[gmx-users] force field parameters clashing

Justin Lemkul jalemkul at vt.edu
Mon Jan 15 15:58:35 CET 2018

On 1/15/18 9:45 AM, Harsha Ravishankar wrote:
> 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.

You do not need to do any of this. CHARMM-GUI provides you with the 
coordinates of the system, a full topology, and the force field files 
necessary to carry out the simulation.


> 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


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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