VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Fri Apr 07 2023 - 11:35:41 CDT

Hello, I discovered this website which answers my own inquiry above i.e.
navigate to BUILDPAR
and then ENTER tab PREPARE PARAMETERIZATION FROM CGENFF PROGRAM OUTPUT:

*https://urldefense.com/v3/__http://adreasnow.com/Cheat*20Sheets*20and*20Play/MD*20Play/NAMDqmmm/__;JSUlJQ!!DZ3fjg!-wMJWTJNkmdFOvFoIOsdknGR-rwaITNC5sZ63qBy5sAP94APKiA2OxCDO_w01Sg3DKXDW-CYEPeyXFpTTl5MjDk9EQ$
<https://urldefense.com/v3/__http://adreasnow.com/Cheat*20Sheets*20and*20Play/MD*20Play/NAMDqmmm/__;JSUlJQ!!DZ3fjg!-wMJWTJNkmdFOvFoIOsdknGR-rwaITNC5sZ63qBy5sAP94APKiA2OxCDO_w01Sg3DKXDW-CYEPeyXFpTTl5MjDk9EQ$ >*

On Fri, Apr 7, 2023 at 2:24 PM Joel Subach <mjsubach_at_alumni.ncsu.edu> wrote:

> ...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!-wMJWTJNkmdFOvFoIOsdknGR-rwaITNC5sZ63qBy5sAP94APKiA2OxCDO_w01Sg3DKXDW-CYEPeyXFpTTl4M9lSFxA$ >*.
> 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 🚀
>>
>>
>>
>>
>>
>>