Re: [modeller_usage] Help with rigid body minimization of protein-protein complex

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

On 2/13/18 7:30 AM, mromero AT bsc.es wrote:
> I have been testing whether I could use Modeller to minimize a 
> protein-protein complex.

Modeller's strength is satisfying a bunch of distance restraints. It's 
not a great general purpose dynamics package - for that you'd be better 
off using something like CHARMM or GROMACS. Your script looks fine but 
you haven't given Modeller any restraints between the receptor and 
ligand, so there's nothing to pull them together. In a regular MD 
package you might expect solvent, dispersion, or electrostatics to do 
this, but Modeller doesn't model any of those interactions.

	Ben Webb, Modeller Caretaker
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