Hello,
While I am running MMPBSA by setting inp=1, then it is giving the warning
message as: "radiopt should be zero for inp=1". But, since "set default
pbradii ..." option was not given during prmtop files generation, so can I
put "radiopt=0" in mmpbsa.in file ?
In amber22 manual, for inp=1, settings is given but that is fro membrane
protein systems. I am not working on membrane proteins. Can I put those
values ?
Thanks
Kankana Bhattacharjee
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08/29/23,
11:02:18 AM
On Tue, Aug 29, 2023 at 12:39 AM Kankana Bhattacharjee <
kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
> 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]
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>>> 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 - 23:00:02 PDT
