > I am trying to reproduce the change in enthalpy of binding of
> >>>>> > protein-ligand complex using MMPBSA . In the paper, Authors'
> used amber12
> >>>>> > version and cavity_surften, cavity_offset were set as 0.005420,
> -1.008
> >>>>> > respectively.
> >>>>> > Whereas, I am using amber22 version, in this case, default values
> of
> >>>>> > cavity_surften, cavity_offset are 0.0378, -0.5692 respectively.
> When my
> >>>>> > calculations were done using the default (cavity_surften,
> cavity_offset
> >>>>> > parameters), the result matched closely enough with the paper. But,
> >>>>> > when I explicitly
> >>>>> > mentioned the cavity_surften, and cavity_offset parameters (based
> on the
> >>>>> > paper) in "mmpbsa.in" file, I am getting positive enthalpy
> change of
> >>>>> > binding !! Could you kindly give suggestions regarding this?
> >>>>> >
> >>>>> > Your suggestions would be highly appreciated.
> >>>>> >
> >>>>> > Thanks and regards
> >>>>> > Kankana Bhattacharjee
> >>>>> > _______________________________________________
> >>>>> > AMBER mailing list
> >>>>> > AMBER.ambermd.org
> >>>>> >
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> >>>>>
> >>>>> Sender notified by
> >>>>> Mailtrack 08/28/23, 12:43:33 AM
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