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Task 4: Calculate the structure of the ligand molecule.
- In the task_4task4_to_5 directory,
create a text file using a text editor, the ".upl" file (mol.upl).
This name is used in the instruction file for CYANA, the reg.cya file in this exercise. - To do that, copy the "Intermolecular NOE" table - the first column contains the 6 columns needed for identification of the atom pair.
- The seventh column has to be the distance calculated above.
Note that the atom numbers and names have to exactly match the MOL.lib file.
Note also, that the distance has to be in a numerical format using "dot" as a decimal separator and not a "comma"!
- Navigate to the task_4task4_to_5 directory in the terminal (command line) and start the CYANA:
$ cyana - In the cyana prompt, call the instruction in req.cya (leaving out the .cya) to perform the structure calculation:
cyana> reg
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- Copy the calc_ligand_structure into a new one.
cp -r task_4task4_to_5task_4 task4_to_5_noSD - Open the mol.upl In the text editor, delete the line with the problematic restrain.
- Repeat the structure calculation in CYANA:
cyana> reg
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