DISI - User contributions [en]

Blastermaster on C7

2026-06-22T21:42:40Z

Buyan:

This page is for C7-specific notes on running Blastermaster for [[DOCK 3.8]].

For general Blastermaster documentation, see [[Blastermaster]], [[Blastermaster_files]], and [[Blastermaster_(pydock3_script)]].

== What Blastermaster does ==

Blastermaster prepares a receptor binding site for docking.

It takes receptor/ligand input files and creates the dockfiles directory used later by DOCK/SUBDOCK.

The final dockfiles directory is what docking needs. The working directory contains intermediate files.

== Inputs ==

Typical required input files are:
rec.pdb
xtal-lig.pdb
Some workflows may use xtal-lig.mol2 instead.

== Outputs ==

Important output directories:
working
dockfiles

dockfiles is the important directory for later docking.

For descriptions of the generated files, see [[Blastermaster_files]].

...

[Category:Buyan]]

Blastermaster on C7

2026-06-22T21:34:05Z

Buyan: Created page with "This page is for C7-specific notes on running Blastermaster for DOCK 3.8. For general Blastermaster documentation, see Blastermaster, Blastermaster_files, and Blastermaster_(pydock3_script). == What Blastermaster does == Blastermaster prepares a receptor binding site for docking. It takes receptor/ligand input files and creates the dockfiles directory used later by DOCK/SUBDOCK. The final dockfiles directory is what docking needs. The working direc..."

SUBDOCK DOCK3.8

2026-06-22T21:23:48Z

Buyan:

Important note- although DOCK 3.8 is in the header of this article, SUBDOCK is perfectly capable of running DOCK 3.7 workloads, though some features of DOCK 3.8 will not be taken advantage of.

== Installing ==

<nowiki>
git clone https://github.com/docking-org/SUBDOCK.git</nowiki>

'''IMPORTANT: subdock.bash expects to live in the same directory as rundock.bash!!!'''

subdock.bash is located @ subdock.bash relative to the repository root.

subdock.bash can be called directly from any location- it is not sensitive to the current working directory.

== What's New? ==

Compared to older scripts, SUBDOCK is easier to use, has more features, and is much more flexible!

==== December 2022 ====

* All jobs platforms (e.g slurm, sge) are supported on the same script

* GNU Parallel is now supported as a jobs platform! Ideal for small-scale local testing. https://www.gnu.org/software/parallel/

* Subdock can now be run on both db2.gz individual files & db2.tgz packages. A batch_size can be set for both types, allowing for more flexibility.

* Arguments can be provided environmentally, e.g "export KEY=VALUE" or on the command line e.g "--key=value"

* Subdock now prints out a superscript to copy-paste on success, convenient for re-submission.

* Fully restartable on all jobs platforms! See below section for an explanation on what this means, why it matters, and instructions on usage.

* INDOCK version header is automatically corrected, as are any file paths referenced by INDOCK.

==== May 2023 ====

* You can provide http(s) URLs to dockable files as your input in lieu of file paths!

* Charity engine is now supported as a jobs platform! More instructions for using this further down. (https://www.charityengine.com/)

* Subdock will automatically detect if your jobs failed- no need to use an extra script to check if your jobs have actually finished or not

==== May 2023 ====

* A [[DOCK3R]] image is now used instead of a DOCK executable, in order to avoid pathological misbehavior witnessed on different systems.

== Supported Platforms ==

There are four platforms currently supported:

# SLURM
# SGE (Sun Grid Engine)
#* '''note for BKS lab: the SGE queue on gimel does not have python3, your jobs will not work!'''
# GNU Parallel (for local runs- ideal for testing)
# Charity Engine

One of these platforms must be specified- SLURM is the default. These platforms can be set by the
<nowiki>
--use-slurm=true
--use-sge=true
--use-parallel=true
--use-charity=true</nowiki>
Arguments, respectively

== C7 users ==

For C7-specific SUBDOCK notes, see [[SUBDOCK_on_C7]].

C7 uses SLURM for SUBDOCK jobs.

==== Using Charity Engine ====

To use charity engine, you must have access to an executable of the charity engine CLI, as well as GNU parallel.

Additionally, you must provide your charity authentication details in the form of the CHARITY_AUTHKEY or --charity-authkey variable.

WIP, more specific instructions to come.

