From: Hideyuki Miyatake (miyatake_at_riken.jp)
Date: Fri Sep 27 2024 - 06:59:30 CDT

Hi, Joe,

Sorry, the ligand was broken due to my mistake in copy & paste.

After fix it, it stopped with the same error message as before, as shown
in below

FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NG2S0 CG301 CG1N1 NG1T1 (ATOMS 11642 11653 11654 11672)

CGenFF can not generate the dihedral angle around the nitrile group, as I said.

    Thank you.

     Hideyuki Miyatake

2024/09/27 18:31、Hideyuki Miyatake <miyatake_at_riken.jp>のメール:

Hi, Joe,

Thank you for the calculation.

I tried with Ligand1.str, but
the ligand was broken in the minimization of QwikMD, as attached.

Do you have some suggestions about that?

     Best regards,

     Hideyuki Miyatake

<スクリーンショット 2024-09-27 18.26.27.png>

2024/09/27 11:04、Klimkowski, V <vklimkow_at_butler.edu>のメール:

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!54P0Qr6DJbTq2i-YkRl5OgJIOp9aE5z97uZ3czD1g0WAWh5WJeq0btXlu9wk6hdC_SUlpzyGfUhVC0l4bBFb$ <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、Josh Vermaas <vermaasj_at_msu.edu>のメール:

ault par_all36_cgenff.prm t

<Ligand1.str><Ligand2.str>