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

[Lara Bunte]

Hi

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. 


Greetings
Lara






----- 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>
CC: 
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

-- 
========================================

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

========================================