Good afternoon,
This is my first time posting a question to the AMBER mailing list. I've found it very useful in the past, finding answers to questions posted by others. Thank you to all of you who support this list!
I have recently been attempting to transition from the use of mm_pbsa.pl to MMPBSA.py to calculate deltaG effective using the Generalized Born model. I previously used GBNSR6 (gbsa=6 with the perl script), and I want to do the same with MMPBSA.py. It is my understanding that if I set igb=66 in the &gb namelist (it's actually the default, but I'm setting it anyway), that GBNSR6 should be used for calculation of surface areas. However, I'm getting "Generalize Bonn ESURF calculated using 'LCPO' surface areas" in my FINAL_RESULTS file. I'm copying the relevant section of that file below. It includes the contents of my input file and the files input at the command line. Am I interpreting the line on use of LCPO correctly that GBNSR6 is not being used? If so, what should I do differently to get MMPBSA.py to use the GBNSR6 model?
Here's the relevant section of the FINAL_RESULTS_MMPBSA.dat file.
| Run on Tue Jul 1 16:15:16 2025
|
|Input file:
|--------------------------------------------------------------
|Input file for MMGBSA
|&general
| startframe=1, endframe=1000, interval=1, keep_files=2,
| netcdf=1,
|/
|&gb
| igb=66, saltcon=0.154, epsin=4, epsout=80, surften=0.005, surfoff=0,
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Solvated complex topology file: 6r9u.top
|Complex topology file: complex.prmtop
|Receptor topology file: protein.prmtop
|Ligand topology file: ligand.prmtop
|Initial mdcrd(s): 6r9u_md1.mdcrd
|
|Receptor mask: ":1-164"
|Ligand mask: ":165"
|Ligand residue name is "JVQ"
|
|Calculations performed using 1000.0 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
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>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 02 2025 - 11:30:01 PDT
