Dear Modeller Team,
I am currently looking for a quick method for calculating the energy of
protein structures. I understand that Modeller utilizes a simplified
version of the CHARMM force field, which suits my needs, as I’m looking for
a fast and approximate energy calculation.
I would like to print out each energy term, but with the current code I’m
using, the Lennard-Jones and Coulomb terms are returning zero. Could you
please advise on how to resolve this issue?
The code that I used:
from modeller import *
from modeller.scripts import complete_pdb
# Initialize MODELLER environment (use Environ instead of environ)
env = Environ()
# Load topology and parameter libraries
env.libs.topology.read(file='$(LIB)/top_heav.lib') # Heavy atom topology
env.libs.parameters.read(file='$(LIB)/par.lib') # Parameter library
# Read in the protein structure
mdl = complete_pdb(env, '3VXU.pdb')
# Calculate energy
mdl.energy()
# Energy calculations are complete
print("\nEnergy calculation completed.")
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Thank you for your help.
Best,
Li
