AMBER: how can I constitute T-phosphotyrosine group ?

From: <luaj.sohu.com>
Date: Tue, 11 Oct 2005 22:25:02 +0800 (CST)

Dear Amber users:
    I dont know how to constitute the follow group:
  
                          O ASN49.....
                          | |
      A1(5')...T9 T10(3')-O-P-O-TRY50
                          | |
                          O Leu51......
      T10(3') bonds to phosphotyrosine. But in pdb, O1P,O2P,O3P and P is in TRY50 residue which is named PTR. so when reading it via xleap, O3 and H was added in T10, and O1P,O2P,O3P and P was not recognized. If I constitute a group containing T10 and phosphotyrosine, how to designate the head and tail atoms, because there are three embranchment in this group. Or there are other solutions?
  
      Aijun Lu
   Center for Drug Discovery and Design
   Shanghai Institute of Materia Medica
   Chinese Academy of Sciences
   luaj.sohu.com


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Received on Tue Oct 11 2005 - 15:53:01 PDT
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