[gmx-users] Homology model refinement

[Amir Zeb]

Hi Mijiddorj,

My target protein size is around 250 residues. It's pretty small and i
don't have issue with time. Can you please let me know the actual command
line for cluster analysis?

Regards!

On Thu, Dec 22, 2016 at 12:59 AM, Mijiddorj Batsaikhan <
b.mijiddorj at gmail.com> wrote:

> Hi,
>
> What is your target structure size? If you want to perform explicit solvent
> simulation for bigger protein, it may be time-consuming simulation.
> My suggestion is that you can run simulation implicitly, it helps you
> remove some bad contacts. Then, you can make cluster analysis and find
> dominating configurations from section that converged to stable rmsd
> values.
>
> Mijiddorj
>
> > > 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
> > > > --
> >
> >
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