Freezes after a while about lightdock HOT 6 CLOSED

Please, could you describe in more detail what is your actual workflow, OS, version of LightDock, input structures..?

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Sorry, of course. OS is Ubuntu 22.04. I have a pdb file for DNA generated from 3D-Dart (consists of chains A and B) and a protein from AlphaFold2. I use a restraints.list. Here is part of the final lightdock_protein.pdb:

ATOM 1 N TYR A 33 -19.338 -2.079 12.345 1.00 89.44 N
ATOM 2 CA TYR A 33 -19.806 -1.688 11.017 1.00 89.44 C
ATOM 3 C TYR A 33 -18.947 -0.554 10.458 1.00 89.44 C
ATOM 4 O TYR A 33 -18.556 -0.584 9.286 1.00 89.44 O
ATOM 5 CB TYR A 33 -21.275 -1.262 11.064 1.00 89.44 C
ATOM 6 CG TYR A 33 -21.838 -0.887 9.712 1.00 89.44 C

And here is part of the final lightdock_dna.pdb:

ATOM 1 P DC A 1 0.564 8.277 -26.794 1.00 0.00 P
ATOM 2 O1P DC A 1 0.592 9.612 -27.432 1.00 0.00 O
ATOM 3 O2P DC A 1 1.424 8.109 -25.601 1.00 0.00 O
ATOM 4 O5' DC A 1 -0.944 7.888 -26.428 1.00 0.00 O
ATOM 6 C5' DC A 1 -1.766 7.259 -27.430 1.00 0.00 C

Everything up and including the setup step works in regular lightdock 0.9.4, so I downloaded lightdock-rust and moved these temporary results over there and wrote a shell script. However, I don't seem to get any models generated when running ant_thony.py:

lgd_flatten.py lightdock_rec.nm.npy rec_nm.npy
lgd_flatten.py lightdock_lig.nm.npy lig_nm.npy

ls *.dat | sed "s/initial_positions_/swarm_/g" | sed "s/.dat//g" > swarmlist.txt

swarmlist1=$(cat swarmlist.txt)

for swarm in $swarmlist1;
do
mkdir "${swarm}"
done

sed -i '1!s/^/..//g' swarmlist.txt

for swarm in $swarmlist1;
do
cd "${swarm}"
cp -r ../data ../setup.json ../restraints.list ../rec_nm.npy ../lig_nm.npy ../lightdock_* ../dna.pdb .
cd ..
done

sed "s/swarm_/initial_positions_/g" swarmlist.txt | sed "s/$/.dat/g" > initial_list.txt

paste swarmlist.txt initial_list.txt > swarmlist_final.txt

sed -i "s/initial_positions_0.dat/../initial_positions_0.dat/g" swarmlist_final.txt

while IFS="$(printf '\t')" read -r swarm initial;
do
cd "${swarm}"
../../../target/release/lightdock-rust setup.json "${initial}" 100 dna
done < swarmlist_final.txt

...

The rest of the script is the exact part that comes after the simulation in the tutorial on protein-DNA docking online

from lightdock.

Did the simulation run? If gso_100.out files are generated, it might be a problem a problem with generate conformations script or the clustering.

from lightdock.

It worked when I changed my script and used the execution.sh script located in one of the example folders as a blueprint instead.

from lightdock.

Then it looks like something related to your custom script. Difficult for me to the debug, see if there is any error or warning on the output.

from lightdock.

Closing for now, feel free to reopen it if you need further assistance.

from lightdock.