Marc Charendoff wrote:
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?
Correct. Angles and dihedrals/impropers require >= 3 atoms.
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.
It shouldn't break anything. As long as you've appropriately defined the
residue in the .rtp and .hdb files (adding one proton, not two, if necessary)
then pdb2gmx should be able to deal with it like anything else.
-Justin
Thanks, Marc
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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