[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 14:07:59 PST 2014


 Sorry I pointed you the wrong, but still relevant, paper. 

Here is the paper on coloring spheres:
http://www.ncbi.nlm.nih.gov/pubmed/7504257?dopt=Abstract


I hope this helps,

Trent

 

 

-----Original Message-----
From: Trent E. Balius <tbalius at aol.com>
To: mirandaisbest <mirandaisbest at gmail.com>; dock-fans <dock-fans at docking.org>
Sent: Wed, Dec 3, 2014 1:38 pm
Subject: Re: [Dock-fans] DOCK3.6 parameters for ion, DNA, and RNA, and question on pharmacophore matching


 Hi Yi,

Q1:
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. 

Q2:
Yes, you can get the parameters from the amber force field files but will need to put them in the dock format.

Q3:
No. you will need to modify both of the files:
prot.table.ambcrg.ambH
vdw.parms.amb.mindock

 
Q4: 
I think that it is ok, just a warning.  Is that the charge you expect for MN?  I think so. 

Q5:
DOCK 3.6 papers:
http://www.ncbi.nlm.nih.gov/pubmed/20735049
http://www.ncbi.nlm.nih.gov/pubmed/22716043

Paper on coloring spheres: 
http://onlinelibrary.wiley.com/doi/10.1002/jcc.540130311/abstract

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



======================================
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
http://wiki.bkslab.org/index.php/BKS_lab_Structure_preparation

, 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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