[gmx-users] Hydrogen bonding pair selection

Binwu Zhao bzhao at ncsu.edu
Thu Mar 17 21:10:46 CET 2016

Dear Gromacs Users,

I was trying to calculate the number of hydrogen bonds between the “O” on Proline (acceptor) and the “N-H” on Glycine (donor) in my system. There are 16 Proline residues and 32 Glycine residues. 

I first used command “make_ndx" to create two groups, PRO_&_O and N_H_&GLY,  corresponding to 16 “O” on Proline, and 32 “N-H” on Glycine, separately. Then I tried to calculate the number of H-bonds between these two groups.

However, I encountered the following issue

Select a group: 15
Selected 15: 'N_H_&_GLY'
Select a group: 17
Selected 17: 'PRO_&_O'
Checking for overlap in atoms between N_H_&_GLY and PRO_&_O
Calculating hydrogen bonds between N_H_&_GLY (64 atoms) and PRO_&_O (16 atoms)
Found 32 donors and 48 acceptors

The “hbond” command is actually picking up the “N-H” on Glycine as acceptors as well. May I ask if there is any way I can let just the “O” on Proline be the acceptor and “N-H” on Glycine be the donor? In other words, I would like to have 32 donors and 16 acceptors.

Is there any way to do that?

Thanks in advance!


More information about the gromacs.org_gmx-users mailing list