[O3A] Possible issue with MMFF94 geometry minimization

[John P. K. <ko...@uw...>]

Hello Dr. Tosco and Open3D community - I recently started using the Open 3D
Align + QSAR pre-built binary distribution for Windows. I am having an
issue with the "qmd" command, I think my problem may be due to MMFF94
geometry minimization during the iterative procedure that "qmd" runs
through. I have attempted to specify prm_dir parameter to the folder where
mmff.prm/mmffs.prm resides as well as simply run "qmd" on default.

*The issue is that the .sdf file that is generated depicts hydrocarbon
chains (for all conformations) as completely linear, without the 'kink'
that we would expect for a minimized geometry. Therefore, it appears I am
not generating force field based minimized structures.*

Am I incorrectly running "qmd"  / is there a possible issue with the
windows pre-built / an issue with the Tinker files?

See attached images of a 2D structure that I imported (before running
"qmd"), and the linear hydrocarbon result after running "qmd" (where FF
optimization did not appear to occur).