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

[Pandya, Akash]

I assumed it meant to select all ligand molecules closest to the protein's centre of mass. I'm not entirely sure if that is correct interpretation.

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 11:34
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

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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