[gmx-users] Hydroxide Attempt

[Justin A. Lemkul]

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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> 
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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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