[gmx-users] Homology model refinement

[Amir Zeb]

Hello,

I have created a homology model for a protein, where the seq. identity
between the template and target is 40%. The template structure also
contains co-factor and an inhibitor in bound form means it is a complex.
I'll have to define the ligand binding site in target (homology model)
based on inhibitor bound in template structure. But before to reach that
stage, i want to simulate the created model to refine the structure which
is a common practice in modelling. I'm not pretty sure that should i
simulate the model structure along with the inhibitor and co-factor from
template, or one of them, or just only the protein structure alone? Please
let me, if you have any referenced answer.

Regards

Amir