[gmx-users] Protein-ligand binding Cut-offs

[Mark Abraham]

Hi,

Gmx select will produce a selection eg of all molecules with an atom within
a cutoff of any atom in another molecule.

Mark

On Fri, 16 Jun 2017 18:15 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:

> Hi all,
>
> I have ran a simulation with a protein and multiple ligand molecules
> inserted randomly inside a box. I want to isolate those ligand molecules
> that are closest to the protein by a cut-off of four angstroms or so. Is
> there a command I could use to do this for me or would I have to use a
> molecular visualizer software for this?
>
> Thanks,
>
> Akash
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