[Zinc-fans] requesting peer suggestions on docking and duplication

[Martin Stoermer]

Mornign everyone,

another thing to remember is that if you do concatenate the zinc  
files (as we do) is that some docking packages will run into memory  
problems after too many ligands. For example we have had problems  
with GOLD. When I concatenated all 113 of the ZINC Druglike sdf  
"chunks" you get a 9.6GB SD file. When I ran a GOLD job on our  
cluster across 8 nodes if dies after ~600K ligands with error  
messages like:

libpvm [t40002]: pvm_pklong(): Value too large
Pvm Function pvm_pklong( (long) start_point, 1, 1), called from  
GOLD_COMM_SendNextDock, caused an error: Value too large

************************************************************************ 
******
warning: Slave process 786433 on host node21.***.***.***.*** failed  
with following error message:
Gold internal failure (3.2) in docking ligand 0 in file /chem_db/ 
Drug_like/GOLD/Drug_like_3d.sdf
************************************************************************ 
******
WARNING: pvm task problem 786433
  Fatal error:
Received interrupt [signal number 15]

I can't speak for how Autodock, Dock and the others handle these  
large datasets, I haven't tried to bludgeon them with 2.5 million  
compounds yet. Maybe others will have that answer. So it may be more  
sensible to limit yourself to smaller sets e.g. one concatentated  
vendor database at a time.

cheers,
Martin


>
> The question is, if we merge all the files into one single giga SDF  
> file, are the ZINC IDs unique to all the entries, meaning, can we  
> safely traceback the ligand of interest to its representative pH  
> subset?
>
>
> With best regards,
> Elite158
>
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> Zinc-fans at docking.org
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