Hi Brittany,
Its been a long time since I used Amber so I wont be able to give you exact
commands or the procedure that I followed.
I assume that you could generate the .lib file for the Linker using
gaff/amber force-field.
In either case use this .lib file to generate .pdb (when you save .pdb
mention the FF to be used) and then superimpose this pdb file on the DNA
using the phosphate group (as was mentioned in the tutorial?). This saves
the copy pasting time. Then you can manually substitute the linker in the
DNA's pdb file and remove the unwanted part.
Also, when you run leap dont forget to source the force-field file
(gaff/amber) you borrowed the atom types from.
Also, it would be better to define a head/tail (probably Phosphorous/Oxygen
in your case) atom for your linker, so that LEAP can automatically connect
the linker to DNA.
Hope this helps.
Best,
Dr. Chandan Patel
On Wed, Dec 3, 2014 at 3:28 AM, Brittany Boykin <
bzb0031.tigermail.auburn.edu> wrote:
> Hello,
>
>
> I am working on trying to attach a organic linker to two single stranded
> DNA at separate ends to mimic the experimental ring-like structure of the
> proximity effect. The linker is attached to the DNA through a phosphate
> group at the 5' and 3' ends. The organic linker has two capped phosphate
> groups. I compared my system to the AMBER tutorial A1. I developed RESP
> charges for the linker. Developing the parameters for the linker was a bit
> of a hassle. Then I proceeded to run the linker through LEAP. This was
> successful after I established unique atom types, but this was done through
> copying and pasting from a .mol2 file to the linker pdb file to run in
> LEAP. How do you develop unique atom types for the molecule using AMBER if
> it does not already do it? I was successful in running the DNA (polyAT
> decamer) in LEAP. LEAP did create a H5T atom but that could easily be
> removed by a visualizer method. I deleted one side of the DNA (polyAT to
> ployA). Before I proceeded to put them together, I deleted the phosphate
> capped ends from the linker and added a phosphate group to the 5' end of
> the DNA. I used Chimera combine command to link the structure. Using Join
> models, I highlighted the two ends I wanted attached and linked them
> together, unfortunately this software did not allow me to construct the
> whole complex. When I tried to run half of the created structure ,the
> biggest problem I feel is AMBER did not see the fixed group (phosphate
> group) that puts two individual structures together.
>
>
> >From all this being said, is there a way to attach DNA to a organic
> linker, have readable atom types, notice the attached groups, develop
> parameters, and run the whole structure though LEAP to start simulations?
>
>
> I know I am not the first to want to attach DNA to a linker at two
> separate ends. I know there is someone who can guide me in the right
> direction.
>
>
> See attached files to get a general idea of what I am trying to accomplish.
>
> Thank you and have a great day!
>
>
>
> Brittany Boykin
> Graduate Student
> Auburn University
> Department of Chemistry and Biochemistry
> e: bzb0031.tigermail.auburn.edu
> c: (404)545.1036
>
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>
>
--
....for afterwards a man finds pleasure in his pains,
when he has suffered long and wandered far.
-Homer
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Received on Tue Dec 02 2014 - 16:30:02 PST
