Thank You very much for your reply. I did as you told me to transform the the upl files and ambiguous map files into actual sander input . however I am still confused about what it actually meant. take peak #74 as example :
The sander input is as follows:# 0 AMB 20-2:74 0 AMB 20-1:74 4.50 (# 74:20 Double Ambig) &rst ixpk= 74, nxpk= 20, iat= -1, -1, r1= 1.30, r2= 1.80, r3= 8.58, r4= 9.08, igr1=2085,2086,2085,2086, 941, 942, 941, 942, 941, 942, 2085,2086, igr2=2043, 899, 916,2060, &end
The UPL file : 0 AMB 20-2:74 0 AMB 20-1:74 4.50 # 74:20 Double Ambig
The Ambiguous map file:AMBIG 20-2:74 = HG1+ 122 HG1- 122 HG1- 55 HG1+ 55 HG1+ 55 HG1+ 122 AMBIG 20-1:74 = HA 120 HA 53 HA 54 HA 121
What am I asking is , is there a clear correspondence between the ambiguous assignment of the first dimension (AMBIG 20-1:74) and the second dimension (AMBIG 20-2:74) like the SANE output below(Its all from peak #74). In other words, how does sander reads double ambiguous map files and translate it into actual upper distance restraints?
Contribution filtering retained 6 possibilitiesMET_120:HA ILE_122:HG1+ MET_120:CA 4.70 6.43 0.14445MET_120:HA ILE_122:HG1- MET_120:CA 4.70 6.43 0.14445MET_53:HA ILE_55:HG1- MET_53:CA 4.83 6.91 0.12251MET_53:HA ILE_55:HG1+ MET_53:CA 4.83 6.91 0.12251MET_54:HA ILE_55:HG1- MET_54:CA 4.99 6.17 0.10036MET_54:HA ILE_55:HG1+ MET_54:CA 4.99 6.17 0.10036MET_121:HA ILE_122:HG1+ MET_121:CA 5.14 6.09 0.08419MET_121:HA ILE_122:HG1- MET_121:CA 5.14 6.09 0.08419Restraint written as :0 AMB 20-2:74 ( HG1+ 122 HG1- 122 HG1- 55 HG1+ 55 HG1+ 55 HG1+ 122 ) --- 0 AMB 20-1:74 ( HA 120 HA 53 HA 54 HA 121 )
For example, a given cross-peak that was assigned to three atom-pairs A-X or B-Y or C-Z. What is the AMBIG definition to turn it into ambiguous map files? and would it create ambiguous map files like AMBIG 20-2:#n = X Y ZAMBIG 20-1:#n = A B Cor would it use some special rule to specify which one of the combination is more probable Since allowing all possible combinations would create 9 upper distances bounds Thanks very much. Your help would be greatly appreciated ----- ÔʼÓʼþ -----
·¢¼þÈË£ºDavid A Case <david.case.rutgers.edu>
ÊÕ¼þÈË£ºtanfei777.sina.cn, AMBER Mailing List <amber.ambermd.org>
Ö÷Ì⣺Re: [AMBER] Help me with double ambiguous noe.map files!!! PLEASE
ÈÕÆÚ£º2016Äê06ÔÂ12ÈÕ 21µã12·Ö
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 - 21:30:03 PDT
