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

Lara Bunte lara.bunte at yahoo.de
Mon Apr 23 19:27:25 CEST 2012


In this case my problem is not solvable with gromacs?

All I have is the my_molecule.pdb which is a small molecule in a water box and my generated index.ndx file, size.xvg file and output.xtc file. 


----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Lara Bunte <lara.bunte at yahoo.de>; Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 19:20 Montag, 23.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule

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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