VMD-L Mailing List

From: Hideyuki Miyatake (miyatake_at_riken.jp)
Date: Tue Sep 24 2024 - 20:55:26 CDT

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