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

[Pandya, Akash]

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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