change the bond in the molecule

[Fatmah]

Hi
I work in Pyrx academic version (not free)
when I do docking for molecules , Pyrx change the bonds in the structure (see attached file)
how to fix this problem ?

[Sarkis Dallakian]

Hi Fatmah ,

Thank you for the message. When converting ligands to pdbqt, PyRx adds hydrogens and then removes non-polar hydrogens. Are there any hydrogens missing or added that makes it appear that PyRx changes the bond structure?

Thank you,
Sarkis

[Fatmah]

Hi
No hydrogen missing or added , just the change the bond structure.

[Sarkis Dallakian]

The bond structure is not stored in the pdbqt file. It is up to the visualization program how to draw the bonding structure. Perhaps you can do energy minimization before docking to see if that helps.

[Fatmah]