[gmx-users] force field parameters clashing

[Harsha Ravishankar]

Hello Justin,

Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating Couldn't
find topology match for atomtype NP.

I am not sure as to what is the source of such errors.

best wishes

Harsha



On Mon, Jan 15, 2018 at 3:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
> -Justin
>
>
> 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
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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>
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-- 
Harsha Ravishankar
Harsha.Ravishankar at scilifelab.se
Doctoral candidate in Biophysics
Theoretical and Computational Biophysics
KTH - Science for Life Laboratory, Stockholm