== Supported File Types ==

DOCK can be run on individual db2.gz files or db2.tgz tar packages.

The file type can be specified via the --use-db2=true or --use-db2-tgz=true arguments. db2.tgz is the default

Each job dispatched by SUBDOCK will consume BATCH_SIZE files, where BATCH_SIZE is equal to --use-db2-batch-size or --use-db2-tgz-batch-size depending on which file type is chosen.

The number of jobs dispatched by SUBDOCK is equal to ceil(N / BATCH_SIZE), where N is the total number of input files.

== Restartability ==

'''ONLY APPLICABLE FOR DOCK 3.8+!'''

Restartability means that we can impose arbitrary time limits on how long our jobs can run *without* losing our progress. Time limits can be as large or as small as we want them to be, even as little as a few minutes per job! This flexibility lets docking jobs efficiently fill in the gaps between longer-running jobs on the same ecosystem, thus they will be preferentially treated by whichever system is in charge of scheduling.

=== How to use for your Job Platform ===

On SLURM, runtime can be defined with the "--time" argument, e.g:

<nowiki>subdock.bash --use-slurm=true --use-slurm-args="--time=00:30:00"</nowiki>

This will allow our job to run for 30 minutes before progress is saved & copied out.

On GNU parallel this is accomplished with "--timeout", e.g:

<nowiki>subdock.bash --use-parallel=true --use-parallel-args="--timeout 1800"</nowiki>

On SGE, the same can be achieved using the s_rt and h_rt parameters, e.g:

<nowiki>subdock.bash --use-sge=true --use-sge-args="-l s_rt=00:29:30 -l h_rt=00:30:00"</nowiki>

This tells SGE to warn the job 30 seconds prior to the 30 minute hard limit.
GNU and SLURM platforms will provide a hard-coded 30 seconds notice, whereas this notice period must be manually defined for SGE jobs.

=== How to continue jobs ===

Run subdock.bash again with the same parameters (particularly EXPORT_DEST, INPUT_SOURCE, USE_DB2, USE_DB2_TGZ, USE_DB2_BATCH_SIZE, and USE_DB2_TGZ_BATCH_SIZE) to restart your jobs! If you saved the superscript SUBDOCK spits out on successful submission, you can simply call that.

You'll know there is no more work to be done if SUBDOCK prints "all N jobs complete!", SUBDOCK will also tell you what proportion of jobs have not yet completed on each submission.

Output files are appended with a suffix indicating how many times the docking task has been resubmitted, e.g OUTDOCK.0 for the first attempt, OUTDOCK.1 for the second, etc.

Be careful not to overlap your submissions- there are no guardrails in place to prevent this from happening if you are not careful.

== Full Example - All Steps ==

This example assumes you have access to a DOCK executable and an installed scheduling system (SGE/SLURM/Parallel), but nothing else.

1. Source subdock code from github
<nowiki>
git clone https://github.com/docking-org/SUBDOCK.git</nowiki>

2. Fetch dockfiles from DUDE-Z- we will use DRD4 for this example.
<nowiki>
# note- SUBDOCK automatically detects your DOCK version & corrects the INDOCK header accordingly
wget -r --reject="index.html*" -nH --cut-dirs=2 -l1 --no-parent https://dudez.docking.org/DOCKING_GRIDS_AND_POSES/DRD4/dockfiles/</nowiki>

3a. Get db2 database subset sample via ZINC-22. Example provided below:
<nowiki>
wget http://files.docking.org/zinc22/zinc-22l/H17/H17P050/a/H17P050-N-laa.db2.tgz
wget http://files.docking.org/zinc22/zinc-22l/H17/H17P050/a/H17P050-N-lab.db2.tgz
wget http://files.docking.org/zinc22/zinc-22l/H17/H17P050/a/H17P050-N-lac.db2.tgz</nowiki>

You can select a db2 database subset via cartblanche22.docking.org- for wget-able files, choose the DOCK37 (*.db2.tgz) format, with URL download type. Multiple download types are supported, for example if you are on Wynton you can download Wynton file paths- removing the need to download the files yourself.

