Re: [O3A] Possible issue with MMFF94 geometry minimization

[Paolo T. <pao...@un...>]

Dear John,

you will need to add hydrogens and generate 3D coordinates for your 2D 
molecule before feeding it into Open3DALIGN. You may conveniently do 
that with obabel:

obabel -i sdf 2d.sdf -o sdf -O 3d.sdf -h --gen3D

See attached for input and output files.

Cheers,
p.

On 03/06/16 00:05, John Paul Kowalski wrote:
> 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).
>
>
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