[gmx-users] Question Regarding Hydrogen Database Error

Justin Lemkul jalemkul at vt.edu
Sun Feb 5 01:13:31 CET 2017

On 2/4/17 7:00 PM, Elise White wrote:
> Hello everyone,
> I am a junior at Binghamton High School amidst researching the Tau protein
> through
> various biomolecular simulations and studies.
> Recently, I introduced the NMA capping group to the force field I am
> working with - Gromos96
> 53a6 - by properly adding it to the residuetypes.dat file and adjusting the
> aminoacids.rtp file as
> depicted below based on a topology of NMA I generated using the ATB. As far
> as I'm concerned, this process was successful, as GROMACS recognized the
> capping group.
> [ NMA ]
>  [ atoms ]
>      H     H   0.258     1
>      N     N  -1.331     2
>     CA   CH3   0.571     3
>    1HA     H  -0.166     4
>    2HA     H  -0.166     5
>    3HA     H  -0.166     6

These charges add up to -1, so something has gone wrong.

Moreover, since Gromos96 is a united-atom force field, I have doubts about 
whether or not there should even be H atoms on this carbon.  The point of a 
capping group is to mimic a peptide bond, and the CH3 is an analog to the 
alpha-carbon of an amino acid.  Gromos96 treats such carbons as uncharged.

You also won't be able to generate H atoms that are named with integers as the 
first character, but again I don't think they should be there.  Their types are 
also wrong, as H is a polar H atom (e.g. -NH or -OH groups) so this isn't 
correct, in addition to the fact that a CH3 atom type means you don't have H 
attached to that carbon.  I'm not sure why ATB would give you such a topology, 
but something seems fishy, starting from the very charges themselves.

>  [ bonds ]
>      H     N
>      N    CA
>     CA   1HA
>     CA   2HA
>     CA   3HA
>  [ angles ]
>     H     N    CA
>     N    CA   1HA
>     N    CA   2HA
>     N    CA   3HA
>   1HA    CA   2HA
>   1HA    CA   3HA
>   2HA    CA   3HA
> However, an error message popped up notifying me that I need to update the
> hydrogen database with the 3 tetrahedral hydrogens attached to the alpha
> carbon- 1HA, 2HA, and 3HA.
> I read chapter 5.6.4 of the manual thoroughly several times, and I am still
> incredibly confused about what a "control atom" is - and am quite unsure
> about what "control atoms" I need to specify before adding my 3 tetrahedral
> hydrogens.

"Control atoms" are atoms that can be used to define a local geometry, i.e. 
there is a simple internal coordinate builder that adds H atoms based on the 
relative positions of existing atoms.  For CHARMM, our NMA capping group (which 
is named NME to avoid a clash with the N-methylacetamide group) is:

NME     2
1   1   HN  N   -C  CH3
3   4   HH3 CH3 N   -C

I would expect a Gromos96 NMA .rtp file to look more like:

[ NMA ]
  [ atoms ]
      H     H   0.310     1
      N     N  -0.310     2
     CA   CH3   0.000     3
  [ bonds ]
      N     H
      N     CA

with an .hdb entry of

NMA     1
1   1   H  N   -C  CH3

It should be rather simple.


> It is my hope that one of you vastly experienced computational biochemists
> could point me in the right direction or clarify my understanding.
> I appreciate you reading my message - it is truly an honor - I respect and
> admire all of you.
> Best regards,
> Elise White


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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