My apologies. I'm new to the mailing list. I pasted a table into my email, and it got mangled. In summary, the value for EEL that is produced by MMPBSA.py is -5.2417 regardless of whether epsin = 1 or epsin = 4, and it does not change between implicit and explicit trajectories. It is also the same for the GB and GB (GBNSR6) outputs.
________________________________
From: Johann, Timothy via AMBER <amber.ambermd.org
Sent: Monday, July 21, 2025 5:16 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] MMPBSA.py results unresponsive to changes in epsin
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Good afternoon,
I've been analyzing protein-ligand trajectories using MMPBSA.py, and I noticed that the results are not responsive to the value of epsin. Here's what I'm seeing for one complex, both for an explicit solvent trajectory and an implicit solvent trajectory. I'm only providing the EEL because I compared changes to those calculated using mm_pbsa.pl, and EEL (ELE for mm_pbsa.pl) was where the major difference was.
Complex
Epsin
Method
EEL-LCPO
EEL-GBNSR6
4mre-imp
1
py
-5.2417
-5.2417
4mre-imp
4
py
-5.2417
-5.2417
4mre-exp
1
py
-5.2417
-5.2417
4mre-exp
4
py
-5.2417
-5.2417
Here are my input files for MMPBSA.py, pulled from the top of the FINAL_RESULTS_MMPBSA.dat file. In putting together this data for this post, I analyzed only one frame. I originally noticed the issue on analysis of all 1000 frames of my trajectories.
4mre-imp epsin1
|Input file:
|--------------------------------------------------------------
|Input file for MMGBSA
|&general
| startframe=500, endframe=500, interval=1, keep_files=2,
| netcdf=1,
|/
|&gb
| igb=66, saltcon=0.154, epsin=1, epsout=80, surften=0.005, surfoff=0,
|/
|--------------------------------------------------------------
4mre-imp epsin4
|Input file:
|--------------------------------------------------------------
|Input file for MMGBSA
|&general
| startframe=500, endframe=500, interval=1, keep_files=2,
| netcdf=1,
|/
|&gb
| igb=66, saltcon=0.154, epsin=4, epsout=80, surften=0.005, surfoff=0,
|/
|--------------------------------------------------------------
4mre-exp epsin1
|Input file:
|--------------------------------------------------------------
|Input file for MMGBSA
|&general
| startframe=500, endframe=500, interval=1, keep_files=2,
| netcdf=1,
|/
|&gb
| igb=66, saltcon=0.154, epsin=1, epsout=80, surften=0.005, surfoff=0,
|/
|--------------------------------------------------------------
4mre-exp epsin4
|Input file:
|--------------------------------------------------------------
|Input file for MMGBSA
|&general
| startframe=500, endframe=500, interval=1, keep_files=2,
| netcdf=1,
|/
|&gb
| igb=66, saltcon=0.154, epsin=4, epsout=80, surften=0.005, surfoff=0,
|/
|--------------------------------------------------------------
I started the analysis at the command line using the following syntax for the implicit trajectory:
MMPBSA.py -O -i mmgbsa.in -cp complex.prmtop -rp protein.prmtop -lp ligand.prmtop -y 4mre_md1.mdcrd
I started the analysis at the command line using the following syntax for the explicit trajectory:
MMPBSA.py -O -i mmgbsa.in -sp 4mre.top -cp complex.prmtop -rp protein.prmtop -lp ligand.prmtop -y 4mre_md1.mdcrd
I'm not sure if the lack of response is a bug in MMPBSA.py or an error on my part somewhere in the process. Any help would be appreciated. I've seen this more broadly than in just the one complex. I'm happy to provide more data as needed.
Cheers,
Tim
—
Dr. Timothy W. Johann
Professor of Chemistry
office 540-375-2364
johann.roanoke.edu<mailto:
johann.roanoke.edu>
www.calendly.com/johann-2<
http://www.calendly.com/johann-2><
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http://www.calendly.com/johann-2>>
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Received on Mon Jul 21 2025 - 15:30:02 PDT
