Gustavo,
That depends a lot of what you're trying to see, how well resolved the
crystal structure is, if your binding site is missing large portion, etc.
If you have a structure that is missing noticeable pieces, especially in
the area you're interested in, it'd be a smart idea to let the
'whole' structure equilibrate before placing the ligand into it and then
carrying out your simulation.
If you're just taking a crystal structure that more or less complete and
has everything you want, then I imagine the ligand should be fine just
being added to the PDB and being considered for minimization.
Best,
Kenneth
On Sat, May 23, 2015 at 9:05 PM, Gustavo Avelar Molina <
gustavoavelarmolina.usp.br> wrote:
> Hi everyone,
>
> I've been asking myself whether it is appropriate to place a ligand in a
> protein (be it through covalent bonding or not) after its minimization or
> equilibration. Or is it more appropriate to do the modification just by
> using the original protein PDB as the atomic coordinates source? I'm
> assuming here that there are no experimental data about the atomic
> coordinates of the bound protein.
>
> I would be grateful if someone could explain it me.
>
> Regards,
>
> Gustavo
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Received on Sun May 24 2015 - 11:00:03 PDT
