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

[Mark Abraham]

Hi,

You aren't getting output because you aren't actually making a selection -
see "gmx help select" and its suggestions for where to look for the rest of
the documentation and explained examples.

Mark

On Wed, Jun 21, 2017 at 12:00 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> I'm not sure if the command I entered (shown below) is correct. No output
> was given. I'm unclear as to how this command will enable me to isolate the
> glycine molecules within 4A of the protein molecule?
>
> gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 15000 -selrpos whole_mol_com
> -seltype dyn_mol_com -pdbatoms all
>
> 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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