The Molecular Graphics Laboratory Forum

Dear All,

I hope that you can help me out. I have just started to use AUTODOCK 4. I want to create a ligand, namely, DYDDDDK (FLAG-TAG antibody epitope). I have tried to use PRODRG, I have drawn the molecule correctly and everything. However, when I save the file, either as .pdb .pdbq .pdbqt .mol2 etc. They don't open!!

An error comes up saying that I have 5 molecules?? I don't understand. I've drawn the molecule and got the co-ordinates but it doesn't seem to open!

Any ideas? Or ideas on how I could use another software to make my ligand on and then integrate it into AUTODOCK??

Thanks guys!!

Hello,
Check out this tutorial http://autodock.scripps.edu/faqs-help/t ... odocktools .
Good luck!

i have problem with ligand.
i have made pdb file for my ligand using prodrg. i prepared ligand in autodock by adding polar hydrogens and kollman charges(charges added -0.376) and i have done rest all thing, after launching the autodock it showing that charges added -0.376 and ligand may be having problem.
but i have done docking successfully by using same pdb file in another system. i am not getting where i am having problem whether in my ligand or in my system(both systems having XP os). please help me.

thank you.