ADL: Nobel prize winning Potassium cation and 18 crown ether complexation and modeling

Jon Wil jonwil6425 at gmail.com
Sun Jan 3 15:44:45 PST 2021


Hi folks
I thought I would see how autodock models the properties of Charles
Peddersons discoveries of crown ethers that led him to be awarded the
Nobel prize for Chemistry in 1987:

*[ https://en.wikipedia.org/wiki/Crown_ether
<https://en.wikipedia.org/wiki/Crown_ether> ].*


So to start with  Iwas trying to dock NaOH with 18 C - 6 i.e.,
[image: image.png]
I have download the NaOH 2D sdf file from pubchem and converted it to PDB
in Pymol but when I try to import it as a ligand I get the following error
messages:


*Sodium cation from pubchem Structure2D_CID_923 : :UNK0:Na and Sodium
cation from pubchem Structure2D_CID_923 : :UNK0:Na have the same
coordinatesERROR*


*and*


*forcing addition of gasteiger charges to molecule with all zero charges
 Sorry, there are no Gasteiger parameters available for atom Sodium cation
from pubchem Structure2D_CID_923 : :UNK0:NaSodium cation from pubchem
Structure2D_CID_923 : :UNK0:Na and Sodium cation from pubchem
Structure2D_CID_923 : :UNK0:Na have the same coordinates*


Here is the NaOH  file info:
[image: image.png]

Any ideas? I tried adding  "Gasteiger charges"  but the error messages just
came up again. I am new to Autodock and have searched hard for any info on
this and for cations as ligands in general and how to dock them; for
example by looking in Autodock's manual and the forum etc., to solve this,
but cant find anything.

Many thanks in advance for your help

Kind regards
Jon


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