Re: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238

From: Kushal Raj Roy (kushalrajroyfc_at_gmail.com)
Date: Fri Nov 12 2021 - 09:20:20 CST

Hi,

Instead of mod.str try to use toppar_water_ions_namd.str. Hopefully, it
will work.

Best,

Kushal

On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas, <vermaasj_at_msu.edu> wrote:

> Hi Zhihong,
>
> What this means is that the parameter set doesn't have nonbonded
> parameters for atom type N238. How to fix it depends on how there came to
> be atoms with type N238. I don't recognize it as being in the standard
> CHARMM parameter sets. Does your system have an components that you needed
> to parameterize (like whatever needs the UNK_DEF6D6.prm file)?
>
> -Josh
>
> On 11/12/21 9:35 AM, 辛志宏 wrote:
>
> Hello!
> An error occured when I run a molecular dynamic using NAMD3,
>
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238
>
>
> I don't know how to solve it, any suggestion will be much appreciate.
>
> The following parameters were used,
> parameters ./common/par_all36_prot.prm
> parameters ./common/par_all36_carb.prm
> parameters ./common/par_all36_cgenff.prm
> parameters ./common/par_all36_lipid.prm
> parameters ./common/par_all36_na.prm
> parameters ./common/UNK_DEF6D6.prm
> parameters ./common/toppar_water_ions_namd.str
> #parameters ./common/toppar_water_ions.mod.str (don't works)
>
>
>
>
> Thanks,
>
> Zhihong xin
>
>
>
> --
> Josh Vermaas
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uVsOD3CDQs066tBFC3xROQI0suhEylSkTmazy6rOp51OzxR7wZIqqHYUPYVE0lv21w$>
>
>

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST