[gmx-users] gmx select

[Mark Abraham]

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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