From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Wed Sep 25 2024 - 09:09:41 CDT

Hi Hideyuki,

When you ran this in NAMD, did you add in the default
par_all36_cgenff.prm to the configuration file? By default, I think
CGenff only gives you parameters that do not already exist in the
standard par_all36_cgenff.prm parameter file.

-Josh

On 9/24/24 9:55 PM, Hideyuki Miyatake wrote:
> Dear VMD users,
>
> Hello, I’m a VMD/NAMD/QwikMD user.
>
> I have a problem I cannot obtain the correct str files for the ligands attached,
> which contain nitrile groups, by using CGENFF3.0 or CHARMM-GUI websites.
>
> The dihedral parameters around the nitrile groups are missing, so we added
> the estimated values to the str files, but the MD simulations failed due
> to the crush of the ligands.
>
> Please advise me on generating the proper str files for the ligands.
>
> Thank you.
>
> Hideyuki Miyatake
>
>
>
>
>

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io