Re: [AMBER] Question about xleap: How to define a linkage between DNA and phosphotyrosine.

From: FyD <>
Date: Mon, 05 Jul 2010 08:44:44 +0200

Dear Catherine,

- I do not think using a central nucleotide fragment in place of a
terminal one (or vice-versa) is a good idea. If you do so it is
unlikely the total charge of your system will remain an integer (what
you want to reach) and you will generate open valencies. For
nucleotide fragments, you need to keep in mind that the central
fragment takes an integer value (not always = -1; see the F-83
R.E.DD.B. project by L. Tao for instance) and the sum of the 3' & 5'
terminal fragments takes also an integer value.
See also the total charge of DA, DA3 & DA5 in the Amber force field
topology database:
> charge DA
Total unperturbed charge: -1.000000
> charge DA3
Total unperturbed charge: -0.692100
> charge DA5
Total unperturbed charge: -0.307900
                 -0.692100-0.307900 = -1.0000 !

- A consequence is that I do not thing you can use the phosphorylated
Tyrosine published by Homeyer et al.: the connections between the
nucleotide & peptide parts do not match: the resulting total charge
will not be an integer and you will have either missing oxygens and
"too much" ;-) oxygens in the connections.

You need to build (a) new fragment(s) for your phosphorylated amino
acid (PAA) in agreement with the nucleotide fragments already
available. If I well understood your system, your PAA is located at
the 3' terminal. But you cannot use the 3' regular terminal fragment
which is 3'OH. Thus, you need to add a PAA fragment which has the same
total charge as DA3, and this PAA fragment is in fact a Tyr-O-PO2

Your case is quite interesting/tricky. I suggest you to use
R.E.D.-III.x to learn how to use intra- & inter-molecular charge
constraints during the charge fit to define molecular fragments. Then,
you might decide to use R.E.D. IV/R.E.D. Server if your case is too


You might find answer in more complex projects:

additional answers are below.

> I would like to define the linkage between a phosphotyrosine and a
> DNA base pair. I make myself clear, I have prepare the model
> structure as the attached pdb file. This is exactly the model that
> I could like to define for amber calculation. I already found the
> parameters for phosphotyrosine (I downloaded from the amber webpage
> previously). I have difficulty to define a linkage between DT and
> PTR. I have serveral questions would like to ask for your guidence.

This is not because you found FF libraries for something that has the
same name that you can apply it to your system! I do not think the PAA
FF libraries from Homeyer et al. are compatible with what you need.

> (1) how to add a bond between O3P of PTR and C3' of DT in xleap?
> What is the text command should be used?

Look at the connecting atoms for DA and the PAA of Homeyer et al.:
they do not match to do what you need.

> (2) there are four predefined residues for DT in ff99SB force
> fields, i.e. DT3, DT4, DTN and DT. however, all of them has a
> Oxygen atom attached to the C3', if I define the pdb file using
> anyone of them. It may be problematic, as PTR will also have an
> additional oxgyen.

Yes so you need to build your own PAA fragment keeping in mind that
the total charge of your new PAA fragment + DA5 (or DX5) takes an
integer value (-1 here).

> (3) I think I should define a new unit (name as DTp) in xleap to
> represent a "DT without Oxygen in C3'".


> In order to maintance the charge of the DTp unit same as DT. I may
> modify the charge of DTp by removing the oxygen atom from DT, and
> share the charge of oxygen to all the rest of atoms in DTp. Do you
> think it is reasonable approach?

I would create (a) new PAA fragment(s)

> (4) I also have to solve the problem head and tail problems in the
> new units. For DTp, the head should be the other base pairs one
> step above DTp. the tail should be PTR. However, for PTR, as it is
> a protein residues, the head and tail should be the residue that
> link the N-terminal or C-terminal of tyrosine. However, do I have
> to define PTR has another tail or head at the O3P atom? If yes, how
> to define more than one tails in xleap?

No problem here; your PAA fragment will have three connect atoms like
CYX in disulfide bridge. Look at CYX and you will have all what you
need for your PAA fragment.

> (5) I also would like to ask the text command should be used to
> remove an atom in xleap, as it could be very difficult to pick an
> atom in edit mode of xleap.

This is not just deleting an atom (or adding one) you also need to get
an integer value for the total charge of your system.

The best here might to re-generate the terminal & central fragments...
This is a little brain storming & this just like playing LEGO ;-) I
hope this helps.

regards, Francois

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Received on Mon Jul 05 2010 - 00:00:03 PDT
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