Dear members: I am currently working on an NMR structure calculation using amber . I am also using SANE to select the most probable NOE assignments based on structure filters. However, I encountered some problems when preparing for distance restraint rst files, more specifically, in understanding double ambiguous noe.map files. For example, for CNOESY peak #74 , SANE outputs includes 0 AMB 20-2:74 0 AMB 20-1:74 4.50 # 74:20 Double Ambigmap file for this peak :AMBIG 20-2:74 = HG1- 155 HG1+ 155 HG1- 55 HG1+ 55 HG1+ 155 HG1+ 55 HB+ 61 AMBIG 20-1:74 = HA 153 HA 53 HA 154 HA 54The dyana format upl corresponding to this peak is :Contribution filtering eliminated 5 possibilitiesMET_153:HA ILE_155:HG1- MET_153:CA 0.016 -0.002 -0.096 4.64 6.07 0.16094MET_153:HA ILE_155:HG1+ MET_153:CA 0.016 -0.020 -0.096 4.64 6.07 0.16094MET_53:HA ILE_55:HG1- MET_53:CA 0.016 -0.002 -0.096 4.92 6.03 0.11371MET_53:HA ILE_55:HG1+ MET_53:CA 0.016 -0.020 -0.096
4.92 6.03 0.11371MET_154:HA ILE_155:HG1- MET_154:CA 0.005 -0.002 -0.092 5.17 6.10 0.08477MET_154:HA ILE_155:HG1+ MET_154:CA 0.005 -0.020 -0.092 5.17 6.10 0.08477MET_54:HA ILE_55:HG1- MET_54:CA 0.005 -0.002 -0.092 5.21 6.11 0.08026MET_54:HA ILE_55:HG1+ MET_54:CA 0.005 -0.020 -0.092 5.21 6.11 0.08026MET_54:HA LEU_61:HB+ MET_54:CA 0.005 -0.022 -0.092 6.03 6.83 0.03365Restraint written as :0 AMB 20-2:74 ( HG1- 155 HG1+ 155 HG1- 55 HG1+ 55 HG1+ 155 HG1+ 55 HB+ 61 ) --- 0 AMB 20-1:74 ( HA 153 HA 53 HA 154 HA 54 )
what I am confused about is the translation rule between the map file and the upper distance restraint
For some peak, it seems that the correspondence of the ambiguous possibilities is one to one, but in this case HG1+ 155 and HG1+ 55 in the indirect dimension in the map file is written twice
Can you please help me with this , Thank you very much!!Yours sincerely
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----------Fei TanBeijing NMR CenterPeking UniversityCollege of Life Science100871
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Received on Sun Jun 12 2016 - 00:30:02 PDT
