I am try to calculate total no of hydrogen bond present in a system. For that I am using gromacs 5.0.2 (gmx hbond ). The problem is that I am unable to specify donor and acceptor during input. I am using Amber coordinate and topology file that is converted to gromacs topology and coordinate through acpype.py. Now how to specify no of donor and acceptor for water molecules.
Total 350 water molecules is there in my system . So there should be two H bond donor and two H bond acceptor, but during calculation it is showing 350 donor and 350 acceptor.
Thanks
By definition, donors and acceptors are heavy atoms, so if you have 350 water molecules, you have 350 oxygen atoms that can act as both acceptors and donors. A schematic representation of an h-bond would be D-H--A.
If you want to specify whether h-bonds formed by the same D-A pairs via different hydrogens are to be considered separate, I believe you should look at the -merge option.
Alternatively, you can create an index file to only consider h-bonds between subsets of your original systems, if this is what you aim to do.
Hi,
If you've already got your topology and coordinates in Amber format, you could try using the 'hbond' command from cpptraj. For example, you could look for all solute-solvent hydrogen bonds with the following input:
parm myparm.parm7
trajin mytraj.crd
hbond HB out nhb.dat avgout solute_avg.dat \
solventacceptor :WAT@O solventdonor :WAT \
solvout solvent_avg.dat bridgeout bridge.dat \
series uuseries uuhbonds.agr uvseries uvhbonds.agr
Hope this helps,
-Dan
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