[gmx-users] File editing - only one layer of water around a molecule

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 22 23:10:43 CEST 2012

On 4/22/12 5:07 PM, Lara Bunte wrote:
> Hi
> I got always the same error. I tried
> trjconv -n index.ndx -s molecule_in_water.pdb -o output
> Could you please send an example command how to get the coordinate file out of
> my index file?
> I typed trjconv -h but I can't filter the knowledge out, thats to much for me.

You should be passing your coordinate file to -f, not -s.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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