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-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical, Applied and Materials Physics, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Mon, Feb 17, 2025 at 5:28 AM Gabriel Ernesto Jara via AMBER < amber.ambermd.org> wrote: > HI all, > > I reported an issue with MMPBSA.py two weeks ago and wanted to follow up. > I have attached a figure showing a negatively charged residue that, based > on expectations, should contribute favorably. However, the decomposition > results indicate the opposite. > I would appreciate your insights on this matter. > Best regards, > Gabriel > > > > --- > Gabriel Ernesto Jara, PhD > Specialist in Scientific Computation - JR. > Brazilian Biosciences National Laboratory - LNBio > Brazilian Center for Research in Energy and Materials - CNPEM > 10,000 Giuseppe Maximo Scolfaro St. > Campinas, SP - Brazil 13083-100 > Phone: +55 19 3512-1255 > lnbio.cnpem.br/en > ________________________________ > From: Gabriel Ernesto Jara via AMBER <amber.ambermd.org> > Sent: Tuesday, February 4, 2025 9:59 AM > To: amber.ambermd.org <amber.ambermd.org> > Subject: [AMBER] Help with MMPBSA.PY Pairwise Decomposition Results > > [You don't often get email from amber.ambermd.org. Learn why this is > important at > https://urldefense.com/v3/__https://aka.ms/LearnAboutSenderIdentification__;!!CzAuKJ42GuquVTTmVmPViYEvSg!OErGBcoJbNObe9vjt20ABoE4k54LA8Qs2xpBP_JD-AoOHO1c6HlsHZbgiU28QMQRLY36ITk4Nsg$ > ] > > Dear all, > > I performed a pairwise decomposition using MMPBSA.PY (version 14.0) on a > system with a very high net charge (-24 e-), protonated using pdb2pqr at pH > 8. I observed that almost all positively charged residues had a strong > favorable contribution, while all negatively charged residues showed a > strong unfavorable contribution—even those at the binding interface. Below > is the input file used for the calculation: > > &general > startframe=1, endframe=300, interval=1, > verbose=2, keep_files=0, entropy=0, netcdf=1, > / > &pb > istrng=0.15, fillratio=4.0, indi=6.0 > / > &decomp > idecomp=1, > #print_res=":375-385,575-585" > / > > I also noticed a similar, though less pronounced, behavior in systems with > a net charge of -6 e-. > > Could anyone help me understand whether I need to adjust my input > parameters, or if this might be an artifact or limitation of the method? > > I appreciate any insights you can provide. > > Best regards, > > Gabriel > > > > --- > Gabriel Ernesto Jara, PhD > Specialist in Scientific Computation - JR. > Brazilian Biosciences National Laboratory - LNBio > Brazilian Center for Research in Energy and Materials - CNPEM > 10,000 Giuseppe Maximo Scolfaro St. > Campinas, SP - Brazil 13083-100 > Phone: +55 19 3512-1255 > lnbio.cnpem.br/en > > > Aviso Legal: Esta mensagem e seus anexos podem conter informações > confidenciais e/ou de uso restrito. Observe atentamente seu conteúdo e > considere eventual consulta ao remetente antes de copiá-la, divulgá-la ou > distribuí-la. Se você recebeu esta mensagem por engano, por favor avise o > remetente e apague-a imediatamente. > > Disclaimer: This email and its attachments may contain confidential and/or > privileged information. Observe its content carefully and consider possible > querying to the sender before copying, disclosing or distributing it. If > you have received this email by mistake, please notify the sender and > delete it immediately. > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!OErGBcoJbNObe9vjt20ABoE4k54LA8Qs2xpBP_JD-AoOHO1c6HlsHZbgiU28QMQRLY36BMIv1e4$ > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > > https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!OErGBcoJbNObe9vjt20ABoE4k54LA8Qs2xpBP_JD-AoOHO1c6HlsHZbgiU28QMQRLY36BMIv1e4$ > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Feb 18 2025 - 11:00:02 PST