How to save in .pdb file with explicit hydrogens

I used Marvin Sketch to draw a molecule which i would be using for docking studies.

I added the explicit hydrogens via structures> add>add explicit Hydrogens. Then I saved the structure in .pdb format.

When I view the saved molecule, it opens in MarvinSpace but the explicit hydrogens are not visible by default. I know I can display them via Display> Draw Type> Ligand> Hydrogen. But is there a way to save it. I mean the structure which has the explicit hydrogens displayed by default. 

I need to save in that format because when I try to use the saved file (the file that doesnt display the explicit hydrogens by default) in the docking software, it gives an error saying that "explicit hydrogens missing".

Hi,

I'm afraid that hydrogen atoms cannot be saved in PDB file, namely, the PDB file format does not support their storage. This is an inherent property of this partical molecular structure file.

Regards

Miklos

Thanks for the reply Miklos, but the problem is that the next software that is to be used for docking displays an error message " explicit H not found"

Could you suggest something which will enable us to use the molecules drawn in MSketch in docking programs, which demand input as .sdf file.?

 

thanks

Hi,

you may try MOL2 perhaps. Most docking programs support that. It is capable of storing hygrogen atoms along with their geometry.

Does this help?

Miklos

too late to reply, but I guess would be useful for the people looking for an answer to the above question:

Well, I had the same problem before and I used autodock to convert my ligand and protein files from pdb to the pdbqt file format. pdbqt file format adds explicit hydrogens to your structure and protein-ligand docking by autodock vina supports that file format. 

Problem would be, if your docking software doesn't support pdbqt file formats, you could try autodock vina.

Thanks,

Abhi

Thank you very much!