From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 20 2017 - 10:55:24 CST

Hi,
  I strongly amplify JC's suggestion to begin using the latest
VMD release. Particularly with recently-developed tools and extensions
in VMD it is critical that users run the latest versions of VMD to
ensure that you have all of the latest bug fixes. I note from the
email below that the version that was being used wasn't even a
production version of VMD, it was an alpha-test version of VMD,
probably one of the earliest versions that included ffTK. In general
users should stop using alpha-test versions immediately after a new
production release of VMD is made available. There is no sense in reporting
problems with old alpha-test versions of VMD when one or more production
releases have been available for multiple years.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 20, 2017 at 11:48:13AM -0500, JC Gumbart wrote:
> I spent 20 minutes refreshing my memory about this issue, although it was
> unnecessary. As you already see, we fixed it over three years ago. So
> why are you using a version of VMD even older than that? Please grab the
> latest VMD, which will contain this fix and numerous other improvements.
> Best,
> JC
>
> On Jan 20, 2017, at 6:02 AM, Sze May Yee <[1]szemayyee_at_gmail.com> wrote:
> Dear All,
>
> I am using ffTK to parameterize an isothiocyanate group following the
> tutorial with VMD-1.9.2a33.
> I read in the VMD development the following fix from V1.9.1:
> VMD 1.9.2 alpha 35 October 24, 2013
>
> * fftk: fix for gaussian hessian calculation, should be version
> independent
>
> Using the default Route on ffTK, Gaussian (g09) outputs with the error:
> The following ModRedundant input section has been read:
> B * * R
> A * * * R
> L * * * * R
> D * * * * R
> Unrecognized coordinate type "O"
> Error termination via Lnk1e in /opt/g09/l101.exe at Fri Jan 20 10:43:03
> 2017.
> Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds.
> File lengths (MBytes): RWF= 10 Int= 0 D2E= 0 Chk= 2
> Scr= 1
>
> From its Gaussian input file:
> %nproc=1
> %mem=1GB
> # MP2/6-31G* Geom=(ModRedundant,AllCheck) NoSymm IOp(7/33=1) SCF=Tight
> Freq Guess=Read
>
> B * * R
> A * * * R
> L * * * R
> D * * * * R
> O * * * * R
> B 2 1 1.0843778848648071
> ...etc.
>
> Again, I am experiencing the same errors after using the recommended
> Route/command line:
> # MP2/6-31G* Geom=(ModRedundant,AllCheck) NoSymm IOp(7/33=1) SCF=Tight
> Freq Guess=Read
> ([2]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22732.html)
> Are there any other recommended routes please?
>
> Many thanks.
>
> Kind regards,
> May
>
> References
>
> Visible links
> 1. mailto:szemayyee_at_gmail.com
> 2. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22732.html

-- 
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/