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

[Mark Abraham]

Hi,

No, that's not a prerequisite, but it is one approach.

Mark

On Tue, Jun 20, 2017 at 8:16 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> 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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