[modeller_usage] absolute position restraints

["Frank Böckler" <>]

Dear all, 
 
I'm trying to keep some part (ligand) fixed in space using the restraint 
features 9, 10 and 11 and the restraint type 34. 
Unfortunately, I was not quite successful with this approach (outlined 
below). 
Can anybody give me an advice, how to proceed correctly (correct syntax 
for the restraints, other approach giving the same result, ...)? 
Any help is highly appreciated! 
 
Thanks in advance, 
 
Frank 
 
My approach was: 
# generating a restraint file from the .ini file of a corresponding run, 
which included the ligand (atom-ids: 1936-1958) using an awk script: 
 
.ini-file: 
 
HETATM 1936  C5  LAE   257      46.483  11.136  15.931  1.00 -0.04       
4SG1940 
HETATM 1937  C4  LAE   257      45.927  12.329  16.596  1.00  0.07       
4SG1941 
[...] 
HETATM 1958  C16 LAE   257      42.378  10.076  17.821  1.00 -0.02       
4SG1962 
END 
 
.rsr-file: 
 
MODELLER5 VERSION: MODELLER FORMAT 
R    3   1    9   34   1   2   0  1936   46.483   0.0 
R    3   1   10   34   1   2   0  1936   11.136   0.0 
R    3   1   11   34   1   2   0  1936   15.931   0.0 
R    3   1    9   34   1   2   0  1937   45.927   0.0 
R    3   1   10   34   1   2   0  1937   12.329   0.0 
R    3   1   11   34   1   2   0  1937   16.596   0.0 
[...] 
R    3   1    9   34   1   2   0  1958   42.378   0.0 
R    3   1   10   34   1   2   0  1958   10.076   0.0 
R    3   1   11   34   1   2   0  1958   17.821   0.0 
 
My idea was to constrain the x, y or z coordinate (feature 9, 10, 11) of 
the ligand with a harmonic potential (3) written into restraint type 34 
and applied on 1 atom (using 2 parameters: the coordinate and the standard 
deviation). I've used both 0.0 and higher values as standard deviations to 
fix the atom position absolutely or to allow some movement, however both 
was unsuccessful. Perhaps the whole syntax is false??? 
 
However, modeller7v7 does not complain about the restraints (as can be 
seen from the .log file), which I read in as part of my rewritten 
'special_restraints' section: 
 
.top-file: 
 
subroutine routine = 'special_restraints' 
[...] 
   read_restraints file = 
'/home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr', 
add_restraints = on 
[...] 
return 
end_subroutine 
 
 
.log-file: 
 
[...] 
make_re_422_> Number of previous, current restraints         :    20593    
20593 
make_re_423_> Number of previous, current selected restraints:    20327    
20327 
[...] 
TOP_________>   218  750 CALL ROUTINE = 'special_restraints'  
[...]  
TOP_________>   223  761 READ_RESTRAINTS FILE = 
'/home/literatur/boeckler/D4proj/t; 
                      op/LIG_posconst_new2.rsr', ADD_RESTRAINTS = ON  
  
openf5__224_> Open       11  OLD  
SEQUENTIAL  /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr 
openf5__224_> Open       11  OLD  
SEQUENTIAL  /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr 
rdcsr2__307_> Number of restraints read    :       69 
              Number of excluded pairs read:        0 
              Number of pseudo atoms read  :        0 
 
Dynamically allocated memory at        amprmcns [B,kB,MB]:     18611512   
18175.305    17.749 
openf5__224_> Open       11  OLD  
SEQUENTIAL  /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr 
openf5__224_> Open       11  OLD  
SEQUENTIAL  /home/literatur/boeckler/D4proj/top/LIG_posconst_new2.rsr 
rdcsr2__307_> Number of restraints read    :       69 
              Number of excluded pairs read:        0 
              Number of pseudo atoms read  :        0 
rdcsrs__304_> Restraints in memory, selected restraints:    20662    20396 
              Explicitly excluded atom pairs in memory :        0 
              Pseudo atoms in memory                   :        0 
[...] 
 
Thus, it seems that the restraints have been read in successfully and no 
errors were reported. However, having a look at the output file shows that 
the ligand has been "exploding", spreading its atoms all in space. 
 
.pdb-file: 
 
HETATM 1936  C5  LAE   257     127.363  17.224  57.224  1.00 57.83       
4SG1940 
HETATM 1937  C4  LAE   257      50.824 -79.520 -76.644  1.00 57.83       
4SG1941 
[...] 
HETATM 1958  C16 LAE   257      66.463  23.642 160.673  1.00 57.83       
4SG1962 
END 
 

-- 
  
------------------------------------------------------------------ 
Dr. Frank Böckler 
Dept. of Medicinal Chemistry 
Emil-Fischer-Center 
Friedrich-Alexander University Erlangen-Nürnberg 
Germany 
------------------------------------------------------------------ 

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