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

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Wed Jun 28 16:57:23 CEST 2017 

I want to see the closest binding glycine molecules so would "within x distance of any protein atom" be more appropriate?

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 15:13
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs

Hi,

You get to choose... do you want everything within some distance of the protein center of mass, or any protein atom, or something else. But don't be suprrised if there are no ligand atoms super close to the protein center of mass ;-)

Mark

On Wed, Jun 28, 2017 at 12:47 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
wrote:

> 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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