prepack_example.sh error message

[Anonymous]

Dear all,

I am running pre pack_example.sh while using FlexPepDocking. I have used almost the same commands and flags as what I have used in the example 2b1z (where 2b1z runs fine) on a new antibody-peptide pair, 2hfg, but I got the following error while running

FlexPepDocking.linuxgccrelease -database $PATH_TO_DB @../prepack_flags. Could someone point out what have I done wrong please?

Error message:

ERROR: this_pose.total_residue() == residue_packstat_.size()
ERROR:: Exit from: src/protocols/toolbox/pose_metric_calculators/PackstatCalculator.cc line: 164

I was wondering if I have tested on a case where there are too many residues for a docking peptide, but as I shortened the peptide to only 9 residues the result is the same.

My test files and error log attached.

Many thanks in advance!!!

[Anonymous]

A) Try the flag -mpi_tracer_to_file (filestem). It will save the output from each processor to a different log file, named filestem_###. This won’t have anything to do with your bug, but it will make your log easier to read.

As for your actual error, it may have something to do with either the insertion codes or nonprotein residues. If there are any nonprotein residues in your input, see what happens if you remove them. You could also try renumbering the pose to not have insertion codes (I think there’s an option something like -renumber_pdb to the score application that will do this). No idea if this will work. I’ve also forwarded this to the flexpepdock guys for comment; unfortunately the packstat code isn’t theirs so it’s not quite in any one person’s domain.

[Anonymous]

Hi smlewis

Thanks for your reply. My colleague found that the numbering of the atom in residue cannot have insertion code. Now it is working.
Cheers,

Alvyn

[Author]

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