Coarse Grain a basic All-Atom structure of Polystyrene

[pranoy-ray]

This might be a pretty novice question but I am trying to coarse grain a basic molecule of styrene. I have it's PDB file as follows:

REMARK   DATE:     2/ 5/21     14:47:31      CREATED BY USER: nathan                  
ATOM      1  CG  STY S   1      -2.373  -0.260  -0.036  1.00  0.00      STYR
ATOM      2  HG  STY S   1      -3.436  -0.447  -0.077  1.00  0.00      STYR
ATOM      3  CD1 STY S   1      -1.891   1.053  -0.076  1.00  0.00      STYR
ATOM      4  HD1 STY S   1      -2.583   1.880  -0.149  1.00  0.00      STYR
ATOM      5  CD2 STY S   1      -1.478  -1.330   0.060  1.00  0.00      STYR
ATOM      6  HD2 STY S   1      -1.850  -2.344   0.094  1.00  0.00      STYR
ATOM      7  CE1 STY S   1      -0.513   1.298  -0.022  1.00  0.00      STYR
ATOM      8  HE1 STY S   1      -0.167   2.322  -0.055  1.00  0.00      STYR
ATOM      9  CE2 STY S   1      -0.099  -1.090   0.114  1.00  0.00      STYR
ATOM     10  HE2 STY S   1       0.571  -1.934   0.193  1.00  0.00      STYR
ATOM     11  CZ  STY S   1       0.402   0.230   0.070  1.00  0.00      STYR
ATOM     12  C1  STY S   1       1.834   0.547   0.132  1.00  0.00      STYR
ATOM     13  H1  STY S   1       2.114   1.583   0.379  1.00  0.00      STYR
ATOM     14  C2  STY S   1       2.867  -0.275  -0.134  1.00  0.00      STYR
ATOM     15  H21 STY S   1       3.901   0.095  -0.077  1.00  0.00      STYR
ATOM     16  H22 STY S   1       2.701  -1.326  -0.415  1.00  0.00      STYR
TER      17      STYR     1
END

I saved the above PDB file as ST.pdb, and ran the following command:

martinize2 -f ST.pdb -x STc.pdb

It gives me the following output:

    INFO - general - Read 1 molecules from PDB file ST.pdb
    INFO - step - Guessing the bonds.
 WARNING - unknown-residue - Can't add bonds based on atom names for residue S-STY1 because 'Residue STY is not known to force field charmm'. Falling back to distance criteria.
    INFO - general - 1 molecules after guessing bonds
 WARNING - general - Mutation "cter" not found. Check target resid!
 WARNING - general - Mutation "nter" not found. Check target resid!
    INFO - step - Repairing the graph.
 WARNING - unknown-residue - Cannot recognize residue 'STY' in  molecule 0. Deleting the molecule.
    INFO - step - Dealing with modifications.
    INFO - step - Read input.
    INFO - step - Creating the graph at the target resolution.
    INFO - step - Averaging the coordinates.
    INFO - step - Applying the links.
    INFO - step - Placing the charge dummies.
    INFO - step - Sorting atomids
    INFO - step - Writing output.
   ERROR - general - 4 warnings were encountered after accounting for the -maxwarn flag. No output files will be written. Consider fixing the warnings, or if you are sure they are harmless, use the -maxwarn flag.

I am confused as to what is going on here, even when I visualized ST.pdb using VMD it looked perfect:

[pckroon]

Hellohello!

I figured this would be better as a discussion rather than code issue.

You need to add styrene as a residue to the data files. There have been several previous issues on how to add new residues (for example #535), and I also wrote something about that in the documentation. https://vermouth-martinize.readthedocs.io/en/latest/tutorials/6_adding_residues_links/index.html. Could you start there? If you have more questions please feel free to ask :)

[pranoy-ray]

@pckroon so where do I get the itp file for Styrene or the FF file for Styrene? (STY)

[pckroon]

You'll need to make those yourself (or find them elsewhere). You can try looking (for example) here: https://github.com/marrink-lab/polyply_1.0 or https://github.com/ricalessandri/Martini3-small-molecules
I can't really help you parametrizing a decent martini3 model; it's been far too long since I had to do that.