Hi Ray Luo,
Sure, it will help me.
I will sent you a email of the list.
Thank you
Best,
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: Ray Luo <rluo.uci.edu>
Sent: Tuesday, February 18, 2025 3:33 PM
To: Gabriel Ernesto Jara <gabriel.jara.lnbio.cnpem.br>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Help with MMPBSA.PY Pairwise Decomposition Results
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Gabriel,
We didn't implement the residue decomposition feature in mmpbsa.py, but we'll be happy to look into your example. Can you share with me off the list your files so I can reproduce your results?
All the best,
Ray
--
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<mailto: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<
http://lnbio.cnpem.br/en>
________________________________
From: Gabriel Ernesto Jara via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>>
Sent: Tuesday, February 4, 2025 9:59 AM
To: amber.ambermd.org<mailto:amber.ambermd.org> <amber.ambermd.org<mailto:amber.ambermd.org>>
Subject: [AMBER] Help with MMPBSA.PY Pairwise Decomposition Results
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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<
http://lnbio.cnpem.br/en>
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Received on Thu Feb 20 2025 - 09:30:02 PST
