From: Lalehan Ozalp (
Date: Mon Dec 11 2017 - 03:01:46 CST


I have a problem with my DNA-ligand complex; that substituents of my ligand
just disappeared when I monitored it on VMD. However, I visualize the same
pdb complex on some other vizualization programs, with no missing

The procedure I followed is:
- Ran a docking.
- Compiled the DNA and my ligand (model1) together in a new pdbqt, thus
formed a complex.
- Converted the pdbqt file > to pdb file using "cut" command (which can be
done through a Linux terminal).
- Opened it on VMD (for running MD) and saw that only the core structure of
my ligand is present, but the substituents are missing. The receptor (DNA)
is intact.

May it be that there's been a sort of parameterization problem since I
visualize the same pdb file by using some other programs?

Any help would be appreciated.