[gmx-users] charmm to gromacs

[Rebeca García Fandiño]

Dear Gromacs users,
I am trying to obtain the .itp files for an organic molecule for a MD simulation in GROMACS using the CHARMM force field.

I am trying to use cgenff_charmm2gmx.py:

python cgenff_charmm2gmx.py MOL1 ligand.mol2 ligand.str charmm36-nov2014.ff

After this step, I obtain several files, among them:
mol1.top:
----------------------------------------
#include "charmm36-nov2014.ff/forcefield.itp"

; additional params for the molecule
#include "mol1.prm"

#include "mol1.itp"

#include "charmm36-nov2014.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "charmm36-nov2014.ff/ions.itp"

[ system ]
; Name
mol

[ molecules ]
; Compound        #mols
MOL1          1
----------------------------------------------------

The file mol1.prm does not contain any value:

-------------------------------------

[ bondtypes ]
;      i        j  func           b0           kb


[ angletypes ]
;      i        j        k  func       theta0       ktheta          ub0          kub


[ dihedraltypes ]
;      i        j        k        l  func         phi0         kphi  mult


[ dihedraltypes ]
; 'improper' dihedrals
;      i        j        k        l  func         phi0         kphi

--------------------------------


And in the mol1.itp file also obtained from cgenff_charmm2gmx.py, the values of c0, c1, c2, c3,...in bonds, angles, and dihedrals are missing:

----------------------------------

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    1   108     1
    1   109     1
    1   110     1
(...)
[ angles ]
;  ai    aj    ak funct            c0            c1            c2            c3
    2     1   108    5
    2     1   109    5
    2     1   110    5
  108     1   109    5
[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
  108     1     2     3     9
------------------------


Any idea of what could be happening?

Best wishes,

Rebeca.

Dr. Rebeca Garcia
Santiago de Compostela University
Spain