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

[Sergio Manzetti]

Yes, remove figure reference, use figures from us, and insert reference at the same place for the Software: 

"Figure made with MacMolPlt" 
http://www.sciencedirect.com/science/article/pii/S1093326399000029 


Sergio Manzetti 

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From: "Mark Abraham" <mark.j.abraham at gmail.com> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Tuesday, June 20, 2017 8:40:33 PM 
Subject: Re: [gmx-users] Protein-ligand binding Cut-offs 

Hi, 

No, that's not a prerequisite, but it is one approach. 

Mark 

On Tue, Jun 20, 2017 at 8:16 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk> 
wrote: 

> Hi, 
> 
> Is the pre-requisite for this command a separate index file for the 
> glycine molecules I have? 
> 
> 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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