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

[Nikolaos Michelarakis]

Hello again,

This what I have been trying to do so far. This is the command to run the
script:

./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff

and this is the error I have been getting along with 2 Notes:

NOTE2: Please be sure to use the same version of CGenFF in your simulations
that was used during parameter generation:
--Version of CGenFF detected in  charmm36-mar2014.ff/forcefield.doc : 2b8

NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include
parameters that are already in CGenFF' option when uploading a molecule
into CGenFF.

error in atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top
96 142


The file names I am using are:
 2e7z-ptc.str          charmm36-mar2014.ff
2e7z-ptc.mol2  cgenff_charmm2gmx.py

These are the contents of the .mol2 and .str files respectively:

https://drive.google.com/file/d/0BzqRbRx4Ynf0TUg3blBOTmV0Qzg/edit?usp=sharing
(mol2)

https://drive.google.com/file/d/0BzqRbRx4Ynf0VThMSnNYMU1XVmM/edit?usp=sharing
(str)

Thanks a lot,

Nicholas