AMBER Archive (2005)

Subject: AMBER: how to constitute T-phosphotyrosine group?

From: luaj_at_sohu.com
Date: Tue Oct 11 2005 - 07:28:38 CDT

Dear Amber users:<p> I dont know how to constitute the follow group:<p> <p> O ASN49.....<p> | |<p> A1(5')...T9 T10(3')-O-P-O-TRY50<p> | |<p> O Leu51......<p> T10(3') bonds to phosphotyrosine. But in pdb, O1P,O2P,O3P and P is in TRY50 residual 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? <p> <p> Aijun Lu <p> Center for Drug Discovery and Design<p> Shanghai Institute of Materia Medica<p> Chinese Academy of Sciences<p> luaj_at_sohu.com
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