cxcalc majorms2 on already protonated 3d structure

User ce5f27518b

30-09-2014 13:31:18

Dear all,

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

User 851ac690a0

02-10-2014 13:19:14



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.