ricalessandri
commented
7 months ago @fgrunewald current version (commit a39c3acb06614d99fa6181a702e62123f823561f) gives the following error:
Traceback (most recent call last):
File "/Users/alessandri/miniconda3/envs/itp_to_ff/bin/polyply", line 281, in <module>
main()
File "/Users/alessandri/miniconda3/envs/itp_to_ff/bin/polyply", line 277, in main
subprogram(**args_dict)
TypeError: itp_to_ff() got an unexpected keyword argument 'tolerance'with commands like:
polyply itp_to_ff -i PS_n4_AA_oplsLigParGen.itp -sm '[CH](c1ccccc1)[CH2]' -rn PS -o new_OK.ff 
fgrunewald
The new utility allows users to extract ff-files automatically from itp files by defining fragments as SMILES. Currently the code only works for linear polymers. Let's look at some examples for how to use this Program.
Say we have a itp that describes any number of PEO oligomers then to extract the parameters for PEO we'd run:
Now of course with PEO there is the challenge of how we treat the termini. They can for example be terminated with an OH group. By default the algorithm will group all atoms that cannot be assigned to a fragment as given by the smile into the next connected fragment. Thus it creates a new bigger fragment. In this example, we would obtain the PEO fragment but also PEOter fragment that describes the termini. If they are asymmetric the code produces 2 new residues describing the termini.
Of course this might not be what we want, since we may want to build a modular ff format. In this case we can also specify the OH terminal explicitly as a fragment. For example, like so:
Note that we need to provide the terminal definitions on both ends, because the code works in blocks. Using this command we obtain definition for the termini as a separate block.
@ricalessandri
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