when calculation the Major Tautomer on smiles:
Marvin 5.2.6 and java 1.6.0_13 is going into an endless calculation. Pushing the "cancel" button does not help, one has to kill the application.
same is true when using the API in Java, either on opensolaris or windows XP... would be nice to have a timeout option for the plugin to stop the calculation.
In 5.3 version this will be fixed.
We do not want to introduce time limit, because it can lead to unreproducible results (on a slow and on a fast computer the results can be different).
Using cxcalc with -M true option is cerating a list of tautomers, instead of giving one.
I typed (v.5.3.1):
/cxcalc probe.smi majorms -H 7.0 -M true -f sdf >probe_out.sdf
In the sdf file there were lines containing smiles of tautomers, and it could not be opened with mview.
The same can be experienced with cxcalc pka -M true
All the bests,
cxcalc probe.smi majorms -H 7.0 -M true -f sdf >probe_out.sdf
It performs major microspecies calculation (not major tautomer).
cxcalc pka -M true
This perform pKa calculation.
In major microspecies and pKa calculations the "-M" options means "take major tautomeric form". When used, the input molecule is converted to its major tautomeric form, and the major microspecies / pKa calculation is performed on the major tautomer. No other tautomers are generated.
Please attach the input and the output files, and explain what would you expect as output.