Molecular oxygen

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    • February 24, 2018 at 2:05 pm #2855
      Anonymous

        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. Molfile_to_params.py gives the following  


        
$ python molfile_to_params.py 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:
        
Traceback (most recent call last):
        
File "molfile_to_params.py", line 1323, in <module>
        
sys.exit(main(sys.argv[1:]))
        
File "molfile_to_params.py", line 1295, in main
        
num_frags = fragment_ligand(m)
        
File "molfile_to_params.py", 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 https://pubchem.ncbi.nlm.nih.gov/compound/977#section=3D-Conformer 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?

        Thanks!

        * 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.

      • February 24, 2018 at 6:41 pm #14055
        Anonymous 

          
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 matters…you can probably just hack up the ZN params into O=O params if you need to?  That’s where I’d start.)

          • February 24, 2018 at 9:44 pm #14056
            Anonymous

              molfile_to_params.py 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 molfile_to_params.py should be able to go from there.

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

          • February 26, 2018 at 10:05 am #14057
            Anonymous

              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. 


              
NAME OXY
              
IO_STRING OXY Z
              
TYPE LIGAND
              
AA UNK
              
ATOM  O2  OOC   X   0.00
              
ATOM  O1  OOC   X   0.00
              
ATOM  X1  VIRT VIRT 0.00
              
BOND  O1   O2
              
BOND  O2   X1
              
NBR_ATOM  O2
              
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

               

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