Hello all,
I wanted to conform Rosetta params for Methane molecule which I have written (as molfile_to_params.py fails to create). Also, is there any specific method to create params compounds with no rotamer?
NAME M3T
IO_STRING M3T Z
TYPE LIGAND
AA UNK
ATOM C1 CH3 X -0.29
ATOM H1 Hapo X 0.07
ATOM H2 Hapo X 0.07
ATOM H3 Hapo X 0.07
ATOM H4 Hapo X 0.07
ATOM V1 VIRT X 0.00
BOND_TYPE C1 H1 1
BOND_TYPE C1 H2 1
BOND_TYPE C1 H3 1
BOND_TYPE C1 H4 1
BOND_TYPE H1 V1 1
NBR_ATOM C1
NBR_RADIUS 2.185002
ICOOR_INTERNAL C1 0.000000 0.000000 0.000000 C1 H1 V1
ICOOR_INTERNAL H1 0.000000 180.000000 1.535419 C1 H1 V1
ICOOR_INTERNAL V1 0.000001 68.822455 1.095891 H1 C1 V1
ICOOR_INTERNAL H2 -59.999912 70.526795 1.535368 C1 H1 V1
ICOOR_INTERNAL H3 -119.998242 70.533101 1.535319 C1 H1 H2
ICOOR_INTERNAL H4 -119.999459 70.527546 1.535390 C1 H1 H3
Category:
Post Situation:
Looks somewhat reasonable to me.
I don't think you'd actually need the virtual atom, though. I think (though haven't confirmed) that you should be fine with just the central carbon and having the hydrogens off it.
As far as rotamers, you don't need a separate rotamers file if you don't need/want to do any conformational sampling. The ICOOR records should be sufficient for specifying the geometry. (molfile_to_params.py should work for ligands with only one conformation. If you had issues, it was likely due to the small size, rather than having only one conformation.)