pKa value calculation of planer and non-planer molecule?

User ec839d1ceb

06-06-2014 02:21:32



want to calculate pKa values of planar (trans) and non-planar (cis) types of a

when I make the structure from IUPAC name (Marvin sketch) and calculate pKa
values, the pKa values predicted by Marvin are the same. But I consider that
these two values should be different.

have stable structures which are calculated by GAMESS. Can I use these coordinates
for Marvin?

I want to know the procedure to put the coordinates obtained by
GAMESS into Marvin to obtain pKa values.

also want to calculate pKa values of a molecule in various solvent.


is another problem.

I select [calculation] and click [pKa], there comes "a license is not
found and this is evaluation mode" in the PC window, and after I push OK
button, the calculated values of pKa come out (Marvin Sketch).

I doing a correct procedure?

can I set a license file for the academic license?



a lot in advance.


User 851ac690a0

12-06-2014 13:57:52


Yes you are right , the cis and the trans isomers  have to have different pKa values. 

I am working on this now. On the first attached figure the "cis" and  the "trans" isomers are drawn in the MarvinSketch. The calculated pKa values are different for the two isomers. These are not the correct values yet.

The improvement will be available in the 6.4 version.


Could you save your 3D structure created in GAMESS in a known file format like the "sdf" for example?


I attached 3 more files about  the "sdf"  file / structure  of the "cis" isomer generated by Marvin's 3D cleaner.  


The solvent effect on the  pKa is a planned feature which will be implemented in the near future.


Your  licence question will be answered by one of my colleague. 



User ec839d1ceb

13-06-2014 03:00:09

Hi, Jozsi

Thank you.

I am looking forward to use 6.4 Version. I would like to calculate the pKa of Methyl Red.

Unfortunately, I do not know the "sdf" format, so I attach the pdf file of structure calculated by GAMESS ( the view is made by Winmoster )

Many many thanks.