Date: Mon, 17 Feb 2025 13:27:45 +0000
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://aka.ms/LearnAboutSenderIdentification ] 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 http://lists.ambermd.org/mailman/listinfo/amber
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