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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