Re: Regarding Parameter file

From: René Hafner TUK (
Date: Mon May 24 2021 - 03:51:05 CDT

     ON3 is an atom type from par_all36_na.prm

     Inside toppar_water_ions.str you only need to comment out any
NBFIXes Lines where "ON3" occurs; may happen for more atom types but
should be solvable the same way.


On 5/23/2021 7:14 PM, Nadira Khatoon wrote:
> Hi,
> I am new at learning NAMD for simulating membrane embedded proteins.
> Will use of different versions of Charmm parameter files cause errors
> in the simulation?
> Also, an error stating "FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR
> ATOM TYPE ON3", is coming, but there are no ON3 atoms in both pdb and
> psf files. I am unable to find a solution to this. Could you please
> help me with this?
> For running this simulation, I have used parameter files as mentioned
> below:
> parameters par_all36_lipid.prm
> parameters par_all36m_prot.prm
> parameters toppar_water_ions.str

Dipl.-Phys. René Hafner
TU Kaiserslautern

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