From: Kushal Raj Roy (kushalrajroyfc_at_gmail.com)
Date: Fri Nov 12 2021 - 11:13:21 CST
Hi,
I think you didn’t get what prof. Vermaas trying to anecdote about your
unknown compound's (UNK_DEF6D6.prm) prm file. For instance, I would like
to suggest you generate all the parameter files by using charmm-gui rather
than LigPargen.
Best,
Kushal
On Fri, 12 Nov, 2021, 10:18 pm 辛志宏, <xzhfood_at_njau.edu.cn> wrote:
>
> Thanks Josh and Kushal.
>
> The ligand parameter(UNK_DEF6D6.prm) was generated by Ligpargen(
> https://urldefense.com/v3/__http://zarbi.chem.yale.edu/ligpargen/__;!!DZ3fjg!q7EpUSeNyEAA-BfOaFAH-SQ-L1v7EEU_87H40lpitko2_O1t9Zzw6RKsXSN8VAoWbw$ ),
> <https://urldefense.com/v3/__http://zarbi.chem.yale.edu/ligpargen/),__;!!DZ3fjg!ph09oszzUS7UYHmeDfrR2wr2796iFD0r0PWWcnbJXZ4ZB1HiXNPvCOw8iX9PWjnq9g$> also
> I try use toppar_water_ions_namd.str. instead, but it failure.
>
> zhihong
>
>
>
>
> 发件人：Kushal Raj Roy <kushalrajroyfc_at_gmail.com>
> 发送日期：2021-11-12 23:20:20
> 收件人：namd-l_at_ks.uiuc.edu,Josh Vermaas <vermaasj_at_msu.edu>
> 主题：Re: namd-l: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238
>
> Hi,
>
> Instead of mod.str try to use toppar_water_ions_namd.str. Hopefully, it
> will work.
>
> Best,
>
> Kushal
>
> On Fri, 12 Nov, 2021, 9:01 pm Josh Vermaas, <vermaasj_at_msu.edu> wrote:
>
>> Hi Zhihong,
>>
>> What this means is that the parameter set doesn't have nonbonded
>> parameters for atom type N238. How to fix it depends on how there came to
>> be atoms with type N238. I don't recognize it as being in the standard
>> CHARMM parameter sets. Does your system have an components that you needed
>> to parameterize (like whatever needs the UNK_DEF6D6.prm file)?
>>
>> -Josh
>>
>> On 11/12/21 9:35 AM, 辛志宏 wrote:
>>
>> Hello!
>> An error occured when I run a molecular dynamic using NAMD3,
>>
>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE N238
>>
>>
>> I don't know how to solve it, any suggestion will be much appreciate.
>>
>> The following parameters were used,
>> parameters ./common/par_all36_prot.prm
>> parameters ./common/par_all36_carb.prm
>> parameters ./common/par_all36_cgenff.prm
>> parameters ./common/par_all36_lipid.prm
>> parameters ./common/par_all36_na.prm
>> parameters ./common/UNK_DEF6D6.prm
>> parameters ./common/toppar_water_ions_namd.str
>> #parameters ./common/toppar_water_ions.mod.str (don't works)
>>
>>
>>
>>
>> Thanks,
>>
>> Zhihong xin
>>
>>
>>
>> --
>> Josh Vermaas
>> vermaasj_at_msu.edu
>> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>> Michigan State Universityhttps://prl.natsci.msu.edu/people/faculty/josh-vermaas/ <https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uVsOD3CDQs066tBFC3xROQI0suhEylSkTmazy6rOp51OzxR7wZIqqHYUPYVE0lv21w$>
>>
>>
>
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST