MiMiCPy does not support topology files prepared for free energy perturbation
The [atoms]
section for the perturbed molecule in a free energy perturbation GROMACS calculation looks something like this
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 c 1 MOL C 1 0.704701 12.0100 c 0.698701 12.0100
2 ca 1 MOL C1 2 0.920902 12.0100 ca 0.922901 12.0100
...
19 hn 1 MOL H5 19 0.439800 1.0080 DUM_hn 0.000000 1.0000
...
thus 1) they have more than 8 columns (which triggers an Exception
in Itp.__read_atoms()
). and 2) depending on the state of the molecule (A or B) the atom type might be different, and this affects the order of the atoms in CPMD.
For 1), the solution could be to allow lines with 11 columns. For 2), to specify as an argument the state of the system ('A'
or 'B'
or something similar).
There might be other differences in free energy perturbation files that are important. I still have to look into that.