I'm preparing a set of ligands for docking, I use majormicrospecies to convert smiles into mol2, then standardizer and corina, is there any way to include the rare protonation forms when using majormicro (e.g. only use form that have an abundancy bigger than 10%)? I believe that in some cases the rare tautomer is actually the active drug form,
can you send us an example file so we can investigate your problem?
Ok, here are three example ligands in SMILEs format, they have two major tautomeric forms/protonation states, one of which is dominant, but I would like the cxcalc majormicrospecies two give me every form which has an abundance higher than 20%, not only the major form,
could please attach the SMILES codes you mentioned?
Sorry, for some strange reason the forum doesnt want to attach my file, where here are the smiles:
you can use the pKa plugin in MarvinSketch to generate the microspecies distribution for your molecule.From here you can see e.g. that molecule #1 has 4, while molecule #2 has 6 microspecies alltogether. You can also see the microspecies with relevant distribution at a given pH.
In cxcalc you can geneate all microspecies with their distribtion at a given pH (default is 7.4) using the
cxcalc microspeciesdistribution test.mol
command. In this case the microspecies distribution is stored in a MSDISTR[pH=...]property. You can use the
command to get a full list of calculations.