How to determine the value corresponding to the strength of a hydrogen bond?

[Andrew Orry]

Q.

The sizes of the spheres and coloring of the hydrogen bonds relates to the strength of the hydrogen bond. I realize that a 0-2 scale is used for weak to strong (what is considered 0 and what is 2?), but how can I determine what the actual value is from my model? 

A.

The coloring of the H-bonds are red (strong - thick spheres) to blue (weak - thin spheres). To return the value that dictates the coloring and size you need to use show hydrogen bond exact as shown here:

http://www.molsoft.com/man/icm-commands.html#show-hbondexact

then the value is reported in the Field() of the atom

Example:

read pdb "1crn"
convertObject a_ yes yes no no yes no yes ""
show hbond exact a_1crn_1.a/^T30/og1 a_1crn_1.a/^C32/hn
Field(a_1crn_1.a/^C32/hn)

There are no absolute units. Absolute value of hydrogen bond strength is not well defined because of competing solvation contributions and because partitioning of interaction energy into hydrogen bonding and other terms is largely arbitrary - e.g. many forcefields don’t have a hydrogen bonding term at all and rely on electrostatic term to account for it.