GROMACS version:2023
GROMACS modification: Yes/No
Hi all,
I am interested in identfying if water molecule may be significant in my active site.
I have done some Hbond analysis between my protein and ligand and found some result. However, when i do Hbond analysis between ligand and Water molecules, i get a very weird result
Hbond Protein-Ligand
Specify 2 groups to analyze:
Selected 1: ‘Protein’
Selected 41: ‘L01’
Checking for overlap in atoms between Protein and L01
Calculating hydrogen bonds between Protein (37524 atoms) and L01 (15 atoms)
Found 3452 donors and 6949 acceptors
Will do grid-search on 33x31x27 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 24 threads.
Average number of hbonds per timeframe 2.646 out of 1.1994e+07 possible
HBond Water-Ligand
Specify 2 groups to analyze:
Selected 44: ‘Water’
Selected 41: ‘L01’
Checking for overlap in atoms between Water and L01
Calculating hydrogen bonds between Water (174123 atoms) and L01 (15 atoms)
Found 58041 donors and 58044 acceptors
Will do grid-search on 33x31x27 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 24 threads.
Average number of hbonds per timeframe 1.213 out of -4.63018e+08 possible
The portion im confused on is Average number of hbonds per timeframe 1.213 out of -4.63018e+08 possible
negative number of hbond possible? why?
i tried to dig into finding the algorithm that gromacs uses to calculate but couldnt find it.
Anyone can point to what went wrong?
Q2) Is it viable to use hx or hbn to find important residues that hbonds with my ligand, instead of having to monitor the whole trajectory?
Kind regards