[gmx-users] force field parameters clashing

[Justin Lemkul]

On 1/15/18 1:27 PM, Harsha Ravishankar wrote:
> 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.

CHARMM-GUI will only provide a topology and subset of the force field 
that is pertinent to the system you provide it. If you subsequently add 
things into the mix, it won't account for necessary parameters. If 
you're going to take this approach, use CHARMM-GUI to build the entire 
system.

-Justin

> 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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>
>

-- 
==================================================

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

==================================================