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:
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:
I saved the above PDB file as ST.pdb, and ran the following command:
martinize2 -f ST.pdb -x STc.pdbIt gives me the following output:
I am confused as to what is going on here, even when I visualized ST.pdb using VMD it looked perfect: