[gmx-users] Hydrogen database

Peter C. Lai pcl at uab.edu
Fri Nov 18 02:37:48 CET 2011

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
       |      |    |   |
       |      |    |   |
      H73    H32  H22  O1-HO1

HDB entry:
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) 
Atom Assignments (from the rtp entry):

         / \
        /   \
 H411-C41   C42-H423
     /  |   |  \
 H412 H413 H421 H422        

HDB entry:
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.

> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

More information about the gromacs.org_gmx-users mailing list