From: Hao Wu (haw4005_at_med.cornell.edu)
Date: Thu Nov 05 2020 - 14:56:21 CST

Hi Mariano,

No problem. Good to know that this email has been picked up. Thanks for checking the issue!

Best,
Hao

Hao Wu, Ph.D.
Postdoctoral Associate

Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065
haw4005_at_med.cornell.edu

________________________________
From: Mariano Spivak <mariano_at_ks.uiuc.edu>
Sent: Thursday, November 5, 2020 3:53 PM
To: Hao Wu <haw4005_at_med.cornell.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>; John Stone <johns_at_ks.uiuc.edu>
Subject: [EXTERNAL] Re: Potential bugs in ffTK dihedral optimization

Hi Hao,

It looks like the October 29th email never got into the vmd-list, sorry for that.
I will take a look into this issues you are describing, we are aware of some issues with the latest macOS Catalina and we are working on fixing those.

Thanks

On Nov 5, 2020, at 2:43 PM, Hao Wu <haw4005_at_med.cornell.edu<mailto:haw4005_at_med.cornell.edu>> wrote:

Hello VMD community,

I just want to follow up whether my previous bug report has been successfully received by VMD mailing list. I sent the email on October 29, but it has not been responded yet. Meanwhile, I found many other emails after mine have been posted and answered on the list.

I used this email to subscribe to the list and sent my email to vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>. Is this the correct way to post on the list?

I look forward to discussing my issues with all the VMD developers and users. Thanks for checking!

Best regards
Hao

Hao Wu, Ph.D.
Postdoctoral Associate

Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065
haw4005_at_med.cornell.edu<mailto:haw4005_at_med.cornell.edu>

________________________________
From: Hao Wu
Sent: Thursday, October 29, 2020 11:11 PM
To: vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Potential bugs in ffTK dihedral optimization

Hello VMD community,

I am using ffTK in VMD 1.9.4 to parameterize a small molecule (an LSD with 50 atoms). I found several potential bugs in the dihedral optimization procedure.

  1. Error in Gaussian dihedral scan input files (most important): In the step of scan torsion, I tried to generate the Gaussian input files for each scan. In all the Gaussian input files created, I found one atom (H45 in this molecule)'s name is incompletely written, and its coordinates are totally missing (please find an attached .gau file as an example). These input files are wrong and cannot be used for conducting correct QM dihedral scans in Gaussian at all.
  2. Toggle atom labels error: When I click "Toggle Atom Labels", an error message "need three numbers for a vector" pops up (see the attached complete error message). Most atom labels still show up. But some atoms are missing their labels. Please see an attached sample figure, in which I used red circles to highlight two hydrogen atoms missing their labels.
  3. Dihedral plots in macOS's dark mode: when macOS is in dark mode, the plots created by "Torsion Explorer" in Scan Torsions panel and "visualize results" in Opt. Torsions are not correctly shown. They both lost their axes, labels, and legend labels, as shown in the attached screenshots. In macOS's light mode, they are totally fine.

Here is my environment info when encountering these problems:
OS version: Mac OS Catalina 10.15.7
VMD version: 1.9.4a48 Rev7 (October 13, 2020)

These issues all go away when using VMD 1.9.3 on a lower version of macOS (10.14.6), with the exact same molecule and setup files. I haven't tested any earlier version of VMD 1.9.4.

I also attached my pdb, psf, and par files that can be used to replicate these issues in dihedral scan/optimization.

Could you please kindly look into these issues? Thanks a lot!

Best regards
Hao

Hao Wu, Ph.D.
Postdoctoral Associate

Weill Cornell Medicine
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065
haw4005_at_med.cornell.edu<mailto:haw4005_at_med.cornell.edu>

<UNK.scan1.neg.gau><toggle_atom_label_error.log><toggle_atom_label_error.tga><torsion_explorer_dark_mode.png><dihOpt_fit_plot_dark_mode.png><lsd.1.pdb><lsd.1.psf><lsd.1.par>