Dear everyone,

I am a new learner of Accelerys DS Visualizer. I am doing molecular docking by using Autodock Vina. After that, I got the docked ligand (file *.pdbqt). Therefore, I tried to use Accelerys DS Visualizer  version 2.5 to open this file to display the molecular structure.

However, I found that with the same version, the molecular structure of file docked ligands are different although I used the same structure of ligand for docking. (for example: I use structure A for docking the first time, after docking I got the result A1, docking the second time I got is A2: I used Accelrys DS Visualizer version 2.5 to open A1, I found there is one double bond, but if I use Accelrys DS Visualizer version 2.5 to open A2, I found there are two double  bonds. (I also consider whether there are convertion of these conformations here or not, however, the answere is no convertion here.)

Anothere thing is with the different version (version Accelrys DS Visualizer 2.0 and version 2.5), I also found there are the different structure like above situation.

Could you give me some suggestions or some ideas to solve the problem?

Many thanks for your help and your time.

Best regards,