[gmx-users] gmx select
akash.pandya.15 at ucl.ac.uk
Wed Jul 12 23:46:59 CEST 2017
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.
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
What are the residue names in your coordinate file? Glyci probably doesn't fit
On Wed, Jul 12, 2017 at 10:36 PM Pandya, Akash <akash.pandya.15 at ucl.ac.uk>
> 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?
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