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
>>> <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$>"
>>> file, I am getting positive enthalpy change of
>>> > binding !! Could you kindly give suggestions regarding this?
>>> >
>>> > Your suggestions would be highly appreciated.
>>> >
>>> > Thanks and regards
>>> > Kankana Bhattacharjee
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> >
>>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!IMjwHDD5PnwYkCEQW4JOWYqk2BejQdfFCDjMXNKyFtUx5-tN9M6tTMrsJT5DAwvbum7Ea8WHqvM$
>>>
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>>> notified by
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>>> <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPfMybHSv$> 08/28/23,
>>> 12:43:33 AM
>>>
>>
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Received on Sun Aug 27 2023 - 22:30:02 PDT
