VMD-L Mailing List

From: Hao Wu (haw4005_at_med.cornell.edu)
Date: Tue Nov 24 2020 - 11:17:18 CST

Hi Mariano,

I am curious about the status of the potential bugs I reported in the previous email on Nov 5th. Please let me know if you have investigated it or any recent progress.

Thanks! Happy Thanksgiving.

Best,
Hao

Hao Wu, Ph.D.
Postdoctoral Associate
Weinstein Lab<https://physiology.med.cornell.edu/training/weinsteinlab/>

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

________________________________
From: John Stone <johns_at_ks.uiuc.edu>
Sent: Thursday, November 5, 2020 4:02 PM
To: Hao Wu <haw4005_at_med.cornell.edu>
Cc: Mariano Spivak <mariano_at_ks.uiuc.edu>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: [EXTERNAL] Re: Potential bugs in ffTK dihedral optimization

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--_000_BL0PR06MB4451FAC4505DF37EC2314CB2E8FB0BL0PR06MB4451namp_--