DISI - User contributions [en]

Zack useful snippets

2026-05-06T03:40:31Z

Zack: Useful DOCK3.8 binaries

These are small tidbits of info collected over time that are too unpolished for their own page, but useful enough for someone at some point, maybe. They may not be fully reliable.

==DB2 to MOL2==

Use the following python2 script:

/nfs/home/zack/software/zack_bks_scripts/db2_to_mol2/db2_to_mol2.py

==MOL2 to DB2==

The Docker image lives on epyc:

(pydock_env) [zack@epyc building_single_mol2]$ docker images | grep building
building_single_mol2 latest cdadaf7a2ffc 6 minutes ago 3.94GB

The script to use is at:

~/software/zack_bks_scripts/build_single_pose.sh

<pre>
#!/bin/bash
# Usage: build_single_pose.sh <input.mol2> <output_dir> [pose_name]
#
# Builds a single-conformer DB2 from a mol2 pose.
# Output: <output_dir>/bundle.db2.tgz (contains <pose_name>.<charge>.db2)

set -euo pipefail

if [ "$#" -lt 2 ] || [ "$#" -gt 3 ]; then
echo "Usage: $0 <input.mol2> <output_dir> [pose_name]" >&2
exit 1
fi

INPUT_MOL2=$(realpath "$1")
OUTPUT_DIR=$(realpath "$2")
POSE_NAME="${3:-}" # optional; derived from mol2 name if blank

if [ ! -f "$INPUT_MOL2" ]; then
echo "Error: input mol2 not found: $INPUT_MOL2" >&2
exit 1
fi

mkdir -p "$OUTPUT_DIR"

# Stage input into a work dir the container will see as /data
WORKDIR=$(mktemp -d /tmp/pose_work_XXXXXX)
chmod 777 "$WORKDIR"
trap "rm -rf $WORKDIR" EXIT

cp "$INPUT_MOL2" "$WORKDIR/input.mol2"

# Scratch dir for the container's /tmp
SCRATCH=$(mktemp -d /tmp/pose_scratch_XXXXXX)
chmod 777 "$SCRATCH"
trap "rm -rf $WORKDIR $SCRATCH" EXIT

docker run --rm \
-u "$(id -u):$(id -g)" \
-v "$WORKDIR:/data" \
-v "$SCRATCH:/tmp" \
-e POSE_NAME="$POSE_NAME" \
building_single_mol2 \
bash -c "source /pyenv/bin/activate && cd /tmp && python /build_single_pose.py"

# Move the result to the requested output dir
if [ ! -f "$WORKDIR/bundle.db2.tgz" ]; then
echo "Error: build failed — no bundle.db2.tgz produced" >&2
exit 1
fi

mv "$WORKDIR/bundle.db2.tgz" "$OUTPUT_DIR/bundle.db2.tgz"
echo "Done: $OUTPUT_DIR/bundle.db2.tgz"
tar -tzf "$OUTPUT_DIR/bundle.db2.tgz"
</pre>

Example usage:

<pre>
# auto-derive pose name from the input mol2
./build_single_pose.sh xtal-lig_4mer_round2.mol2 /path/to/output

# or override the pose name explicitly
./build_single_pose.sh xtal-lig_4mer_round2.mol2 /path/to/output 4mer_WT
</pre>

Make sure the final bundle is in the format:

bundle.db2.tgz/{LIG_NAME}.dock.db2

''Alternative method''

This approach runs on n-1-21 but has not been fully verified:

<pre>
# on n-1-21
conda deactivate
source /nfs/soft/dock/versions/dock37/DOCK-3.7.5.0/env.sh
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
$DOCKBASE/ligand/generate/build_ligand.sh xtal-lig_4mer_round2.mol2 \
--name="4MER" \
--smiles="NC(=[NH2+])NCCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](N)CO)C(=O)NCCC(N)=O"

# Last step will break. Exit out of n-1-21.
conda deactivate
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
source /nfs/soft/dock/versions/dock385/env.sh

# Go back to the dir and re-run:
$DOCKBASE/ligand/generate/build_ligand.sh xtal-lig_4mer_round2.mol2 \
--name="4MER" \
--smiles="NC(=[NH2+])NCCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](N)CO)C(=O)NCCC(N)=O"

# It should error out earlier, but package the results into db2
</pre>

Again, make sure the final bundle is in the format:

bundle.db2.tgz/{LIG_NAME}.dock.db2

==Scoring a Single MOL2==

Based on the [https://wiki.docking.org/index.php?title=Rescoring_with_DOCK_3.7 Rescoring with DOCK 3.7] wiki page, specifically using <code>rescoring.tar.gz</code>.

