[gmx-users] doubt regarding make_ndx

[Venkat Reddy]

Dear all,
I try to make my residues of interest as an index group using the
command make_ndx -f conf.gro -o index.ndx. I have entered my residues as
>  r 15 23 27 30 82 84 125 127 129 140 143 184 187 188 191 194 195 198 201
205 206 208 211 228 236 261 263 273 277 282 283 428 429 432 433 438 441 457
459 463

then I renamed the index file using

> name 26 tunnel
>q

When I checked back my index file, I found some water molecule atoms also
inserted in the tunnel group. What could be the problem?
Am I doing in the proper way?

Thanks a lot for your valuable time.

-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036