[gmx-users] Question Regarding Hydrogen Database Error

Elise White elisenwhite at gmail.com
Sun Feb 5 01:00:31 CET 2017

Hello everyone,

I am a junior at Binghamton High School amidst researching the Tau protein
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
 [ 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

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

More information about the gromacs.org_gmx-users mailing list