Run the following steps in order on n-1-21:

<pre>
# Set up environment
conda deactivate
source /nfs/soft/dock/versions/dock385/env.sh
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
source /nfs/soft/dock/versions/dock37/DOCK-3.7.5.0/env.sh

cp -r /nfs/home/zack/software/zack_bks_scripts/pose_build_and_rescore_dock3/ ./
python convert_anyMol2_to_dockMol2.py {YOUR_MOL2} {DOCKABLE_MOL2} {LIG_NAME}
csh 1.run.rescore_prep.csh {DOCKABLE_MOL2}

# There should now be: poses.mol2.gz, amsol.txt.gz, vdw.txt.gz
# The dock binary included is for convenience only
# INDOCK has search_type and other fields that point to the built pose
./dock64 INDOCK > OUTDOCK
</pre>

==Environment for AMSOL==

<pre>
conda deactivate
source /nfs/soft/dock/versions/dock385/env.sh
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
source /nfs/soft/dock/versions/dock37/DOCK-3.7.5.0/env.sh
</pre>

==Generating More Conformers in Ligand Building==

A new Docker image <code>building_configurable_omega</code> was created to expose OMEGA tuning parameters as environment variables. Only epyc has this image. It also prints the number of conformers saved into db2 in the log.

Example SLURM script:

<pre>
#!/bin/bash
#SBATCH --output=active_building/logs/slurm-%A_%a.out
#SBATCH --array=1-2
#SBATCH --time=01:00:00
#SBATCH --mem=2500M
#SBATCH --nodelist=epyc

TMPDIR=$(mktemp -d /scratch/job_${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID}_XXXXXX)
trap "rm -rf $TMPDIR" EXIT
export INDIR="/mnt/nfs/exk/work/zack/npsr1/UCSF_DOCK/setup_prep/round2/decoys/built_decoys/active_building/${SLURM_ARRAY_TASK_ID}"
newgrp docker << EOF
docker run --rm -u $(id -u):$(id -g) -v ${INDIR}:/data -v ${TMPDIR}:/tmp \
-e OMEGA_MAX_CONFS=2000 \
-e OMEGA_MAX_SEARCH_TIME=3600.0 \
building_configurable_omega bash /dock/ligand/submit/build-docker.sh
EOF
</pre>

''Available OMEGA tuning knobs:''

{| class="wikitable"
|-
! Variable !! Default !! Notes
|-
| <code>OMEGA_MAX_CONFS</code> || 600 || Set to 0 for rotor-dependent auto-scaling
|-
| <code>OMEGA_ENERGY_WINDOW</code> || 12 || kcal/mol; tighter = fewer confs
|-
| <code>OMEGA_RMSD</code> || 0.5 || Å; larger = fewer confs (more pruning)
|-
| <code>OMEGA_TORLIB</code> || GubaV21 || Or "Original"
|-
| <code>OMEGA_FF</code> || MMFF94Smod || Force field
|-
| <code>OMEGA_HARD_CODED_TOR_PATTERN</code> || 1 || Amide/guanidinium planarity constraints
|-
| <code>OMEGA_MAX_SEARCH_TIME</code> || 120.0 || Previously hardcoded; now configurable
|}

==Useful DOCK3.8 binaries==
On gimel / bks cluster:
<pre>
(base) -sh-4.2$ pwd
/nfs/home/zack/software/dock_binaries
(base) -sh-4.2$ ls
dock64_light_mol2 dock64_no_maxnode_limit_divya dock64_verbose_no_viable_poses dock64_verbose_no_viable_poses_and_safe_db2_load_fail
</pre>

Zack useful snippets

2026-04-29T20:44:51Z

Zack: typo

Zack useful snippets

2026-04-29T20:43:58Z

Zack: initial page

These are small tidbits of info collected over time that are too unpolished for their own page, but useful enough for someone at some point, maybe. They may not be fully reliable.

