Hydrogen bond output from CHARMM is wrong
In version 4.5.4, running g_hbond on a trajectory using CHARMM27 results in incorrect output. g_hbond only detects the terminal amino group as an H-bond donor and no others. I have found that the reason is due to the fact that in CHARMM27, the amide proton is named "HN" for all residues. If one changes the names of these protons in the topology to simply "H" then g_hbond works correctly. I guess the fix would either be to expand the names that g_hbond accepts when identifying H-bond donors, or to change the way the atoms are named in the CHARMM27 residues (.rtp file).
Adjusted construction of default index groups
The CHARMM convention of naming the H atom bonded to backbone N as
"HN" led to erroneous construction the MainChain+H and (complementary)
SideChain groups. Protein, Protein-H and SideChain-H were fortuitously
#3 Updated by Mark Abraham almost 9 years ago
- Status changed from New to Feedback wanted
I couldn't reproduce this with my own CHARMM27 trajectory+tpr. 8 donors and 15 acceptors were found for ACE-ARG-ALA-ALA-GLU-NAC, which sounds about right.
Moreover, the test in
src/tools/gmx_hbond.c looks for the first letter of various atom names, and so "H" and "HN" both satisfy.
#4 Updated by Justin Lemkul almost 9 years ago
It finds some, but not all. I'm attaching a test case to see if you can replicate it. With "correct.tpr," the H names are changed to "H" instead of "HN." For "wrong.tpr," the original "HN" name is retained.
g_hbond -s wrong.tpr -f frame.gro ... (select MainChain+H for both groups) Average number of hbonds per timeframe 4.000 out of 16.5 possible
g_hbond -s correct.tpr -f frame.gro (again, MainChain+H) Average number of hbonds per timeframe 29.000 out of 280.5 possible