Plugin Major Microspecies: somes molecules eliminates

Hello,


I have a problem with the plugin "Major Microspecies" for some of my molecules. I give an exemple of molecule that is not consider by the "Major Microspecies" calculation in the attached file "molecule_majormspb.sdf" (another structures that are not considered are attached in a topic "Problem with the clean option in Standardizer" in the section "Structure canonicalization / standardization" of the forum ).


I use the Calculator version 4.0.1 and my command line was the one below:


cxcalc -N hi -v -o molecule_majormspb_mjms.sdf majorms -H 7.4 -f sdf molecule_majormspb.sdf


I obtained the following message:


> Calculation warnings:





1: majorms:


and the resulting file "molecule_majormspb_mjms.sdf" is empty.


Could you help me to understand why I obtain this result?


Best regards,


Samia ACI

The problem is that your input molecule contains too many (more than 8) ionizable atoms, the warning is:


1: majorms: The number of ionizable atoms (9) exceeds the specified limit (8).





In this case the current version cannot calculate the microspecies.


In the next Marvin release we will solve that in this case the major microspecies would be produced by a different calculation.