Fixed (positive) charges not counted by Marvin pKa tool

User 0bc0889614

17-05-2013 22:04:38

If there are more than a certain number (10?) of titratable protons on a molecule, then Marvin switches from showing individual protonation states to showing the distribution of charges (i.e. all configurations with the same net charge are grouped together). That would be fine, but Marvin doesn't take into account fixed charges when labeling the curves. So, I have a molecule with a fixed positive charge on a quaternary amine. Because Marvin doesn't take into account this fixed positive charge, the calculated charges are all off by -1. The curve labeled -2 should be labeled -1, the curve labeled -1 should be labeled 0, etc.

I've demonstrated this bug here:

User 851ac690a0

20-05-2013 11:47:44



Thanks for reporting this bug.  The fix "+"  charge was not taken into account  on the graphic label.

I have fixed this bug. The fix will be available in the next bug-fix release. 


A little trick sometimes can help to jump from  macro distribution  to micro distribution. The boundary of the upper and the lower pKa values to be calculated  and  plotted on the screen can be adjusted by changing of the min. basic and max. acidic  pKa parameters.

 I attached two  figures. Both the micro and the macro distributions are drawn  by setting the pKa options as it is shown.  



User 0bc0889614

20-05-2013 23:49:47

Thanks, Jozsi!