VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Fri Apr 07 2023 - 07:24:56 CDT

..and that attached Documentation Website within the above pdf tutorial
indicates the below:Build Menu
The Build Menu provides a number of options for construction and atom
typing of the new molecules.

*Export and Import topologies to CGenFF <https://urldefense.com/v3/__https://cgenff.umaryland.edu/__;!!DZ3fjg!-fJcjZYG9ZDtKy_xMD17q7s_2UFMDzFnaZqeI7GsH4uScwvSa_pfLYyLUeMAJeu3JRrTsx4uEcbh_cJ38UJidtuUSQ$ >*.
Using this menu, the user can export MOL2 files to be submitted to the
server or local executable of CGenFF. The submission can be done
automatically if the username and password of the CGenFF Server is defined
(please see Settings), or if the path to the local executable is defined.
*The user authentication in the direct communication of VMD and the CGenFF
Server is still being developed by the developers team. We will update this
information once this process is finalized.

Accordingly maybe this importing of the CGenFF .str file into VMD has not
be established as of yet, it's not clear nor are the instruction i.e.
Exporting and Importing topologies

to CGenFF, it should be Importing topologies FROM CGenFF?

On Thu, Apr 6, 2023 at 12:59 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> Hello towards the above topic:
>
> I am on fftk-Tutorial Section 2 System Preparation generating psf and pdb
> files
> from the .str file generated via CGenFF, tutorial link below:
>
> http://www.ks.uiuc.edu/Training/Tutorials/science/ffTK/fftk-tutorial.pdf
>
> following the below step from the tutorial:
>
> 1. Launch the Molefacture GUI in VMD: Extensions → Modeling → Molefacture
> When the startup dialog pops up, leave the selection blank and click the
> Start Molefacture button.
>
> subsequently I clicked sequentially:
> BUILD...TOPOLOGY & PARAMETERS...IMPORT CGENFF TOPOLOGY (see-screenshot-1).
>
> and input my CGenff generated 14C+H_fix.str file
>
> 2. via this command I then generated Error: Cannot find molecule-1 in
> atomselect´s `molld´
> (see screenshot-2), within this screenshot is the beginning lines of my
> .str file. (This same error occurred even when instead inputting the
> 14C+H_fix.mol2 generated via Gromacs which was used to generate the
> 14C+H_fix.str file.)
>
> Any assistance towards solving this error would be appreciated:)
>
> Best,
> Joel 🚀
>
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