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

Lara Bunte lara.bunte at yahoo.de
Sun Apr 22 23:07:19 CEST 2012


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


 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 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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