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

Lara Bunte lara.bunte at yahoo.de
Mon Apr 23 19:13:37 CEST 2012

If I use 

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

I got this error again

Can not open file:

Whats now the problem?


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 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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