[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

[Nikolaos Michelarakis]

Hey,

Thanks a lot, I fixed the file but I am now getting a python error, I think.

Traceback (most recent call last):
  File "./cgenff_charmm2gmx.py", line 792, in <module>
    m.read_mol2_coor_only(mol2_name)
  File "./cgenff_charmm2gmx.py", line 720, in read_mol2_coor_only
    atomi = int(entry[0])-1
ValueError: invalid literal for int() with base 10: ''

something wrong with the coordinates?

the new mol2 file is:

https://drive.google.com/file/d/0BzqRbRx4Ynf0SV9rZnhhTmxGRmM/edit?usp=sharing

cheers!

Nicholas