batch mode pKa calculation

Hi ;





I am a newbie to marvin and was planing to use the pKa plugin to calculate pKa value for a set of chemical compound which are in .mol file format. I want to run it for a range of pH values and not sure how do you do that for a batch mode using cxcalc command.








Thanks in Advance

Hi,








Results of the pKa calculation will be written into the result.txt file with the next command line:

Code:

cxcalc  pka  "your .mol file"  > result.txt

Additional help information of the pka calculator available with the next command line:

Code:

cxcalc pka -h

Jozsi

See also this earlier post: http://www.chemaxon.com/forum/viewpost2811.html#2811.





Zsolt

Thanks for the reply . it was helpful but basically i wanted to know wheteher there is any way to get the table reporting various pH values and corresponding pKa value,which is bieng reported when runing the GUI for a single compound. I wanted to get this table in batch mode.

Hi,





Do you mean microspecies distribution chart?





It can not be generated with cxcalc, but the functionality is available via Java API. Here is an example that calculates microspecies distributions at a single pH value: http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/marvin/calculations/pKaPlugin.html (see the "Another example showing microspecies distributions at a single pH value").





You can also use microspeciesdistribution calculation in cxcalc to get the microspecies distribution at a single pH.





I hope this helps,


Zsolt