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

[Mark Abraham]

Is the radius of your protein greater than 0.4 nm?

Mark

On Wed, 28 Jun 2017 12:05 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:

> 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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