Params file for Methane

[Anonymous]

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

 

[Anonymous]

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.)

[Author]

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