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.
Mark
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