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tips & tricks: planar amides

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. Steps to undertake are described here:

1. if necessary: decrypt the static data files. An encrypted file looks like this:

   #encrypt flexx
   11fcfeee9f59f079a3b2e8aae446cd4e1b6c58a9b295aff5de7fa3af6a96d930bae502cda2637def
   4e76e7301aa0e29a3cefd3208d6daa3e6328e62ab5c82918acd9b2e947c7bad7a2cc8fc9358659c9
   749ecec5e95577bdeaaa63240be17b9884a93e1e5a221ba2416d7e08a47852ca1c77fd9e2ac74032

2. Decryption is done in FlexX in the menu DATABASE/DECRYPT. For details on decryption, please refer to the user guide, page 92. Upon decryption, FlexX generates new files with the ending *dcr.dat.
3. 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**
4. 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.
5. save the file as torsion_FIX_planar-amide.dat.
6. 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.
7. re-run the docking with the new static data file.