ADL: Using ADCP with custom peptide?
sanner at scripps.edu
Mon Nov 30 18:02:57 PST 2020
ADCP uses a coarse representation with a single bid for the side chain of each amino acid and relies on a library of rotamers to construct full atom models evaluated with the AutoDock scoring function. Hence, it cannot currently handle custom peptides containing non-standard amino acids. We are working on making this possible but we do not have working code for that yet.
Sorry for he inconvenience.
From: <autodock-bounces at scripps.edu> on behalf of Gustavo Seabra <gustavo.seabra at gmail.com>
Reply-To: "autodock at scripps.edu" <autodock at scripps.edu>
Date: Tuesday, November 24, 2020 at 5:44 PM
To: "autodock at scripps.edu" <autodock at scripps.edu>
Subject: ADL: Using ADCP with custom peptide?
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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