[gmx-users] File editing - only one layer of water around a molecule
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:
> 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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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