3b. If you downloaded the db2.tgz files yourself, create an sdi.in file from your database subset, which will serve as a list of files to evaluate. For example:
<nowiki>
find $PWD -type f -name '*.db2.tgz' > sdi.in</nowiki>

4. Export the parameters we just prepared as environment variables. '''You need a DOCK executable!''' This can be found via our download server if you have a license, otherwise lab members can directly pull https://github.com/docking-org/dock3.git. On BKS cluster, some curated executables have been prepared with labels @ /nfs/soft/dock/versions/dock38/executables. DOCK 3.7 executables may be found here as well!

<nowiki>
export INPUT_SOURCE=$PWD/sdi.in
export EXPORT_DEST=$PWD/output
export DOCKFILES=$PWD/dockfiles
export DOCKEXEC=/nfs/soft/dock/versions/dock38/executables/dock38_nogist</nowiki>

5. Choose a platform. You must select only one platform - mixing and matching is not supported.
<nowiki>
export USE_SLURM=true|...
export USE_SGE=true|...
export USE_PARALLEL=true|...</nowiki>

Any value other than exactly "true" will be interpreted as false.

6a. Run docking!
<nowiki>
bash ~/SUBDOCK/subdock.bash</nowiki>

6b. You can also use command line arguments instead of environment export, if desired. These can be mixed and matched.
<nowiki>
export DOCKEXEC=$PWD/DOCK/ucsfdock/docking/DOCK/dock64
bash ~/SUBDOCK/subdock.bash --input-source=$PWD/sdi.in --export-dest=$PWD/output --dockfiles=$PWD/dockfiles --use-slurm=true</nowiki>

7. After executing subdock, it will print out a convenient "superscript" to copy & paste, for any future re-submissions.

== Mixing DOCK 3.7 and DOCK 3.8 - known problems ==

'''Headline: Though SUBDOCK is compatible with DOCK 3.7, and will allow docking of ligands built for 3.8 in 3.7, it is NOT RECOMMENDED to do this without using a specially prepared 3.7 executable!'''

If you're running DOCK 3.8 against recently built ligands, you may encounter error messages that look like this:
<nowiki> 1 2 bonds with error
Error. newlist is not big enough</nowiki>

Or worse, like this:
<nowiki> Warning. tempconf = 0
1597 -> 0 -> 0</nowiki>

The latter error messages have the potential to cause some serious damage, as they are emitted very frequently & may consume excessive disk space. SUBDOCK will check for these messages periodically during DOCK's runtime & kill the process if they are found.

If you are on 3.8 and are encountering these messages still, use the dock38_nogist executable described in [[How_to_install_DOCK_3.8#Prebuilt_Executable]]. This version voids the code related to the GIST scoring function, which is responsible for these errors.

If you are using 3.7 still, it is possible to prepare a version that keeps everything the same, except without the dangerous "tempconf" message.

== SUBDOCK help splash - all argument descriptions & defaults ==
<nowiki>
[user@machine SUBDOCK]$ ./subdock.bash --help
SUBDOCK! Run docking workloads via job controller of your choice
=================required arguments=================
expected env arg: EXPORT_DEST, --export-dest
arg description: nfs output destination for OUTDOCK and test.mol2.gz files

expected env arg: INPUT_SOURCE, --input-source
arg description: nfs directory containing one or more .db2.tgz files OR a file containing a list of db2.tgz files

expected env arg: DOCKFILES, --dockfiles
arg description: nfs directory containing dock related files and INDOCK configuration for docking run

expected env arg: DOCKEXEC, --dockexec
arg description: nfs path to dock executable

=================job controller settings=================
optional env arg missing: USE_SLURM, --use-slurm
arg description: use slurm
defaulting to false

optional env arg missing: USE_SLURM_ARGS, --use-slurm-args
arg description: addtl arguments for SLURM sbatch command
defaulting to

optional env arg missing: USE_SGE, --use-sge
arg description: use sge
defaulting to false

optional env arg missing: USE_SGE_ARGS, --use-sge-args
arg description: addtl arguments for SGE qsub command
defaulting to

optional env arg missing: USE_PARALLEL, --use-parallel
arg description: use GNU parallel
defaulting to false

optional env arg missing: USE_PARALLEL_ARGS, --use-parallel-args
arg description: addtl arguments for GNU parallel command
defaulting to

