we would like to calculate pKa values with the command-line tool in
Marvin. This works very well. The only problem we have is that we would
also like to see the table with the micropsecies distribution of the
different protomers at different pH, as it is shown in the graphical
interface, also in the output of the comand-line tool. Is it possible to
print this table with an identification of the different protomers
(perhaps as SMILES)?
Thank you very much for your help.
Microspecies and microspecies distribution calculations are accessible also from cxcalc, but no table output for these.
Major microspecies of alanine at pH 4.0:
$ cxcalc majorms -H 4.0 alanine
More major microspecies calculations can be run simultaneously. The output is a table, in each row with the SMILES string of the correspondig major microspecies:
$ cxcalc majorms -H 1.0 majorms -H 7.4 majorms -H 14.0 alanine
id major-ms major-ms major-ms
1 C[C@H]([NH3+])C(O)=O C[C@H]([NH3+])C([O-])=O C[C@H](N)C([O-])=O
Same without table header and molecule ID
$ cxcalc -N ih majorms -H 1.0 majorms -H 7.4 majorms -H 14.0 alanine
C[C@H]([NH3+])C(O)=O C[C@H]([NH3+])C([O-])=O C[C@H](N)C([O-])=O
The output of microspecies distribution calculation is an SDF file, with distribution values in SDF fields (see attached msdistribution.sdf):
$ cxcalc -o msdistribution.sdf msdistr -H 7.4 alanine
See also: http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html#Protonation
I hope this helps.