The Molecular Graphics Laboratory Forum

Hello,

my problem is "simple", viewing the docking between my ligand and protein of choice on PyMol, you can see that the docking is matched according to rigid structure (... can i tell vina to accept H-bond possibility?)..there are no Hydrogen-bonds between the two, you would think that the pdb/pdbqt file would contain electrostatic parameters...if it is the problem?

i tried uploading my ligand in PMV and assign acceptor/donor by: "Build-->show acceptor/donor" and saving it as an output pdbqt file... but no notable change accounted for...should i still try it with PMV? and how?

i read some other questions in this forum asking for ph adjustment which may be the same issue here...protonation; would you suggest trying other software as Open Babel?...if so which command may change the electron accaptor/donor possibility?

i would appreciate your expert opinion on the matter
Sincerely
Ofir.