The Molecular Graphics Laboratory Forum

Please, is there a documentation about how ADT treats non-standard residues?

I have chloride anions ligands, to which ADT assigns charge zero. I manually set -1.000 charge to them in the pdbqt file. Don't know if VINA takes that modification into account.

I also have small peptides from my experimental work that contain a non-standard amino acid. I have two mode to build the pdf file:

(1) cutting the non-standard amino acid into two residues, one named as one of the 20 amino acids, and the other one called NHE (Amber naming, I suppose).

(2) naming the whole non-standard amino acid with a single fictitious name.

Neither works. In both cases ADT does not understand and badly treats the molecules. In case (1) VINA reads the ligand file but the poses obtained are incorrect (bond connections, angles and lengths). In case (2) VINA is unable to open the ligand pdbqt file. CHIMERA opens it, showing that the peptide has been cut into three pieces. All that is also clear by examining the pdbqt file with a text editor.

I have carried out simulations for these peptides with the said files on a number of codes, including NAMD, AMBER, etc.

I am using MGLTools-1.5.4 on Debian GNU/LINUX amd64-GNU/GNOME

thanks
francesco pietra

Hi,

Did you could solve the problem with your chlorides? I wanted to perform docking in a pdb that has an inorganica phosphate in the binding site and your experience could possibly help me.

Thanks in advance,