[gmx-users] make_ndx bug?

gromacs query gromacsquery at gmail.com
Fri Sep 19 14:43:09 CEST 2014

Hi All

I have some pdb file and I removed hydrogens. When I try to make ndx file
using some residue option then rather printing atom numbers in that residue
it prints line number where that residue starts and ends.

make_ndx -f no_H.pdb -o test.ndx

selecting as:

r 300-330

Then in ndx file I get the line number where residue number 300 starts (not
the atom number). I think hydrogens were missing so it just uses line
Though I can handle this just wanted to know if this is a bug?


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