VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 17 2020 - 09:37:00 CST

Yes, any time your email changes (automatically or otherwise) you'll
need to resubscribe to the mailing list.

Best regards,
  John Stone

On Thu, Dec 17, 2020 at 02:51:45PM +0000, Hamish Swanson wrote:
> Hi John,
> Thanks for your help!
> Also, regards syntax I have been looking at a somewhat old users
> guide. I'll keep that in mind for further projects.
> Do I need to resubscribe to the mailing list? I think my email has
> recently been changed automatically.
> Best Wishes,
> Hamish
>
> --------------------------------------------------------------------------
>
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: 17 December 2020 06:44
> To: Hamish Swanson <hamish.swanson_at_strath.ac.uk>
> Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> Subject: Re: vmd-l: Dipole Moment Measurement
>
> CAUTION: This email originated outside the University. Check before
> clicking links or attachments.
>
> Hi,
> I had to manually approve your posting due to a mismatched submission
> vs. subscription email address.
>
> Your script should instead be written with modern VMD syntax and
> in particular with "waitfor all" to prevent evaluation of the dipole
> moment prior to completion of file loading:
> mol new uc000.psf waitfor all
> mol addfile uc000.pdb waitfor all
> set sel [atomselect top all]
> set outfile [open dipolet.dat w]
> puts $outfile catch [measure dipole $sel -debye -masscenter]
> close $outfile
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Dec 16, 2020 at 02:04:59PM +0000, Hamish Swanson wrote:
> > Hi there,
> > I am trying to determine the dipole moment of a small molecule (c000
> > arbitrary name) using the following .tcl script:
> > > mol load psf uc000.psf #molecule psf
> > > mol load pdb uc000.pdb #molecule pdb
> > > set sel [atomselect top all]
> > > set outfile [open dipolet.dat w] #desired output
> file
> > name
> > > puts $outfile catch [measure dipole $sel -debye -masscenter]
> > > close $outfile
> > VMD returns [0.0 0.0 0.0] as the dipole moment vector. However, when
> I
> > load the molecule to VMD and repeat the procedure by hand a dipole
> moment
> > as expected is returned by the Tk console. This gives me confidence
> in the
> > validity of the .psf and .pdb files, I have also used these in the
> setup
> > water box equilibration simulations previously, so I do not think
> they are
> > the cause of the issue.
> > It is my plan to determine the dipole moment for a series of
> molecules
> > quickly, hence the script and doing this by hand is not viable.
> > I am new to VMD and TCL so any input would be much appreciated.
> > Thanks,
> >
> > Hamish Swanson
> > PhD Student
> > The University of Strathclyde
> > Glasgow
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [1]https://eur02.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~johns%2F&amp;data=04%7C01%7Chamish.swanson%40strath.ac.uk%7C09e0773eef4143a447dd08d8a2573a62%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637437843571061399%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=OwpiJDJU6AHdb3QZQh0u2gZaHZ%2FHPO0kTf0vDQsFjAQ%3D&amp;reserved=0
> Phone: 217-244-3349
> [2]https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2F&amp;data=04%7C01%7Chamish.swanson%40strath.ac.uk%7C09e0773eef4143a447dd08d8a2573a62%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637437843571061399%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=CiajpaMQTG%2FwxzpZM3%2F9YH1FdcglkxT%2BwTLTRcFhWC4%3D&amp;reserved=0
>
> References
>
> Visible links
> 1. https://eur02.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.ks.uiuc.edu%2F~johns%2F&amp;data=04%7C01%7Chamish.swanson%40strath.ac.uk%7C09e0773eef4143a447dd08d8a2573a62%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637437843571061399%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=OwpiJDJU6AHdb3QZQh0u2gZaHZ%2FHPO0kTf0vDQsFjAQ%3D&amp;reserved=0
> 2. https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2F&amp;data=04%7C01%7Chamish.swanson%40strath.ac.uk%7C09e0773eef4143a447dd08d8a2573a62%7C631e0763153347eba5cd0457bee5944e%7C0%7C0%7C637437843571061399%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=CiajpaMQTG%2FwxzpZM3%2F9YH1FdcglkxT%2BwTLTRcFhWC4%3D&amp;reserved=0 

-- 
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/