Re: Regarding Parameter file

From: René Hafner TUK (
Date: Mon May 24 2021 - 09:51:14 CDT

Hi Nadira,

    no, atom types NOT present while present in the prm file in the
    simulation will not influence it. BUT the NBFIX part that might
    contain atom of yours at the very end will still be applied (which
    might not be what you want).

    *BUT this error *indicates that your structure HAS this DIHEDRAL and
    REQUIRES to have it defined inside a parameter file you pass to NAMD.

    Though it seems you have a
    (;!!DZ3fjg!vdCetnlO5lhkwRgRUyAats6ukszTSchq4yPSapx7P-jlml2aAV4jeEDEQ0rg88ZT_w$ ) lipid there that cannot
    be describe by "par_all36_lipid.prm" only.

    That's why you need the "toppar_all36_lipid_sphingo.str" .

    Make sure that this the kind of lipid you actually want to simulate.


On 5/24/2021 4:26 PM, Nadira Khatoon wrote:
> Thanks for the help René. Your suggestion solved the issue. However,
> now I am getting a new error stating, "FATAL ERROR: UNABLE TO FIND
> gets solved if I use toppar_all36_lipid_sphingo.str as one of my
> parameter file in addition to the par_all36_lipid.prm ,
> par_all36m_prot.prm, and toppar_water_ions.str.
> I am unable to understand the reason behind it. Will unnecessary
> parameter file affect simulation results?
> -------- Original Message --------
> Subject: Re: namd-l: Regarding Parameter file
> Date: 24.05.2021 14:21
> From: René Hafner TUK <>
> To:, Nadira Khatoon
> <>
> Hi,
>     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.
> Cheers
> René
> 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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