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If you feel that amides in your particular application should be treated as planar, you can force them to be so by adjusting the corresponding section in the static data file torsion.dat.
1. First you need to decrypt the file torsion.dat which is done in FlexX in the menu DATABASE/DECRYPT. For details on decryption, please see the question “How can I use the information in the decrypted static data files?” or refer to the user guide, and look for the DECRYPT command. Upon decryption, FlexX generates new files with the ending *dcr.dat.
2. open torsion*dcr.dat in an editor and go to the very end of this file to the section starting with
@subgraph user_defd 4 **PLANAR_N(H)_amides**
3. this section is commented out:
# @subgraph user_defd 4 **PLANAR_N(H)_amides**
# atom 1 C.*
# atom 2 N.AM
# atom 3 C.2
# atom 4 C.*
# atom 5 H
# atom 6 O.2
# bond 1 2 1
# bond 2 3 am
# bond 4 3 1
# bond 5 2 1
# bond 6 3 2
# data
# tangle/te 180 0
# period 360
# symmetry 180
# end
erase the comment-signs '#' to activate this code.
4. save the file as torsion_FIX_planar-amide.dat.
5. now open the file config.dat. In the section @STATIC_DATA comment out the line
TORSION static_data/torsion_standard.dat
and point to the altered FIX_planar-amide.dat file by typing
TORSION my_path/torsion_FIX_planar-amide.dat
Replace 'my_path' with your corresponding path to this file.
6. re-run the docking with the new static data file.
Alternatively, you can work with SMARTS in Step 3:
This expression would for example, exclude lactames and the like and alow +/- 15° tolerance from the 180° torsional angle:
@subgraph user_defd
4 **slightly_tolerant_planar_amides**
SMARTS [H]~[#7;!R]~[#6;!R]~[#8D1]
data
tangle/te 180 0
tangle/te 175 0
tangle/te 170 0
tangle/te 165 0
period 360
symmetry 180
end
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