ADL: Using ADCP with custom peptide?
gustavo.seabra at gmail.com
Tue Nov 24 17:43:45 PST 2020
I wonder if it is possible to use ADCP with a custom peptide, maybe by
giving the pdb file of the peptide, instead of having ADCP build the peptide
itself from sequence.
I'm trying to run it as:
$ adcp --target target.trg \
--input ligand.pdb \
--numSteps 5000000 \
--nbRuns 100 \
--maxCores 8 \
--natContacts 0.8 \
But I keep getting errors in the log file, for example:
$ cat docked.out
found external potential parameters 1
found external potential parameters 4
setting constrained list file constrains
found external2 potential parameters 4
setting cyclic peptide constrains
Building protein from sequence: ABCDEFGHIGKLMNGPQRSTGVWGYZ.
Building protein from sequence: ABCDEFGHIGKLMNGPQRSTGVWGYZ (26 amino acids,
INFO: Attempting a serial MC simulation.
Found a chain break (chain d -2->-3) return
Found a chain break (chain d -2->0) return
[lots of similar lines]
Found a chain break (chain d 4->6) return
Found a chain break (chain d -7->-8) return
ERROR! ERROR! EOF while reading in from input PDB file.
ramaprob initialise success
I wonder if anyone here would have an idea on what could I be doing wrong.
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