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

Trent E. Balius tbalius at aol.com
Fri Dec 5 08:08:58 PST 2014


 Hi Miranda,

I forgot to say that you will also have to update the charge file: amb.crg.oxt

You can run dock3.6 without openeye.  

Sounds like you are on the right track with the force field stuff. 
It might be reasonable to use analogy to assign the VDW parameters.
To get the charges sum up  the heavy atom charge with its attached non-polar hydrogens. 

I think that we are using an united atom force feild for historic reasons.  
But, It might be hard to modify vdw prams. 

Once you get it working if you could send us your files that would be very useful.  

Note that DOCK 6 might be easer to set up and run, but it is slower.  

I hope this helps, 

Take care,

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: Trent E. Balius <tbalius at aol.com>
Cc: dock-fans <dock-fans at docking.org>
Sent: Wed, Dec 3, 2014 9:09 pm
Subject: Re: [Dock-fans] DOCK3.6 parameters for ion, DNA, and RNA, and question on pharmacophore matching


Hi Trent,
Do I just use the all-atom DNA ff? I did not find united-atom ff for DNA.


I can update prot.table.ambcrg.ambH with atom number and charge found in nucleic12.lib, but I am not sure how to update  vdw.parms.amb.mindock. In  vdw.parms.amb.mindock there are 26 atom types defined, so if I need to add new atom types, I have to define for each atom type, for example atom 27, elsewhere I guess. 


I also tried the way described here:
http://wiki.bkslab.org/index.php/BKS_lab_Structure_preparation

, but /DOCK/dockenv/trunk/etc/file2file.py needs openeye license. Do you think I can run DOCK3.6 without openeye license, if I supply the parameters myself?



Thank you!



On Wed, Dec 3, 2014 at 5:07 PM, Trent E. Balius <tbalius at aol.com> wrote:

 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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-- 


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












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