ADL: Using ADCP with custom peptide?

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ADL: Using ADCP with custom peptide?

Gustavo Seabra
Hi,

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 \
                  --overwriteFiles \
                  --natContacts 0.8 \
                  -o docked

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,
1 chains).
ABCDEFGHIGKLMNGPQRSTGVWGYZ 26
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
eof 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.

Thanks!
--
Gustavo Seabra


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

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Re: ADL: Using ADCP with custom peptide?

Michel Sanner
Hello Gustavo

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.

-Michel

From: <[hidden email]> on behalf of Gustavo Seabra <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Tuesday, November 24, 2020 at 5:44 PM
To: "[hidden email]" <[hidden email]>
Subject: ADL: Using ADCP with custom peptide?

Hi,

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 \
                  --overwriteFiles \
                  --natContacts 0.8 \
                  -o docked

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,
1 chains).
ABCDEFGHIGKLMNGPQRSTGVWGYZ 26
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
eof 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.

Thanks!
--
Gustavo Seabra


________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---