Warning message during lowestenergyconformer calculations

User a83787b4e1

10-07-2011 16:30:13

Hi


I am constructing compound library for virtual screening, and while I was calculating lowest energy conformer of the compounds, one of the compounds received a warning message like


"WARNING! CIS/TRANS bond(s) has extra ligands (1-2)"


It did not give me the index number, so I could not track back this problematic molecule.


Could you explain me what this warning meant?


My command for lowest energy conformer calculation was:


cxcalc lowestenergyconformer -f sdf -O 3 <Input file> > <Output file>


Sincerely,

ChemAxon e08c317633

14-07-2011 13:52:43










baramsite wrote:

It did not give me the index number, so I could not track back this problematic molecule.



 We will improve this, cxcalc will display the index of the molecule.











baramsite wrote:

Could you explain me what this warning meant?



My colleague will explain the meaning of the warning message.


Zsolt

ChemAxon 8b644e6bf4

09-08-2011 15:25:49

 


"WARNING! CIS/TRANS bond(s) has extra ligands (1-2)"  - Could you explain me what this warning meant? 


 


This warning message is printed during the initialization phase of 3D coordinate generation initialization (identifying stereo requirements for the generated conformers) if the input structure contains (or might contain) inconsistent information.


"WARNING! CIS/TRANS bond(s) has extra ligands (<ATNO1>-<ATNO2>)" printed when the bond connecting <ATOM1> and <ATOM2>



Could you send us the molecule(s) provoking this warning - if they are not confidential?


 


Regards,


Gabor

User 8fbca62edf

15-11-2011 08:21:25

Please, what do i do first to put in place a chemical data base?

ChemAxon afdac7b783

15-11-2011 19:37:02

You can start with one of our documentation pages e.g., http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/ijcTOC.html


and


http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/tutorials/import/htmlFiles/import_sd_file.html.


I hope you will find the answers
you
have requested in these documents.


If you have any further questions, do not hesitate to contact us.


 


Best Wishes,


Viktoria