VMD-L Mailing List

From: Klimkowski, V (vklimkow_at_butler.edu)
Date: Thu Sep 26 2024 - 21:04:11 CDT

Hello Hideyuki,

  I took your PDB files, assigned bond orders, & did brief minimization. Using exported mol2 files I submitted these to the CGenFF website & got the attached stream files. Maybe they are the same as what you generated, but it might be worth trying these to see if these work.

Best,

V Joe Klimkowski, PhD
Chemistry Research Affiliate
Butler University
Indianapolis, IN
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Hideyuki Miyatake <miyatake_at_riken.jp>
Sent: Wednesday, September 25, 2024 10:14 PM
To: Josh Vermaas <vermaasj_at_msu.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: .str file generation of nitrile group containing ligands

Hi, Josh,

Thank you for the message.

Yes, par_all36_cgenff.prm is involved in the calculation.

I use QwikMD, which requires stream-style parameter files of the ligands.

I tried to generate the stream files by CGenFF (https://urldefense.com/v3/__https://cgenff.com/__;!!DZ3fjg!5BztIbJJAUXlhpuhtP35r51DV0daU_ShzzqWygPH2qRbESMVF7PdiAjoFDV9ELNj8erPw9NIzt2acg7wS8jTmg$ <https://urldefense.com/v3/__https://cgenff.com/__;!!DZ3fjg!9jTLl1OV3CsIUnDhxxSCLd_FmPJEyWbr_DTznLeQAvmsbUh4XijGOzVrM62aYYyRagjoRm-40Yo-2mmGOQ2U$>),
it only generated the files without dihedral angles around the nitrile groups.

Do you have any suggestions about this?

             Hideyuki Miyatake

2024/09/25 23:09$B!"(BJosh Vermaas <vermaasj_at_msu.edu>$B$N%a!<%k(B:

ault par_all36_cgenff.prm t