On Sun, Jun 12, 2016, tanfei777.sina.cn wrote:
> 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
I don't have a detailed solution, but you might try adding
LISTIN=POUT
to your input file. This generates a detailed description of what each
restraint is doing. (It creates lots of input, so try it with just the
restraints you are having trouble with.)
Roughly equivalent scheme is to examine the actual sander input, not
the makeDIST_RST input. Again, this will show you exactly what sander
is seeing, and allow you to hand-edit it if it seems wrong.
...good luck...dac
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Received on Sun Jun 12 2016 - 06:30:02 PDT
