[gmx-users] Why the index file does not contain the indices I want?

ZHANG Cheng 272699575 at qq.com
Wed Nov 22 20:08:25 CET 2017

Dear Gromacs,
After running 
echo r 66 q|gmx make_ndx -f md_0_1.tpr -o index.ndx

I got the index.ndx file. However, all the sections are those default ones, without the 66th residue atoms I want:

[ System ]
[ Protein ]
[ Protein-H ]
[ Ion ]
[ NA ]
[ CL ]
[ Water_and_ions ]

May I ask how to obtain the indices for the residue 66?

In addition, my protein has light chain (L) and heavy chain (H). So how to specify the 66th residue within the light chain by using "echo"?

Thank you.

Yours sincerely

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