From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Fri Nov 12 2021 - 08:59:35 CST
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 University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uVsOD3CDQs066tBFC3xROQI0suhEylSkTmazy6rOp51OzxR7wZIqqHYUPYVE0lv21w$
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