[AMBER] How do define phospho-tyrosine-DA linkage?

From: Catein Catherine <askamber23.hotmail.com>
Date: Sun, 4 Jul 2010 01:38:41 +0800

Dear All AMBER users,


I am trying to do a MD for a system with phosphated Tyrosine linked to the 10th DNA base pairs, which induce a DNA single strand break between 10th and 11st base pairs.


I got the parameters (lib and frcmod) of phosphated tyrosine from AMBER webpage. I have done the parts for phosphated tyrosine.


I also added a ter card between base pairs 10th and 11st.


I define the 11st base pairs as DA3 so that it is a terminal one.


However, I have difficulty to define the 10th base pairs. When I define it as DA5, an additional O was defined (as both phosphates tyrosine and DA5 got O3P atom defined. When I define it as DA, as there is a ter card, it automatically changed to DA5.


Can I simply delete one of the O3P in xleap window? What is the command line should be used to remove one of the atom, given the residue name is DA10?


If it is not a properly procedures to be used, how can I define the DA linked to a phosphated tyrosine?


By the way is the webpage of amber has been slow down these two days. As I found sometime, I cannot see the webpage at all or connect slowly.


Best regards,

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Received on Sat Jul 03 2010 - 11:00:03 PDT
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