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

Yi Shang mirandaisbest at gmail.com
Wed Dec 3 21:09:53 PST 2014


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
>
>
>        _______________________________________________
> Dock-fans mailing listDock-fans at docking.orghttp://mailman.docking.org/mailman/listinfo/dock-fans
>
>


-- 
Yi  Shang,   Ph.D.
postdoctoral research associate
Icahn School of Medicine at Mount Sinai
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20141204/275028b1/attachment.html 


More information about the Dock-fans mailing list