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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 23 18:39:17 CEST 2012

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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