[Zinc-fans] need help for modifying ligand files of ZINC database

Shreekant Mantri bioinfoman3 at gmail.com
Wed Nov 1 05:58:58 PST 2006

hi all,
i am working on designing of inhibitors  for phosphodiesterase.I want
to do virtual screening of Zinc database using Dock.

i want to know that is it required to do following things to the
molecules in ZINC database.

#  add hydrogens
# assign partial charges
# write files in Mol2 format

or we can directly use the mol2 files of ZINC database for screening.

On the website of DOCK they hav mentioned to use
http://blaster.docking.org/zinc/upload.shtml for database
preparation.But this fecility is currently unable.

I tried using Chimera.But it was not working with the big files of
ZINC database.

Shrikant Mantri
M.Tech. (IT) Specialization in Bioinformatics
Indian Institute of Information Technology Allahabad

Mail :shrikant_mantri at bi.iiita.ac.in
"Memory feeds imagination & imagination feeds IT"......IT's life!!

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