Hi Thomas,
This is a single docking poses produced by Autodock Vina. I did get several
poses, but all of them look similar and a flat structure. I am thinking of
that this might be due to the 2D (not 3D) structure of the lipid which I
used for protein docking as I was not able to get a 3D for
Hi Wei,
Is this an ensemble of docking poses all overlayed in the same PDB file, and
not separated by MODEL records? PyMOL does distance based bonding when loading
data from PDB files. Which docking program generated this file?
Cheers,
Thomas
> On Jul 9, 2018, at 4:57 PM, Wei Song wrote:
>
Hello,
I got a structure (attached figure) of a lipid after docking it with a
protein. The original structure before the docking is in SDF file, not
regular PDB. I've never seen a docked structure like this with many of
the atoms having more bonds than they actually can have like some carbons
