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

Lara Bunte lara.bunte at yahoo.de
Mon Apr 23 09:46:04 CEST 2012


that worked. I used

trjconv -n index.ndx -f my_molecule.pdb -o output

After this I got an trajectory file output.xtc 

Now I have to get really a coordinate file, i.e. pdb file. I used the command

trjconv -s -f output.xtc -o output.pdb

to convert it to pdb, as I read it in this tutorial: 


But I got this error:

Can not open file:

I don't have a topol.tpr file. How do I got my coordinates out of this .xtc file?


Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 23:10 Sonntag, 22.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule

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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