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

[Lara Bunte]

Hi Justin

First: 

It works, thank you :-)

Second: 

You wrote:
>Again, as has been stated several times, giving any Gromacs program a 
command line option (like -s or -f) in the absence of an explicit file 
>name, will cause the program to look for a default file name (which are 
listed in the manual or with -h).  In the first case, with no file name 
given >to -s, trjconv looks for topol.tpr and fails.  In the second case, -f is looking for traj.xtc and fails.  Provide explicit file names for 
all options, unless >you actually have used the default names (which in 
your case, you haven't).
>
>Please go back to my previous advice: 
"Supply your .pdb file to the -s flag." That doesn't mean add -s to the 
command line and expect magic >to happen ;)  It means you need to invoke 
the -s flag to signal that you are providing a file there, and then name
 that file. 

This is the first time that I understand what you are talking about. I had problems because I don't understand your englisch, but now I got it. For every Gromacs Option I have to give a file for it and what file type this is I got out of help. 

Thanks for being such patient with me.

Greetings
Lara






----- Ursprüngliche Message -----
Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
CC: 
Gesendet: 18:35 Montag, 30.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule



On 4/30/12 12:29 PM, Lara Bunte wrote:
> 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?
> 

Again, as has been stated several times, giving any Gromacs program a command line option (like -s or -f) in the absence of an explicit file name, will cause the program to look for a default file name (which are listed in the manual or with -h).  In the first case, with no file name given to -s, trjconv looks for topol.tpr and fails.  In the second case, -f is looking for traj.xtc and fails.  Provide explicit file names for all options, unless you actually have used the default names (which in your case, you haven't).

Please go back to my previous advice: "Supply your .pdb file to the -s flag." That doesn't mean add -s to the command line and expect magic to happen ;)  It means you need to invoke the -s flag to signal that you are providing a file there, and then name that file.  For pedantic purposes:

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

The -f flag specifies the file that is being operated on.
The -s flag specifies a file from which (in this case) atom and residue names are being read.  It is necessary because your output format (.pdb) requires this information.

-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

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