[gmx-users] Hydrogen bonding pair selection
erik.marklund at chem.ox.ac.uk
Thu Mar 17 22:18:40 CET 2016
Is there really a problem? With your selections you will not register any hbonds with N_H_&GLY as the acceptor, since the other group contains no donors.
> On 17 Mar 2016, at 20:10, Binwu Zhao <bzhao at ncsu.edu> wrote:
> 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!
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