I realised "flags" is not part of the command.
!! Sorry for the silly question. It's the end of a long day and I'm tired!
Quoting Jennifer Williams <jennifer.willi...@ed.ac.uk>:
Hi,
Is there some way of making the make_ndx file interactive so that I can
include it in a script?
I would usually type in "a C_O and O_C" to select my atoms
I've tried altering the example on the webpage for making commands
interactive:
make_ndx -flags <<EOF
a C_O OC
q
EOF -f nn_1.pdb
but -flags doesn't seem to be recognized. Does anyone know a work around?
Thanks
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