Hello,
I have a question pertaining to when the hbond command in cpptraj considers a hydrogen bond to be formed. On page 662 of the Amber18 manual, it states “If the A to D distance is less than the distance cutoff and the A-H-D angle is greater than the angle cutoff a hydrogen bond is considered formed.” Also, when entering ‘help hbond’ within cpptraj, the help message includes the statement “Hydrogen bond is formed when A to D distance < dcut and A-H-D angle > acut”. However, various lines (such as line 750) within the script Action_HydrogenBond.cpp have the condition “if ( !(dist2 > dcut2_) )”, which is analogous to <=, not <. In case I didn’t understand the script, I constructed a model system with a hydrogen bond with an A-D distance of 5.0000 angstroms and an A-H-D angle of 90.0000 degrees. Cpptraj counts this hydrogen bond as being formed when running the hbond command on this system with dcut and acut set to 5.0000 angstroms and 90.0000 degrees, respectfully. So, it seems that a hydrogen bond is considered to be formed when the A-D distance is <= (not <) and the A-H-D angle is >= (not >). Is this correct?
While this makes no real practical difference in the results of an analysis, it’s helpful to know the true definition for documenting purposes.
Thanks,
Drew
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Received on Wed Sep 22 2021 - 11:30:02 PDT
