Cis/Trans conformations generated for amide bonds with cxcal

User 635b7487d4

16-03-2015 16:23:16

Dear ChemAxon team,

First of all, thank you very much for your great tools!

I need to generate conformers for several molecules. I use the following command, with cxcalc 6.3.1:

cxcalc conformers -m 50 -f mol2 mymolecule.mol2 > myconformers.mol2

It happens that a large part of the amide bond generated this way are in the cis configuration instead of the most favourable trans configuration. In the same generated conformers for one single molecule, it is possible to find a mixture of cis and trans amide bonds.


One example where random cis/trans conformers are generated is the ligand of the PDB entry 3B2W:


I get the same results whether I start the calculations from the mol2 file or from a SMILES. In the case of the above example, the 2 to 4 first conformers are correct. The rest contain cis amide bonds.


Is there a way to control this? Is it possible to get only trans amide bonds?

Thank you very much for your help.


Best regards,



ChemAxon 2cd598e7ad

17-03-2015 18:30:03


We've started to investigate the issue and will reply you soon.

Regards, Domi

ChemAxon 8b644e6bf4

20-03-2015 15:48:40

Dear Vincent,


Amide dihedral can not be constrained. Cxcalc output is not ordered by energy (this is actually a bug). If you invoke conformer generation from msketch (Calculations - Conformation - Conformers) the contents of the result window is; this moves the  favorable to the beginning of the list.

You might use "cxcalc dihedral" to implement filtering of generated conformers.




User 635b7487d4

25-03-2015 06:52:57

Dear Gabor,

Thank you for your reply. I will use "cxcalc dihedral" to filter the conformers.

Do you have an idea when the bug of cxcalc, relative to the non-ordered list of conformers, generated will be corrected? 


Have a nice day,


ChemAxon a202a732bf

08-04-2015 07:58:42

Dear Vincent,

I have moved the topic to the 'Structure based predictions: Calculator Plugins & Chemical Terms' forum, my colleagues will answer your question soon.

Best regards,


ChemAxon 8b644e6bf4

08-04-2015 16:16:13

Dear Vincent,


Sorry, we did not scheduled the fix of this bug yet.