[gmx-users] Homology model refinement

[Mark Abraham]

Hi,

What us the purpose in doing MD on the homology model? That'll tell you
whether you need a model with the other parts.

Mark

On Thu, 22 Dec 2016 16:51 Amir Zeb <zebamir85 at gmail.com> wrote:

> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>