==DB2 to MOL2==

Use the following python2 script:

/nfs/home/zack/software/zack_bks_scripts/db2_to_mol2/db2_to_mol2.py

==MOL2 to DB2==

The Docker image lives on epyc:

(pydock_env) [zack@epyc building_single_mol2]$ docker images | grep building
building_single_mol2 latest cdadaf7a2ffc 6 minutes ago 3.94GB

The script to use is at:

~/software/zack_bks_scripts/build_single_pose.sh

<pre>
#!/bin/bash
# Usage: build_single_pose.sh <input.mol2> <output_dir> [pose_name]
#
# Builds a single-conformer DB2 from a mol2 pose.
# Output: <output_dir>/bundle.db2.tgz (contains <pose_name>.<charge>.db2)

set -euo pipefail

if [ "$#" -lt 2 ] || [ "$#" -gt 3 ]; then
echo "Usage: $0 <input.mol2> <output_dir> [pose_name]" >&2
exit 1
fi

INPUT_MOL2=$(realpath "$1")
OUTPUT_DIR=$(realpath "$2")
POSE_NAME="${3:-}" # optional; derived from mol2 name if blank

if [ ! -f "$INPUT_MOL2" ]; then
echo "Error: input mol2 not found: $INPUT_MOL2" >&2
exit 1
fi

mkdir -p "$OUTPUT_DIR"

# Stage input into a work dir the container will see as /data
WORKDIR=$(mktemp -d /tmp/pose_work_XXXXXX)
chmod 777 "$WORKDIR"
trap "rm -rf $WORKDIR" EXIT

cp "$INPUT_MOL2" "$WORKDIR/input.mol2"

# Scratch dir for the container's /tmp
SCRATCH=$(mktemp -d /tmp/pose_scratch_XXXXXX)
chmod 777 "$SCRATCH"
trap "rm -rf $WORKDIR $SCRATCH" EXIT

docker run --rm \
-u "$(id -u):$(id -g)" \
-v "$WORKDIR:/data" \
-v "$SCRATCH:/tmp" \
-e POSE_NAME="$POSE_NAME" \
building_single_mol2 \
bash -c "source /pyenv/bin/activate && cd /tmp && python /build_single_pose.py"

# Move the result to the requested output dir
if [ ! -f "$WORKDIR/bundle.db2.tgz" ]; then
echo "Error: build failed — no bundle.db2.tgz produced" >&2
exit 1
fi

mv "$WORKDIR/bundle.db2.tgz" "$OUTPUT_DIR/bundle.db2.tgz"
echo "Done: $OUTPUT_DIR/bundle.db2.tgz"
tar -tzf "$OUTPUT_DIR/bundle.db2.tgz"
</pre>

Example usage:

<pre>
# auto-derive pose name from the input mol2
./build_single_pose.sh xtal-lig_4mer_round2.mol2 /path/to/output

# or override the pose name explicitly
./build_single_pose.sh xtal-lig_4mer_round2.mol2 /path/to/output 4mer_WT
</pre>

Make sure the final bundle is in the format:

bundle.db2.tgz/{LIG_NAME}.dock.db2

''Alternative method''

This approach runs on n-1-21 but has not been fully verified:

<pre>
# on n-1-21
conda deactivate
source /nfs/soft/dock/versions/dock37/DOCK-3.7.5.0/env.sh
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
$DOCKBASE/ligand/generate/build_ligand.sh xtal-lig_4mer_round2.mol2 \
--name="4MER" \
--smiles="NC(=[NH2+])NCCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](N)CO)C(=O)NCCC(N)=O"

# Last step will break. Exit out of n-1-21.
conda deactivate
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
source /nfs/soft/dock/versions/dock385/env.sh

