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

[Pandya, Akash]

Hi,

I want to select all the ligands in my box within 4A of my protein. I looked at gmx help select and I used the command below but nothing appeared. It didn't show my default groups which correspond to the "14" for ligand and "1" for protein. Please advise me on what to do? Am I missing something?

gmx select -f md_0_1.xtc -s md_0_1.tpr -dt 10000 -tu ns -select `group "14" and within 0.4 of com of group "1"'

Many thanks, 

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: 21 June 2017 11:56
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

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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