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

[Pandya, Akash]

Hi,

Is the pre-requisite for this command a separate index file for the glycine molecules I have?

Akash

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark Abraham
Sent: 16 June 2017 17:22
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

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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