problems in pli

[Former user]

1-I tried to run pli example and got errors finding files (they actually don't exist) examples$ $PLI_DIR/bin/pli -settings 1a9u_score.pli WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type3/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type36/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type22/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type23/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type66/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type96/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type1/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type10/type122.pliff could not be opened WARNING:read_nonbonded_ff: Using surrogate file as /home/cresset/b/ff/nonbonded/type29/type122.pliff could not be opened {"system":{"name":"ligand","natoms":27,"min_dx":0.0000,"min_ds":0.0000,"pliff_score":-3.389368,"pliff_nb_score":-6.196110,"pliff_cscore":-2.768310,"pliff_gscore":-3.427800,"pliff_tscore":0.000000,"pliff_iscore":2.806743}} 2-Can you please give an example how to make fragment mapping

[Fred Ludlow]

Sorry for very slow reply - it seems notification emails didn't get through...

For certain atom-type pairs we don't have parameters, so it generalizes to a more generic atom type. The warnings have been changed to be a bit clearer, but they're not a cause for concern.

We have added an example of fragment mapping in the examples directory: https://bitbucket.org/AstexUK/pli/src/pli-snapshot/examples/1a9u_fragmap.pli?fileviewer=file-view-default

Cheers,

Fred

[Prakash Chandra Rathi]

The issue is resolved -- see Fred's comment.