majorms hydrogens

Hello,





I would like to convert major microspecies SMILES to PDB files containing hydrogens on heteroatoms. Could you suggest a procedure to do this?


I was unable to export hydrogens on nitrogen atoms in 3D.





Thanks,


Zsolt

Hello, SMILES is not the best format when you are dealing with 3D structures, why aren't you using sdf file or something similar that can be easier converted to PDB?

Hello,


you are right, in fact I use sdf. But I was unable to convert SDF (the result of a majorms calculation) to a PDB with hydrogens on the heteroatoms. I mentioned SMILES, because I can see the results of the majorms calculations only in 2D.





Zsolt

Try:





cxcalc -N ih majorms --pH 7.4 -f pdb:H infile.mol . Alternatively you can clean it in 3D:





cxcalc -N ih majorms --pH 7.4 -f pdb:H infile.mol | molconvert pdb -3