VMD-L Mailing List

From: Mcguire, Kelly (klmcguire_at_UCSD.EDU)
Date: Sun Oct 23 2022 - 11:53:16 CDT

So, for those of you trying to get ORCA 5 working with the NAMD/VMD QMMM interface and to view the orbitals, you'll need the "grab_orca.sh" file, but you'll want to comment out lines 3-5 (they don't work anymore). Uncomment line 7 and leave line 8 uncommented. This script is called with the qmSecProc in your QMMM config files. You should make sure it has the correct permissions. I found moving this script file into the qmmm_exec/QMMM-Min/0/, or qmmm_exec/QMMM-Ann/0/, or qmmm_exec/QMMM-Equi/0/ (i.e. the directory the ORCA files are reading and writing to), directory after the job has started (but before the first QM step is complete) to work the best. This file concatenates the "qmmm_0.input.TmpOut" into one big file at the end in ".orc" file type. This is the file that you can load using the "orcaviewer.tcl".

One problem though, ORCA is on version 5.0.3 currently, but the orca viewer or orca file type in VMD (currently 1.9.4a55) only supports versions older than ORCA 5. The solution is to find and replace all instances of Program Version 5.0.3 in the ".orc" output with Program Version 4.0.0.2 using the sed command. This string is right below each instance of the big ORCA logo and rights reserved box at the top of each output. You should be able to view all orbitals this way and watch it play each step like you would a trajectory for and MD simulation.

Now I'm trying to get VMD to read MOPAC outputs. The "mergefile.sh" that comes with the setup works fine to concatenate the MOPAC outputs, just need to make sure the "#!/usr/bin/env bash" is at the top or it will fail. It comes with comments at the top and that shebang line below, which makes it fail. But, all current versions of VMD cannot recognize the MOPAC output file. It would be nice to use PM7 in MOPAC because it's so much faster (GPU accelerated) than say HF or B3LYP, but also quite accurate in many cases. I don't have the skills to write a VMD plugin to read MOPAC outputs, so if anyone has a start on that let me know.

Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017
________________________________
From: Mcguire, Kelly
Sent: Friday, October 21, 2022 9:36 AM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: QMMM Update

I finally got both MOPAC 22.0.4 and ORCA 5.0.3 working for QMMM in NAMD 2.14. I can even run the "mergefile.sh" and grab_orca.sh files with qmSecProc without it crashing. However, if I try to open the MOPAC or ORCA outputs to view the orbitals, VMD 1.9.4a55 either complains that it can't open Orca version 5.0.3 even though it's a .orc output or no file type for the MOPAC output which is .out. Does anyone have a way to view the orbitals in VMD from both ORCA and MOPAC outputs? It seems like there hasn't been an update in years for utility. Thanks!

Dr. Kelly McGuire
Herzik Lab - Postdoc
Chemistry/Biochemistry Department
Natural Science Building, 4104A, 4106A, 4017