[gmx-users] force field parameters clashing
harsha.ravishankar at scilifelab.se
Mon Jan 15 15:45:10 CET 2018
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 POPE chain topology
: Include POPS chain topology
: Include PSM chain topology
: Include POPI chain topology
with DDPC, POPE, POPS, PSM, POPI being the different lipid molecules that
are present in the membrane.
In the forcefield.itp file I specify,
; Nucleic acids nonbonded and bonded parameters"
; #include "ffnanonbonded.itp"
; #include "ffnabonded.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
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.
Harsha.Ravishankar at scilifelab.se
Doctoral candidate in Biophysics
Theoretical and Computational Biophysics
KTH - Science for Life Laboratory, Stockholm
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