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Molecular oxygen

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Molecular oxygen

I am planning on docking a ligand in a cavity with a heme and a constrained oxygen. Whereas I can make params of ligands and non-canonical residues, I cannot for molecular oxygen (OXY). It is not in the database either. gives the following 

$ python oxy.sdf -n OXY
Centering ligands at (   0.000,    0.000,    0.000)
Atom names contain duplications -- renaming all atoms.
WARNING:  structure contains double bonds but no aromatic bonds
  Aromatic bonds must be identified explicitly --
  alternating single/double bonds (Kekule structure) won't cut it.
  This warning does not apply to you if your molecule really isn't aromatic.
Total naive charge -1.520, desired charge 0.000, offsetting all atoms by 0.760
Fragment 1: [' O1 ', ' O2 ']
Traceback (most recent call last):
  File "", line 1323, in <module>
  File "", line 1295, in main
    num_frags = fragment_ligand(m)
  File "", line 535, in fragment_ligand
    raise ValueError("Fragment %i has %i atoms; merge with another fragment or add virtual atoms to make 3 total" % (frag_id, num_atoms))
ValueError: Fragment 1 has 2 atoms; merge with another fragment or add virtual atoms to make 3 total

The molecular oxygen is from although there is a structure of oxy-myoglobin in the PDB, but the latter has only a single CONECT bonding*.

What is a `virtual atom` that the py-script is requesting?


* I know that molecular oxygen actually resonates between O=O and O.-O. making it blue and paramagnetic. But for now, I am happy with a sloppy double bonded oxygen.

EDIT. I forgot to mention that running `relax` crashes due to the `OXY` so its not handled implicitly. Running the same on a structure with `OXY` removed but with other ligands (`-extra_res_fa HEM.params -extra_res_fa LG.params`) works fine.

Post Situation: 
Sat, 2018-02-24 06:05
ValueError: Fragment 1 has 2 atoms; merge with another fragment or add virtual atoms to make 3 total


You have two atoms.  You need 3 or more.  Each residue needs to be able to define a local coordinate frame, which requires 3 atoms for 3 DOFs for 3 dimensions.  It's a consequence of Rosetta using internal coordinates (length-angle-torsion) for most of its work; you need at least 3 atoms per residue to make that work.

I don't know if there are any diatomic types already in the database, but I know there are monatomic metals.  If you look at them you will find they fill out their parameters with "virtual" atoms - they're ghosts w/r/t phyiscs, no effects, but they provide the extra handles the math requires.  I don't know if there is a way to do this automatically, but that's where I'd start.  (Since your system is two atoms, only the both length can probably just hack up the ZN params into O=O params if you need to?  That's where I'd start.)

Sat, 2018-02-24 10:41
smlewis recognizes "V" atoms as virtual ones. You should be able to add a spurious V atom to your input sdf/mol2 file, connect it to the oxygens with a pseudo-bond (a single bond will work), and should be able to go from there.

Otherwise, hacking one of the monoatomic metal types probably would work too.

Sat, 2018-02-24 13:44

Thanks! I did as R Moretti recomended —adding a vanadium bounded to one of the oxygen— and doublechecked against zinc as suggested. The params file works and does behave weirdly.

Hopefully, I will not have to work with an organovanadate and stumble across the inverse issue!

Here is the OXY.params (O1=O2 molecule) for any future reader.

ATOM  O2  OOC   X   0.00
ATOM  O1  OOC   X   0.00
BOND  O1   O2 
BOND  O2   X1 
NBR_RADIUS 0.825000
ICOOR_INTERNAL    O2     0.000000    0.000000    0.000000   O2    O1    X1 
ICOOR_INTERNAL    O1     0.000000  180.000000    0.825000   O2    O1    X1 
ICOOR_INTERNAL    X1     0.000000   59.991521    0.824989   O2    O1    X1 


Mon, 2018-02-26 02:05