how to calculate energy using modeller
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.") --- Thank you for your help. Best, Li
On 1/21/25 6:11 PM, Li Xue via modeller_usage wrote: > 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 scores are zero because by default the Modeller scoring function does not include them; see https://salilab.org/modeller/10.6/manual/node109.html#SECTION001031100000000... Rather than Lennard-Jones, a simpler and faster soft-sphere interaction is calculated instead. Electrostatic terms are not calculated at all (the assumption is that usually your template structure will implicitly encode this interaction). You could try adding env.edat.dynamic_sphere = False env.edat.dynamic_lennard = True env.edat.dynamic_coulomb = True after you create your Environ object. Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
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Li Xue -
Modeller Caretaker