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

From: Catein Catherine <askamber23.hotmail.com>
Date: Sun, 4 Jul 2010 16:06:27 +0800

Dear Amber users,


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.


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


(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.


(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?


(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?


(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.


Many thanks in advance.


best regards,



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Received on Sun Jul 04 2010 - 01:30:04 PDT
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