[gmx-users] Hydrogen database

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 18 15:46:04 CET 2011

On 18/11/2011 3:11 AM, Ehud Schreiber wrote:
> Hi,
> 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.

True, though attempting to model pyramidal inversion with the usual MM 
tool kit sounds like a recipe for trouble anyway.

> A better example for two planar hydrogens would be =CH2 such as in 
> ethylene or vinyls.

True, I'll add that to the manual ahead of amide -NH2.

> 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.

Yeah I'd use method 2 for both of these and rely on EM to fix it, but 
some hints are in order.

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

That's a potentially useful feature, but method 2 would still be 
acceptable with due care.

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

I would think so.

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