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

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 23 19:20:40 CEST 2012

On 4/23/12 1:13 PM, Lara Bunte wrote:
> 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?

Apparently you need a .tpr file supplied to the -s flag to do such a 
transformation.  I'm not sure why it's necessary in this case, but it is.



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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