I need to do some modifications in a set of 20k PDB files for the same complex (solutions of Brownian dynamics) so that they are suitable for runnig some calculations in a NMR prediction program. To do that, I'm using BASH. One of the modifications that I need consists of renumbering residues from a certain point (not all of them), because I need two chains with consecutive residue numbering.
I'm trying to do it with awk, but I can´t find the way to do it.
Any help?
Thanks in advance!
Hi Miguel, I think you can write a simple python script to read 20000 pdb files and do whatever changes you want and save with new name and then you can feed this modified pdb fiels into NMR prediction program.
I am not really an expert with awk, but if your required changes are similar for all PDB files, then a python script will do the job just fine. However, before that a careful review of the data files in terms of the position of the required changes and the type of changes, is needed.
I can personally help write the script if the change is symmetrical across all PDB files. Then a simple for loop would do the job!
DM me if needed.
I don't think that awk is useful to modify files.
Instead you can use the sed stream editor.
sed -h
man sed
see this tutorial: https://www.linuxtechi.com/20-sed-command-examples-linux-users/
or google for more
You can combine sed and awk in same script, and use conditionals to establish every end of coordinates. Awk can be used indeed to change numbers, and you have also print formatting.
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