Custom Search
-- 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 10:41 PM Kankana Bhattacharjee < kankana.bhattacharjee_phd21.ashoka.edu.in> wrote: > 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 > <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!M44HDsO75s5K9pK7j2u_ss10tETZtmks4wVKK9N_DcjG_MvMsYs5hE4awf7aP9rukW7ZuDHM9XIT-lVCbWoqgWJOuHz3$> > file ? > In amber22 manual, for inp=1, settings is given but that is fro membrane > protein systems. I am not working on membrane proteins. Can I put those > values ? > > Thanks > Kankana Bhattacharjee > > > > [image: Mailtrack] > <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!CzAuKJ42GuquVTTmVmPViYEvSg!M44HDsO75s5K9pK7j2u_ss10tETZtmks4wVKK9N_DcjG_MvMsYs5hE4awf7aP9rukW7ZuDHM9XIT-lVCbWoqgbWPg-yy$> Sender > notified by > Mailtrack > <https://urldefense.com/v3/__https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&__;!!CzAuKJ42GuquVTTmVmPViYEvSg!M44HDsO75s5K9pK7j2u_ss10tETZtmks4wVKK9N_DcjG_MvMsYs5hE4awf7aP9rukW7ZuDHM9XIT-lVCbWoqgbWPg-yy$> 08/29/23, > 11:02:18 AM > > On Tue, Aug 29, 2023 at 12:39 AM Kankana Bhattacharjee < > kankana.bhattacharjee_phd21.ashoka.edu.in> wrote: > >> Thanks a lot for your suggestions. Authors dint mention the pbradii value >> in the paper. Also, I dint mention the pbradii option during making the >> prmtop files. As while doing the amber ras-raf tutorial i mentioned the >> pbradii option during creating prmtop files then mmpbsa was giving errors >> by saying inconsistent prmtop files. When I removed that option then mmpbsa >> ran fine and took default pbradii value. So, in this case, what pbradii >> value I have to mention in mmpbsa.in >> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!M44HDsO75s5K9pK7j2u_ss10tETZtmks4wVKK9N_DcjG_MvMsYs5hE4awf7aP9rukW7ZuDHM9XIT-lVCbWoqgWJOuHz3$> >> 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 >>>>> >>>> _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Aug 29 2023 - 15:00:01 PDT