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

[Mark Abraham]

How are you interpreting "within 4A of my protein?" What has your protein's
center of mass got to do with it?

Mark

On Wed, Jun 28, 2017 at 12:16 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> Yes it is. So that means I need a cut-off greater than right?
>
> 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: 28 June 2017 11:08
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Protein-ligand binding Cut-offs
>
> 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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