How many iterations for Clean 3D?

User b85e2e3247

20-02-2012 18:32:25

Hello,


How many low energy conformers does the Clean 3D option use by default?


 


Thanks,


Graham

User b85e2e3247

25-02-2012 22:29:53

I have been using the command line code:


 


molconvert -3:[ca]{1}{50}
sdf lib1.sdf -o lib1_3D


 


which generates 50 conformers and selects the lowest energy conformer, but was wondering how many LECs marvin uses when choosing the 'Clean 3D' option?

ChemAxon 8b644e6bf4

26-02-2012 01:14:32

Dear Graham,


Sorry for the late answer. Default Clean3D functionality is equivalent with "-3:[ca]{1}{1}" setting: the first conformer found for the input structure is returned. (Note that internally each fragment fuse step iterates through the possible fuses and the most favorable is selected. You can find a brief introduction on internal workings at https://docs.google.com/document/pub?id=1dgaNFWpBNqexlTRMmWF48II9qkL9e8ALdyFpoIlJfUY )


Regards,


Gabor