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Working 1czy full example with ANM and restraints
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example/1czy/1czy_peptide.pdb

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@@ -51,5 +51,3 @@ ATOM 4275 CB ASP D 210 -22.519 10.036 21.181 1.00 31.88 C
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ATOM 4276 CG ASP D 210 -22.603 9.980 22.689 1.00 32.06 C
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ATOM 4277 OD1 ASP D 210 -21.544 9.791 23.316 1.00 34.58 O
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ATOM 4278 OD2 ASP D 210 -23.711 10.130 23.249 1.00 32.64 O
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ATOM 4279 OXT ASP D 210 -24.157 7.904 20.034 1.00 31.53 O
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TER 4288 HOH D6324

example/1czy/1czy_protein.pdb

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@@ -1279,5 +1279,3 @@ ATOM 1278 CB LEU A 501 -3.277 -2.730 31.996 1.00 29.73 C
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ATOM 1279 CG LEU A 501 -4.698 -2.203 32.216 1.00 29.63 C
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ATOM 1280 CD1 LEU A 501 -5.034 -1.222 31.100 1.00 28.91 C
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ATOM 1281 CD2 LEU A 501 -5.700 -3.351 32.236 1.00 28.46 C
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ATOM 1282 OXT LEU A 501 -0.401 -3.512 33.022 1.00 32.93 O
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TER 1420 HOH A6390

example/1czy/execution.sh

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#!/bin/bash
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# Edit only the number of cores to use for this simulation
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NUM_CORES=4
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# LightDock setup
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lightdock3_setup.py 1czy_protein.pdb 1czy_peptide.pdb 400 200 --noxt --noh -anm -rst restraints.list
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# Convert ANM data
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lgd_flatten.py lightdock_rec.nm.npy rec_nm.npy
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lgd_flatten.py lightdock_lig.nm.npy lig_nm.npy
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# Calculate number of swarms
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s=`ls -d swarm_* | wc -l`
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swarms=$((s-1))
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# Create a task.list file for ant_thony
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for i in `seq 0 $swarms`;do echo "cd swarm_${i}; cp ../lightdock_1czy_protein.pdb .; cp ../lightdock_1czy_peptide.pdb .;cp ../rec_nm.npy .;cp ../lig_nm.npy .;../lightdock-rust ../setup.json ../init/initial_positions_${i}.dat 10; rm -rf lightdock_*.pdb *.npy;" >> task.list; done
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# Let ant_thony run
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ant_thony.py --cores ${NUM_CORES} task.list
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example/1czy/lig_nm.npy

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example/1czy/rec_nm.npy

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example/1czy/swarm_0/gso_1.out

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example/1czy/swarm_0/gso_10.out

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example/1czy/swarm_1/gso_1.out

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example/1czy/swarm_1/gso_10.out

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example/1czy/swarm_2/gso_1.out

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