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
[ 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.
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