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
>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
>> and "Final-mmpbsa.dat", "energy.dat" files herewith.
>>
>> Thanks & Regards
>> Kankana Bhattacharjee
>>
>> ---------- Forwarded message ---------
>> From: Ray Luo <rluo.uci.edu>
>> Date: Sun, Aug 27, 2023 at 11:13 AM
>> Subject: Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:
>> To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>,
>> AMBER Mailing List <amber.ambermd.org>
>>
>>
>> Dear Bhattacharjee,
>>
>> Can you share your "mmpbsa.in
>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
>> 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
>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
>> 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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>> 12:43:33 AM
>>
>
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Received on Sun Aug 27 2023 - 21:00:02 PDT
