[modeller_usage] Re: how to calculate energy using modeller

[Modeller Caretaker <modeller-care@ucsf.edu>]

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#SECTION001031100000000000000

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
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