VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Nov 05 2020 - 15:02:19 CST

Yeah, just FYI, the mailing list blocks large attachments beyond the
equivalent of 40,000 lines of text, so that's why it probably didn't
post last week.

Best,
  John Stone

On Thu, Nov 05, 2020 at 08:56:21PM +0000, Hao Wu wrote:
> 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 <[1]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 [2]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
> [3]haw4005_at_med.cornell.edu
>
> --------------------------------------------------------------------------
>
> From: Hao Wu
> Sent: Thursday, October 29, 2020 11:11 PM
> To: [4]vmd-l_at_ks.uiuc.edu <[5]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
> [6]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>
>
> References
>
> Visible links
> 1. mailto:haw4005_at_med.cornell.edu
> 2. mailto:vmd-l_at_ks.uiuc.edu
> 3. mailto:haw4005_at_med.cornell.edu
> 4. mailto:vmd-l_at_ks.uiuc.edu
> 5. mailto:vmd-l_at_ks.uiuc.edu
> 6. mailto:haw4005_at_med.cornell.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/