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-- 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 >> > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Aug 28 2023 - 11:00:02 PDT