Hi: Never I got this error. Are u working with same unusual atom? Regards.

Juan-Sebastián Gómez-Jeria

Hi sir,

For me also am getting the same error. 

I have a set of 30 ligands to get docked.

Out of this 30,  two ligands showing similar problem.

One ligand showing the exact problem what i mentioned above and the second one showing the similar error, where instead of D its showing some other atom type

 .

With regards 

Sajin

Hi: What is the difference between these two ligands and the others?

Sajin..What you do when you find Br, Cl, F etc. in ligands? try placing D in set atoms directly and see the results. Although it may be more like trial and error. Otherwise you need to identify the atom type properly and update it. You can also attach the ligand file here if it is not confidential.

Juan-Sebastián Gómez-Jeria 

for the second ligand, I am getting like this sir.

unknown ligand atom type Si

add parameters for it to the parameter library first!

With regards

Sajin

Pankaj Mishra,

Thank you for the reply.

When i gave set map types > directly, the autogrid will run correctly but i will get this error while running autodock.

IF i gave set map types > Choose/open ligand, autogrid will show this error.

The atomtype may be 'deuterium' since its showing ligand atom type D

Am also attaching the ligands here.

Juan-Sebastián Gómez-Jeria

Hi sir ,

Am also attaching the compound here. 

If you are using deuterium simply change it by hydrogen for docking. Finally they have the same electronic structure. Regards.

Hi sir,

I tried with that too !!!

But i don't know why, again showing same error.

May be because i didn't change all deuterium. 

Obviously you must change all D atoms by H ones. Regards.

I sir, so what about the other case where the atom type is Si???

Hi: I do not know. You must ask this question in the mailing list of Autodock or contact the programmer. Regards, Juan

check your ligand .pdbqt file in notepad. U understand the problem in format.