Plugins for Jchem

User 9700cbb5ff

22-01-2008 17:15:48

Hello, I am new to Jchem but am currently working on builiding small molecule libraries for virtual screening. I am interested in calculating the protonation state(s) of the molecules in the library so that I am able to accuratley predict their charge. I am having trouble getting the plugins necessary to do so. Could someone please send me in the right direction.



ChemAxon fa971619eb

22-01-2008 17:23:11

I moved this to the structure based predictions and chemical terms forum as this is more appropriate for this sort of question.

ChemAxon e08c317633

23-01-2008 14:14:31


You need Major Microspecies Plugin for this. It can be accessed through Marvin GUI, cxcalc batch processing tool (see majormicrospecies calculation), Chemical Terms (see majorMs function) and API.

To calculate the total charge of a molecule at a specified protonation state in Instant JChem you can simply add a Chemical Terms column with this expression:


This expression will generate the major microspecies of the molecule at pH=4.0 first and then calculate its total charge.

See also: using Chemical Terms fields in Instant JChem animation.