Thanks a lot for your suggestions. Authors dint mention the pbradii value
in the paper. Also, I dint mention the pbradii option during making the
prmtop files. As while doing the amber ras-raf tutorial i mentioned the
pbradii option during creating prmtop files then mmpbsa was giving errors
by saying inconsistent prmtop files. When I removed that option then mmpbsa
ran fine and took default pbradii value. So, in this case, what pbradii
value I have to mention in mmpbsa.in file ? Salt concentration for inp=1 is
0.15 M, what I have to mention in radiopt option ?
On Mon, Aug 28, 2023, 23:24 Ray Luo <rluo.uci.edu> wrote:
> To reproduce the inp=1 result in the paper, please follow the suggested
> parameters while setting inp=1 in amber22/amber23.
>
> In addition to cavity_offset and cavity_surften, make sure you're using
> the same radius definition as mentioned in the paper. Set radiopt=0 so the
> radii are read from the prmtop file as you specified in tleap. Set
> istrng in M for ionic strength and also dielectric constants (exdi, indi)
> for water and solute.
>
> I suppose you are not working on a membrane protein ... Otherwise, there
> are additional settings.
>
> You can read the chapter on PBSA for more details on the PB keywords.
>
> 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 Mon, Aug 28, 2023 at 10:15 AM Kankana Bhattacharjee <
> kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
>
>> 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 ?
>>
>>
>>
>> [image: Mailtrack]
>> <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Il4MNEjlvM46MO3TltglVvwcaIsbz_aSutKfjJ8FJLIVwBUgPP3XftzwhxUtTZ0U6o96xMptBfz6pBZKmlrgBl20DbPj$> Sender
>> notified by
>> Mailtrack
>> <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Il4MNEjlvM46MO3TltglVvwcaIsbz_aSutKfjJ8FJLIVwBUgPP3XftzwhxUtTZ0U6o96xMptBfz6pBZKmlrgBl20DbPj$> 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
>>> <https://urldefense.com/v3/__https://doi.org/10.1021/jp073399n__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Il4MNEjlvM46MO3TltglVvwcaIsbz_aSutKfjJ8FJLIVwBUgPP3XftzwhxUtTZ0U6o96xMptBfz6pBZKmlrgBi1QWRzn$>
>>>
>>> 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
>>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Il4MNEjlvM46MO3TltglVvwcaIsbz_aSutKfjJ8FJLIVwBUgPP3XftzwhxUtTZ0U6o96xMptBfz6pBZKmlrgBj8lgiEY$>"
>>> 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!Il4MNEjlvM46MO3TltglVvwcaIsbz_aSutKfjJ8FJLIVwBUgPP3XftzwhxUtTZ0U6o96xMptBfz6pBZKmlrgBj8lgiEY$>"
>>> and also the result output files?
>>> >>>>>
>>> >>>>> All the best,
>>> >>>>> Ray
>>> >>>>>
>>> >>>>> All the best,
>>> >>>>> Ray
>>> >>>>> --
>>> >>>>> Ray Luo, Ph.D.
>>> >>>>> Professor of Structural Biology/Biochemistry/Biophysics,
>>> >>>>> Chemical and Materials Physics, Chemical and Biomolecular
>>> Engineering,
>>> >>>>> Biomedical Engineering, and Materials Science and Engineering
>>> >>>>> Department of Molecular Biology and Biochemistry
>>> >>>>> University of California, Irvine, CA 92697-3900
>>> >>>>>
>>> >>>>> On Fri, Aug 25, 2023 at 12:48 PM Kankana Bhattacharjee via AMBER
>>> >>>>> <amber.ambermd.org> wrote:
>>> >>>>> >
>>> >>>>> > Dear AMBER users,
>>> >>>>> >
>>> >>>>> > I am trying to reproduce the change in enthalpy of binding of
>>> >>>>> > protein-ligand complex using MMPBSA . In the paper, Authors'
>>> used amber12
>>> >>>>> > version and cavity_surften, cavity_offset were set as
>>> 0.005420, -1.008
>>> >>>>> > respectively.
>>> >>>>> > Whereas, I am using amber22 version, in this case, default
>>> values of
>>> >>>>> > cavity_surften, cavity_offset are 0.0378, -0.5692 respectively.
>>> When my
>>> >>>>> > calculations were done using the default (cavity_surften,
>>> cavity_offset
>>> >>>>> > parameters), the result matched closely enough with the paper.
>>> But,
>>> >>>>> > when I explicitly
>>> >>>>> > mentioned the cavity_surften, and cavity_offset parameters
>>> (based on the
>>> >>>>> > paper) in "mmpbsa.in
>>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!Il4MNEjlvM46MO3TltglVvwcaIsbz_aSutKfjJ8FJLIVwBUgPP3XftzwhxUtTZ0U6o96xMptBfz6pBZKmlrgBj8lgiEY$>"
>>> 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 - 12:30:02 PDT
