[gmx-users] Hydrogen database

Ehud Schreiber schreib at compugen.co.il
Thu Nov 17 17:11:52 CET 2011


I have recently studied the hydrogen database format of .hdb files (page
118, section 5.6.4 in the manual version 4.5.4). I would like to make a
few remarks that, if correct, may need addressing.

1)      Method 3 of adding the hydrogens, that of two planar hydrogens,
gives -NH2 as the example. I think this is misleading, as although this
is true for an amide group -C(=O)NH2 such as in an asparagine and
glutamine side chains, the nitrogen is tetrahedral in the R-NH2 case or
in the amino acid N-terminus. A better example for two planar hydrogens
would be =CH2 such as in ethylene or vinyls.  

2)      The provided methods for adding hydrogens are not covering the
whole set of possibilities. In particular, it seems to me that three
methods are lacking, although admittedly they are less common:

a.       One tetrahedral hydrogen connected to atom i which is in turn
connected to two atoms j,k such that n is on the plane bisecting angle
j-i-k; n-i-j = n-i-k = 109.47 degrees; and dihedral n-i-j-l > 90
degrees. Example: secondary amines R2NH. This case can be mimicked by
method 2 with i,j,l atoms so is perhaps superfluous.

b.      One planar hydrogen connected to atom i which is connected to
only one other atom j such that n-i-j = 120 degrees and n-i-j-k is
trans. Example: R2C=NH.

c.       One linear hydrogen such that n-i-j is a straight line.
Example: #CH where # is a triple bond.

3)      I haven't checked this, but can the k atom be a hydrogen added
in an earlier line of the same .hdb file?

What do you say?


Ehud Schreiber. 

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