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

[Lara Bunte]

Hi

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: 


http://www.mpibpc.mpg.de/groups/de_groot/compbio/p1/index.html

But I got this error:

Can not open file:
topol.tpr


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

Thanks
Greetings
Lara






________________________________
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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================
-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists