[Zinc-fans] missing NCI compounds in zinc?

John Irwin jji at cgl.ucsf.edu
Tue Aug 23 15:20:48 PDT 2005


Hi David and Jose

The current version of ZINC has (incorrectly) MMFF94S charges on atoms. The
version now in preparation has (correctly) AMSOL charges as we use in our
work and publish in our papers. You should be able to fix the charges in the
files you have (to AM1, AM1BCC, or others) with "molcharge" which is part of
OpenEye's QuacPac package.

John
 

> >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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