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

[Lara Bunte]

Hi
If I use 

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

I got this error again

Can not open file:
topol.tpr

Whats now the problem?


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: 18:39 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule



On 4/23/12 11:01 AM, Lara Bunte wrote:
> 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?
>

When I was referring to your "original command," I meant this one:

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

At this point, trjconv expects that you want an .xtc (trajectory) file, since 
you did not explicitly specify an extension.  An .xtc file contains no 
information regarding atom names, so converting it back to a .pdb file requires 
a .tpr file, as the error you got (below) indicates.  If you want to make your 
life simple, be more specific in what you tell trjconv.  Want a .pdb file?  Tell 
it so:

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

-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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