Most of the issues should wash out after energy minimization anyway, so
I wouldn't care about bond angles too much. Just remember: the topology
controls the geometry not the hydrogen database. Yes the hdb file format
isn't too intuitive but after awhile I figured it out. Here some examples
of hydrogens connected to SP and SP3 hybridized heavy atoms.
I parameterize saturated hydrocarbon backbones a lot, so here is an example
of 1-heptanol (HPOH):
Atom Assignments (from the rtp entry):
H72 H31 H21 H12
| | | |
H71--C7--..--C3--C2--C1-H11
| | | |
H73 H32 H22 O1-HO1
HDB entry:
HPOH 8
1 2 HO1 O1 C1 H11
2 6 H1 C1 C2 O1
2 6 H2 C2 C3 C1
2 6 H3 C3 C4 C2
2 6 H4 C4 C5 C3
2 6 H5 C5 C6 C4
2 6 H6 C6 C7 C5
3 4 H7 C7 C1 O1
Here is isopentyl acetate (isoamyl acetate) (3-methyl-1-butyl-ethanoate)
(IPAC):
Atom Assignments (from the rtp entry):
H12
|
H11-C1-H13
|
C=O
/
OM
\
H21-C2-H22
|
H31-C3-H32
|
C4-H41
/ \
/ \
H411-C41 C42-H423
/ | | \
H412 H413 H421 H422
HDB entry:
IPAC 6
3 4 H1 C1 C O
2 6 H2 C2 C3 OM
2 6 H3 C3 C4 C2
1 2 H41 C4 C41 C3
3 4 H41 C41 C4 C3
3 4 H42 C42 C4 C3
On 2011-11-17 10:11:52AM -0600, 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. 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?
> Thanks,
> Ehud Schreiber.
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==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
[email protected] | Birmingham AL 35294-4461
(205) 690-0808 |
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