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

[Lara Bunte]

Hi

What do you mean with 


>Specify a .pdb file as the output of your original command.

I wrote in 


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


in the last part output.pdb. What should I specify more?

Thanks
Greetings
Lara




----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
CC: 
Gesendet: 13:02 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule



On 4/23/12 3:46 AM, Lara Bunte wrote:
>
>
> 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?
>

Specify a .pdb file as the output of your original command.

-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

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