[gmx-users] gmx select

[Pandya, Akash]

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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