[gmx-users] Hydroxide Attempt

Marc Charendoff mcharend at sbcglobal.net
Mon Aug 17 21:38:57 CEST 2009


    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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