I have a 3D molecule file in SD format, composed of one main molecule and a smaller fragment (HCl), called 6603610_3D_protonated.sdf
I first look at the dominant tautomer distribution at pH 7.4, getting the result 6603610_tautomers.sdf. For now I am only interested in the first tautomer, so I save it as 66603610_Part1.sdf
When I look at the file 66603610_Part1.sdf, the first line has the molecule name (66603610). But as it is in 2D and explicit hydrogens are missing, I do the following to add explicit hydrogens and convert to 3D:
cxcalc conformers -m 1 -s true 66603610_Part1.sdf > 66603610_Part1_cleaned.sdf
When I look at the result, the HCl is gone and the name of the molecule is also gone (as the first line of the sdf file is empty). What's happening? How can I retain the molecule name? And is there an "official" recommended way to desalt molecules with Marvin?