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Bug #517

hdb documentation error

Added by Mark Abraham about 9 years ago. Updated about 9 years ago.

Status:
Closed
Priority:
Normal
Category:
documentation
Target version:
Affected version - extra info:
Affected version:
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Description

In the GROMACS 4 manual on page numbered 103, in the list of hydrogen database types, type 6 refers to a pair of hydrogen atoms built from an aliphatic C and its two heavy-atom neighbours.

The wording

"6 two tetrahedral hydrogens, e.g. C-CH2 -C
two hydrogen atoms (n1,n2) are generated at a distance of 0.1 nm from atom i in
tetrahedral conformation on the plane bissecting angle i-j-k with angle (n-i-n2)=(n1-i-j)=(n1-i-k)=109.5"

doesn't seem to describe the process correctly. If the H atoms are indeed built near atom i, then they should be "on the plane bisecting angle j-i-k" (spelling and ordering errors) and I think the first angle equal to 109.5 degrees should be "(n1-i-n2)".

Alternatively, if the atoms are actually built near atom j, then the i-j-k angle bit is right and all three angles equal to 109.5 degrees are mis-labelled.

I tried to see which way it is, but got rapidly lost in the hackblock nightmare :-)

The wording is still incorrect in git manual, though I happen to have fixed the spelling error during some recent house-keeping.

History

#1 Updated by David van der Spoel about 9 years ago

Fixed in commit 3de0830e71bfbfd3baf1f86b55799c040e8588d5. The "truth" became clear when looking at the HB atoms in the oplsaa.ff/aminoacids.hdb file.

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