[Zinc-fans] missing NCI compounds in zinc?

David Evans david.evans at ulsop.ac.uk
Mon Aug 22 01:30:33 PDT 2005


Hi,

>2) I still haven't been able to upload my own molecules (a humble 20)
>into zinc to get them ready for docking. how are the upgrades coming?
>I read sybyl is not recomended for small molecule charge
>adding...should I use sybyl to get mol2 files with charges from the
>PDB files I have?  or is it worth the wait?
>
>  
>
Last time I checked, Zinc had some inconsistencies in the charges
it added. In mol2 files the charges were MMFF, whereas in the dock db files
they were AMSOL charges, as described in the Zinc article
J. Chem. Inf. Model. 45 177-182.
I don't know if this has been corrected.

Sybyl is fine for adding MMFF charges. If you want AMSOL charges,
it is possible to get a stand alone copy of AMSOL and adapt scripts
from the supplemental info of JMB, 322 339-355 (as cited in the above
article). Or there are many other approaches to assign small molecule
charges, most of which are feasible for only 20 molecules.

Dave
--
Dr David Evans
School of Pharmacy
University of London



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