From: 辛志宏 (xzhfood_at_njau.edu.cn)
Date: Fri Nov 12 2021 - 10:15:57 CST
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!ph09oszzUS7UYHmeDfrR2wr2796iFD0r0PWWcnbJXZ4ZB1HiXNPvCOw8iX8LuzE6JA$ ), 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 University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!ph09oszzUS7UYHmeDfrR2wr2796iFD0r0PWWcnbJXZ4ZB1HiXNPvCOw8iX_ASHUGFQ$
This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:12 CST