Script for Smallest Maximum Intramolecular Distance (SMID)

[Andrew Orry]

Q. How to calculate Smallest Maximum Intramolecular Distance (SMID) as described in this publication https://pubs.acs.org/doi/10.1021/acs.jcim.9b00692 ?

Please see the script below:

1. First generate conformers using _confGen http://www.molsoft.com/man/_confGen.html or in GUI Chemistry/Generate 3D Conformers

2. So if you have table 'conformers' (result of _confGen) the script below will select conformations with minimum max inter-atomic distance. You can cut and paste this into the terminal window in the GUI.

add column conformers Rarray(Nof(conformers) ) name="mxdi"
for i=1,Nof(conformers); conformers.mxdi[i]= Max(Max(Distance( Xyz( conformers.mol[i] ) ))); endfor
group conformers.MOL_NUM conformers.mxdi "min,"  all "refmin"  header  name="conformers_minmax_di"

3. You will see a new table called conformer_minmax_di

If needed Right click on the 'mol' column header and choose set 3D browse mode