# Go back to the dir and re-run:
$DOCKBASE/ligand/generate/build_ligand.sh xtal-lig_4mer_round2.mol2 \
--name="4MER" \
--smiles="NC(=[NH2+])NCCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](N)CO)C(=O)NCCC(N)=O"

# It should error out earlier, but package the results into db2
</pre>

Again, make sure the final bundle is in the format:

bundle.db2.tgz/{LIG_NAME}.dock.db2

==Scoring a Single MOL2==

Based on the [https://wiki.docking.org/index.php?title=Rescoring_with_DOCK_3.7 Rescoring with DOCK 3.7] wiki page, specifically using <code>rescoring.tar.gz</code>.

Run the following steps in order on n-1-21:

<pre>
# Set up environment
conda deactivate
source /nfs/soft/dock/versions/dock385/env.sh
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
source /nfs/soft/dock/versions/dock37/DOCK-3.7.5.0/env.sh

cp -r /nfs/home/zack/software/zack_bks_scripts/pose_build_and_rescore_dock3/ ./
python convert_anyMol2_to_dockMol2.py {YOUR_MOL2} {DOCKABLE_MOL2} {LIG_NAME}
csh 1.run.rescore_prep.csh {DOCKABLE_MOL2}

# There should now be: poses.mol2.gz, amsol.txt.gz, vdw.txt.gz
# The dock binary included is for convenience only
# INDOCK has search_type and other fields that point to the built pose
./dock64 INDOCK > OUTDOCK
</pre>

==Environment for AMSOL==

<pre>
conda deactivate
source /nfs/soft/dock/versions/dock385/env.sh
export DOCKBASE="/nfs/soft/dock/versions/dock38/DOCK/ucsfdock"
source /nfs/soft/dock/versions/dock37/DOCK-3.7.5.0/env.sh
</pre>

==Generating More Conformers in Ligand Building==

A new Docker image <code>building_configurable_omega</code> was created to expose OMEGA tuning parameters as environment variables. Only epyc has this image. It also prints the number of conformers saved into db2 in the log.

Example SLURM script:

<pre>
#!/bin/bash
#SBATCH --output=active_building/logs/slurm-%A_%a.out
#SBATCH --array=1-2
#SBATCH --time=01:00:00
#SBATCH --mem=2500M
#SBATCH --nodelist=epyc

TMPDIR=$(mktemp -d /scratch/job_${SLURM_JOB_ID}_${SLURM_ARRAY_TASK_ID}_XXXXXX)
trap "rm -rf $TMPDIR" EXIT
export INDIR="/mnt/nfs/exk/work/zack/npsr1/UCSF_DOCK/setup_prep/round2/decoys/built_decoys/active_building/${SLURM_ARRAY_TASK_ID}"
newgrp docker << EOF
docker run --rm -u $(id -u):$(id -g) -v ${INDIR}:/data -v ${TMPDIR}:/tmp \
-e OMEGA_MAX_CONFS=2000 \
-e OMEGA_MAX_SEARCH_TIME=3600.0 \
building_configurable_omega bash /dock/ligand/submit/build-docker.sh
EOF
</pre>

''Available OMEGA tuning knobs:''

{| class="wikitable"
|-
! Variable !! Default !! Notes
|-
| <code>OMEGA_MAX_CONFS</code> || 200 || Set to 0 for rotor-dependent auto-scaling
|-
| <code>OMEGA_ENERGY_WINDOW</code> || 12 || kcal/mol; tighter = fewer confs
|-
| <code>OMEGA_RMSD</code> || 0.5 || Å; larger = fewer confs (more pruning)
|-
| <code>OMEGA_TORLIB</code> || GubaV21 || Or "Original"
|-
| <code>OMEGA_FF</code> || MMFF94Smod || Force field
|-
| <code>OMEGA_HARD_CODED_TOR_PATTERN</code> || 1 || Amide/guanidinium planarity constraints
|-
| <code>OMEGA_MAX_SEARCH_TIME</code> || 120.0 || Previously hardcoded; now configurable
|}