[gmx-users] Make_ndx for gmx hbond

rose rahmani rose.rhmn93 at gmail.com
Mon Sep 3 18:33:49 CEST 2018


I want yo do gmx hbond analysis. I have an capped tyrosine amino acid in a
box of water. I want to calculate number of hydrogen bonds that amino acid
make with the waters around it. But i couldn't understand the manual
description about how make an index file for this purpose. If i choose
group protein and sol in make_ndx command does it give me what i want? Or i
should specify the O and N atoms in amino acid and make index for it
seperately? If yes, i couldn't understand how to choose an atom from the
help which comes with make_ndx command( should i write
atom type O
atom type N )?

Would you please help me? I couldn't understand the manual.

Best regards

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