[modeller_usage] Re: Close contacts between protein and ligand

[Modeller Caretaker <>]

On 7/21/23 4:08 AM, majort--- via modeller_usage wrote:
> Hi I'm modeling protein with ligands (using the "." options in the
> sequence file). However, in the final models the contacts between
> protein side chains and ligands are too close (the template and
> target have differently sized ligands; the template target ligand has
> a smaller ligand). Is there a way to avoid this, like giving less
> weight to the homology terms and greater weight to the standard FF
> terms?

When using the '.' syntax Modeller copies the ligand and its 
protein-ligand interactions directly from template to target so - as 
you've seen - it won't work very well if the environment differs from 
template to target. Your main options here would be

1. Find a different template that has the ligand in the same environment 
as the target.

2. Define force field terms for the ligand and try to model it flexibly 
rather than as a rigid body.

3. Take your Modeller-generated model and try to refine the 
protein-ligand interactions with a good MD package.

	Ben Webb, Modeller Caretaker
-- 
             https://salilab.org/modeller/
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