Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:

From: Ray Luo via AMBER <amber.ambermd.org>
Date: Mon, 28 Aug 2023 08:46:35 -0700

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
>>>>> > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!IMjwHDD5PnwYkCEQW4JOWYqk2BejQdfFCDjMXNKyFtUx5-tN9M6tTMrsJT5DAwvbum7Ea8WHqvM$
>>>>>
>>>>> Sender notified by
>>>>> Mailtrack 08/28/23, 12:43:33 AM
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Received on Mon Aug 28 2023 - 09:00:02 PDT