[gmx-users] gmx select

[Pandya, Akash]

gmx select -f output.gro -select "Close to protein" resname Glyci and within 0.5 of group "Protein"'

-----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: 13 July 2017 00:04
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] gmx select

Hi,

Can you please copy, paste and post your actual commands. I don't think your use of quote marks would have led to a valid shell command. The whole selection text will need to be inside some quotes.

Mark

On Wed, 12 Jul 2017 23:47 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:

> I have used the same name in my coordinate file. For Glycine it is 
> spelt as Glyci, so the word has been cut off. I know this is correct 
> because I use the same name in VMD.
>
> -----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: 12 July 2017 22:42
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] gmx select
>
> Hi,
>
> What are the residue names in your coordinate file? Glyci probably 
> doesn't fit
>
> Mark
>
> On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash 
> <akash.pandya.15 at ucl.ac.uk>
> wrote:
>
> > Hi all,
> >
> >
> > I am trying to select all the glycine molecules with 0.5nm of my protein.
> > I tried both of these commands I got from the gromacs website:
> >
> > gmx select -f output.gro -select "Close to protein" resname Glyci 
> > and within 0.5 of group "Protein"' -ofpdb
> >
> > gmx select -f output.xtc -s output.tpr (my converted input file) 
> > -select "Close to protein" resname Glyci and within 0.5 of group 
> > "Protein"' -ofpdb
> >
> >
> > Nothing comes up when I enter them. Please could someone help me 
> > with
> this?
> >
> >
> > Akash
> > --
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