[gmx-users] Procedure for processing docked complex from Autodock vina

Prasanth G, Research Scholar prasanthghanta at sssihl.edu.in
Sun Dec 30 08:48:01 CET 2018

Dear all,

I am trying to run a simulation of protein docked with ligands of interest.
I have used autodock vina for the docking. Do i need to convert the
receptor.pdbqt to receptor.pdb before proceeding?
Do i need to add missing hydrogens in this step?

Also the protein of interest has four co-factors in the following order:
(Co-factor A x 4no.s)
HEM (Heme)
Co-factor B.

GROMOS identifies HEM. My doubt is weather I can retain the HEME group with
protein and add the co-factor.gro files (obtained from ATB server) at a
later stage or is it better to delete all the co-factors and add them

Thanks in advance.


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