[gmx-users] force field parameters clashing

[Harsha Ravishankar]

Dear All,

I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs parameters for the different lipids were also obtained.

I first generate a .gro file from the pdb of the membrane using editconf.
Then I run pdb2gmx to obtain .gro and topology files of the aligned protein
molecule. I then combine the gro files of both the membrane and the protein
and create a box using editconf with the combined gro files as input.

I then edit the topology file of the protein to include the different lipid
topologies and numbers as follows,

: Include DDPC chain topology
#include "./charmm.ff/DDPC.itp"

: Include POPE chain topology
#include "./charmm.ff/POPE.itp"

: Include POPS chain topology
#include "./charmm.ff/POPS.itp"

: Include PSM chain topology
#include "./charmm.ff/PSM.itp"

: Include POPI chain topology
#include "./charmm.ff/POPI.itp

with DDPC, POPE, POPS, PSM, POPI being the different lipid molecules that
are present in the membrane.

In the forcefield.itp file I specify,

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
; #include "ffnanonbonded.itp"
; #include "ffnabonded.itp"
#include "charmm_gui_membrane.itp"

The "charmm_gui_membrane.itp" file mentioned above contains the topologies
of the different lipid molecules generated by Charmm-GUI .With solvate I am
able to successfully solvate the prepared membrane-protein complex box with
SOL molecules.

However when I attempt to add ions using gmx grompp -f ions.mdp -c
solvate.gro -p topol.top -o ions.tpr, I receive a number of errors stating


"Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
multiple lines. This is not supported."

I do not quite understand why this should be the case. Any help here would
be sincerely appreciated.

Thanking everyone in advance.

Sincerely,

Harsha Ravishankar



-- 
Harsha Ravishankar
Harsha.Ravishankar at scilifelab.se
Doctoral candidate in Biophysics
Theoretical and Computational Biophysics
KTH - Science for Life Laboratory, Stockholm