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

Trent E. Balius tbalius at aol.com
Wed Dec 3 13:38:42 PST 2014

 Hi Yi,

Yes, dock uses an united-atom (no non-polar hydrogen) amber force field file for the receptors. 
I think that it is based on a force field from the 90's. 

Yes, you can get the parameters from the amber force field files but will need to put them in the dock format.

No. you will need to modify both of the files:

I think that it is ok, just a warning.  Is that the charge you expect for MN?  I think so. 

DOCK 3.6 papers:

Paper on coloring spheres: 

You can color your spheres. there is a perl script that does this in the distribution.  
Coloring is based on receptor environment. 

I would say that DOCK orienting is shape matching, 
However, if you color your spheres, then it is pharmacophore-like shape matching.   

I hope that this helps,


Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius



-----Original Message-----
From: Yi Shang <mirandaisbest at gmail.com>
To: dock-fans <dock-fans at docking.org>
Sent: Wed, Dec 3, 2014 9:52 am
Subject: [Dock-fans] DOCK3.6 parameters for ion, DNA, and RNA, and question on pharmacophore matching

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 file

, 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 using?
2. Can I copy and paste amber nuclei acid parameters to prot.table directly? 
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 generation.
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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