Re: [AMBER] Doubt about ligand binding in proteins

From: Kenneth Huang <>
Date: Sun, 24 May 2015 13:51:22 -0400


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.



On Sat, May 23, 2015 at 9:05 PM, Gustavo Avelar Molina <> 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
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