I am running docking by using Autodock 4.2 software. However, I am not able to run autodock at the final stage and this type of command error appears in the terminal,
Missing atom Na, please add atom in parameter library first.
There are two types of atoms that could not be recognize in ligand which are sodium(Na) and Arsenate (As). How can I add in an atom in the parameter library? I had already tried to edit dpf and gpf files by adding Na and As atom. Besides, I had also tried to edit the grid map types by adding those atoms but it still does not work.
Thanks in advance.
Sketch those ligands freshly in any molecule editor, optimize them as required and try , hope error wont appear !!
I had tried it too.But, still does not work.
Basically I am using sodium arsenate as a ligand. And I had convert this sdf file to pdb file by using this molecular converter.
http://www.webqc.org/molecularformatsconverter.php
I think that you should read this link
http://autodock.scripps.edu/faqs-help/faq/how-do-i-add-new-atom-types-to-autodock-4
I also can't find shared link to follow current error..
I edited the autodock parameters tool, But still I faced current problem
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