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

Yi Shang mirandaisbest at gmail.com
Fri Dec 12 14:33:59 PST 2014


By the way the DNA RNA parameters come from Weiner et al. 1984 JACS paper
entitled "A New Force Field for Molecular Mechanical Simulation
of Nucleic Acids and Proteins", which corresponds to ff84 in AMBER. I think
the protein ff in DOCK3.6 uses the same reference.

On Fri, Dec 12, 2014 at 5:31 PM, Yi Shang <mirandaisbest at gmail.com> wrote:

> Hi All,
> I managed to add nucleic acids parameters to DOCK3.6, the
> prot.table.ambcrg.ambH is attached. The existing vdw parameter is good
> enough to cover nucleic acids so I did not modify.
>
> The docking went fine. I did have weird broken ligands in topdock.py pdb
> output, which I would ask in an separate email threads. But the receptor
> preparation seems fine.
>
> On Tue, Dec 9, 2014 at 4:48 PM, Yi Shang <mirandaisbest at gmail.com> wrote:
>
>> Hi Trent,
>> I was trying to map the polar H naming. And I sum up charges in
>> prot.table.ambcrg.ambH for each amino acids:
>>
>> ALA charge: -2.77556e-17
>> ARG charge: 1
>> ASN charge: -1.337
>> ASP charge: -1
>> CYS charge: 0
>> GLN charge: -1.337
>> GLU charge: -1
>> GLY charge: 0
>> HIS charge: 0.535
>> HIE charge: -0.465
>> HID charge: -0.442
>> HIP charge: 0.773
>> ILE charge: 0
>> LEU charge: -5.55112e-17
>> LYS charge: 1
>> MET charge: 0
>> PHE charge: 0
>> PRO charge: 0
>> SER charge: -5.55112e-17
>> THR charge: -5.55112e-17
>> TRP charge: 5.55112e-17
>> TYR charge: -5.55112e-17
>> VAL charge: 0
>>
>> I am confused by the charges of histidine (different protonations), ASN,
>> GLN, could you explain why HIE, HID, ASN, and GLN are not neutral?
>>
>> Thank you!
>>
>> On Fri, Dec 5, 2014 at 11:08 AM, Trent E. Balius <tbalius at aol.com> wrote:
>>
>>>  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
>>>>
>>>>
>>>>        _______________________________________________
>>>> 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
>>>
>>>
>>>
>>
>>
>> --
>> Yi  Shang,   Ph.D.
>> postdoctoral research associate
>> Icahn School of Medicine at Mount Sinai
>>
>>
>>
>
>
> --
> Yi  Shang,   Ph.D.
> postdoctoral research associate
> Icahn School of Medicine at Mount Sinai
>
>
>


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