Beggining with an already protonated and 3d structure of a molecule, I want to reprotonate it at pH 7.4 with cxcalc majorms2, because of some protonation issue.
Unfortunately, the output contains no explicit H atoms.
How can I re-add these hydrogens in the connection table?
PS: Input file attached
Probably the "-K true" option of the major microspecies calculator is applicable in this case.
In batch mode I would propose to use this command line:
-o output.sdf majorms -H 7.4 zinc05185552.sdf -K true -f sdf
"-o output.sdf" is the output file name can be specified here, this is optional. Without specification of the output file name and path , the generated file will be written to the standard output , usually your screen.
"majorms" the major protonation form ought to be calculated
"-H 7.4" the major protonation form will be calculated at this pH
"zinc05185552.sdf" is the name of the input molecule which is the subject of the calculation
"-K true" explicit hydrogens are not disturbed ,except if it is mandantory due to ionization
"-f sdf" specification of the output file format, in this case the "sdf" choosen
In case of MarvinSketch the "keep explicit hydrogens" options should be thick off as it is shown on the attached figure.