[Dock-fans] DOCK3.6 parameters for ion, DNA, and RNA, and question on pharmacophore matching

Yi Shang mirandaisbest at gmail.com
Wed Dec 3 09:51:44 PST 2014

Hi All,
I wanted to use DOCK3.6 to screen small ligand database. My receptor
contains protein, DNA, RNA, and ions.

In grids/prot.table.ambcrg.ambH there are no parameters for DNA and RNA. I
found some info online on adding non-standard residue into the prot.table
, but I am not sure if this is the way to add parameters for nucleic acids
and ions.

1. Is DOCK3.6 using amber force field? Which protein/ion force field it is
2. Can I copy and paste amber nuclei acid parameters to prot.table
3. For each non-standard residue, is prot.table.ambcrg.ambH the only file I
need to modify?  I see vdw.parms.amb.mindock is also used for grid
4.  The MN ion was read in successfully, but I saw warning in delphi.log
"!!! WARNING:  MN 300 has a net charge of   2.0000", Should I be worried?
MN having charge of 2 seems fine to me.

5. Which is the original paper describing DOCK3.6 algorithms? I was
wondering if ligand sphere generation takes into account the ligand atom
type. For the ligand docking is it shape matching or pharmacophore matching?

Thank you !

Yi  Shang,   Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
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