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

[Lara Bunte]

Hi

I got always the same error.  I tried

trjconv -n index.ndx -s molecule_in_water.pdb -o output


Could you please send an example command how to get the coordinate file out of my index file? 


I typed trjconv -h but I can't filter the knowledge out, thats to much for me. 


Thanks for helping

Greetings
Lara





________________________________
 Von: Justin A. Lemkul <jalemkul at vt.edu>
An: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Gesendet: 22:37 Sonntag, 22.April 2012
Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule
 


On 4/22/12 3:55 PM, Lara Bunte wrote:
> Hi Justin
>
> You wrote:
>
>  >If you do not specify any output file, the default is this .xvg file that
> tells you how many atoms satisfied the >criterion specified in the selection
> string. If you want a coordinate file, it's a two-step process.
>  >
>  >1. Run g_select using the -on flag to produce an output index file of the
> atoms that satisfy your criterion.
>  >
>  >2. Use trjconv with that index file in and your coordinate file to generate
> the structure with those atoms.
>
> I used the command:
>
> g_select -s molecule_in_water.pdb -select '"Close to ISO" resname SOL and within
> 0.5 of resname ISO' -on
>
> And got the size.xvg file and an index.ndx file. Than I want to make my
> coordinate file by
>
> trjconv -n index.ndx
>
> and got the error
>
> Can not open file:
> traj.xtc
>
> I have no traj.xtc file.
>

If you do not specify any other options, trjconv (like all Gromacs programs) 
searches for default file names (listed in the manual and/or the help 
information printed with -h).  You need to provide explicit file names for -s 
and -f in this case, and perhaps -o to choose an appropriate file name and 
format if for some reason you do not wish to use the default name.

-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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