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

[Lara Bunte]

Hi Justin

I got the error 


Can not open file:
topol.tpr


if I type trjconv -n index.ndx -f molecule.pdb -o output.pdb -s


and I got the error

Can not open file:
traj.xtc

if I type trjconv -n index.ndx -f -s molecule.pdb -o output.pdb 


What is the problem? 

Greetings and thank you for helping me.
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: 18:07 Montag, 30.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule



On 4/30/12 11:41 AM, Lara Bunte wrote:
> Hi
>
> I have the command
>
>
> trjconv -n index.ndx -f molecule.pdb -o output.pdb
>
>
> that don't work because of the missing topol.tpr file. You wrote:
>
>> Supply your .pdb file to the -s flag
>
> Where exactly do I have to write -s in my command?
>
>

Anywhere.  Order of arguments is irrelevant to all Gromacs commands.

-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

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