Hello,
I am attempting to see if I can process and run a hydroxide ion using the
ffG43a1 force field. In doing this I have read through chapter 5 of the manual
and have a couple of questions. I do realize that the chemistry and physics of
this will need to be justified, but at this point I'm just trying to make sure
my thought process is right with regards to topology processing by GROMACs.
1) I am first looking to approximate the atomtype by using the OW and H
designated atoms names from ffG43a1.atp.
2) Next ,with regards to residue type, I am looking to designate a new residue
[-OH] in the ffG43a1.rtp files. My real question comes here. For example, for
[HOH] format,
[ HOH ]
[ atoms ]
OW OW -0.82000 0
HW1 H 0.41000 0
HW2 H 0.41000 0
[ bonds ]
OW HW1 gb_35
OW HW2 gb_35
HW1 HW2 gb_41
[ angles ]
; ai aj ak gromos type
[ impropers ]
; ai aj ak al gromos type
[ dihedrals ]
; ai aj ak al gromos type
I understand how I would designate the atoms and bonds, but do I have to bother
with the angles, impropers and dihedrals subsections as shown since I have a
diatomic entity? If yes, I assume GROMACs will know I have a diatomic and
obviously not attempt to assign any of these values?
Last, if I designate this hydroxide and it works, will this prevent pdb2gmx
from automatically assigning a proton to my hydroxide(thus making water)? This
is important as I am looking to observe hydroxide behavior as an anionic ligand
to ZN2+Any guidance you could provide would be appreciated.
Thanks, Marc
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