=================input settings=================
optional env arg missing: USE_DB2_TGZ, --use-db2-tgz
arg description: dock db2.tgz tar files
defaulting to true

optional env arg missing: USE_DB2_TGZ_BATCH_SIZE, --use-db2-tgz-batch-size
arg description: how many db2.tgz to evaluate per batch
defaulting to 1

optional env arg missing: USE_DB2, --use-db2
arg description: dock db2.gz individual files
defaulting to false

optional env arg missing: USE_DB2_BATCH_SIZE, --use-db2-batch-size
arg description: how many db2.gz to evaluate per batch
defaulting to 100

=================addtl job configuration=================
optional env arg missing: MAX_PARALLEL, --max-parallel
arg description: max jobs allowed to run in parallel
defaulting to -1

optional env arg missing: SHRTCACHE, --shrtcache
arg description: temporary local storage for job files
defaulting to /scratch

optional env arg missing: LONGCACHE, --longcache
arg description: longer term storage for files shared between jobs
defaulting to /scratch

=================miscellaneous=================
optional env arg missing: SUBMIT_WAIT_TIME, --submit-wait-time
arg description: how many seconds to wait before submitting
defaulting to 5

optional env arg missing: USE_CACHED_SUBMIT_STATS, --use-cached-submit-stats
arg description: only check completion for jobs submitted in the latest iteration. Faster re-submission, but will ignore jobs that have been manually reset
defaulting to false
</nowiki>

[[Category:DOCK_3.8]]

How to install DOCK 3.8

2026-06-22T21:20:52Z

Buyan:

Many of the tutorials on how to use DOCK software assume you have access to an executable DOCK program- sometimes referred to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program.

== C7 users ==

On [[Cluster 7]], DOCK is already installed. Use:
module load dock

For a quick C7 test, see [[DOCK_3.8_testing_on_C7]].

For SUBDOCK on C7, see [[SUBDOCK_on_C7]].

== Obtaining a License ==

Please obtain a license via the DOCK license server [[https://license.docking.org/application]] and download the software.

== Compiling from source ==

See this page: [[How_to_compile_DOCK]]

If you are a BKS cluster member, you should follow the instructions for compiling via pgf. The DOCK 3.8 source can be found on github:

<nowiki>git clone https://github.com/docking-org/dock3.git</nowiki>

For any others without a PGF license, follow the gfortran instructions.

== Prebuilt Executable ==

DOCK is constantly being modified & fine-tuned, sometimes there may be a special version of DOCK floating around you want to use, or perhaps you have a special version of your own you'd like to share. We collect all custom DOCK executables on the BKS cluster at this location (which is world-writable):

<nowiki>/nfs/soft/dock/versions/dock38/executables</nowiki>

Here is a brief description of the various executables here at the time of writing:
<nowiki>
dock37_vanilla : standard DOCK 3.7 executable
dock38_vanilla : standard DOCK 3.8 executable
dock37_matchcap : DOCK 3.7 executable that more strictly caps the number of matches DOCK generates - slightly faster!
dock38_matchcap : Same as above, but for 3.8
dock38_nogist : DOCK 3.8 sans error messages that sometimes occur when using recently built ligand libraries</nowiki>

You are encouraged to also included the source code in this directory as a tar.gz file with the same base name as your executable.

[[Category:DOCK 3.8]]
[[Category:Developers]]

SUBDOCK ON C7

2026-06-22T21:15:59Z

Buyan: Buyan moved page SUBDOCK ON C7 to SUBDOCK on C7

#REDIRECT [[SUBDOCK on C7]]

SUBDOCK on C7

2026-06-22T21:15:59Z

Buyan: Buyan moved page SUBDOCK ON C7 to SUBDOCK on C7

SUBDOCK on C7

This page is for C7-specific notes on [[SUBDOCK_DOCK3.8|SUBDOCK]]. For the full SUBDOCK documentation, see [[SUBDOCK_DOCK3.8]].

== C7 setup ==

Load DOCK:

module load dock
echo $DOCK_INSTALL_PATH
echo $DOCKBASE

SUBDOCK is inside the DOCK install:

${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash
${DOCK_INSTALL_PATH}/SUBDOCK/rundock.bash

`subdock.bash` expects `rundock.bash` to be in the same directory.

== Scheduler ==

C7 runs this workflow through SLURM (`sbatch`). Set the controller explicitly:

export USE_SLURM=true
export USE_SGE=false
export USE_PARALLEL=false
export USE_CHARITY=false

If more than one controller is enabled, SUBDOCK exits with:

cannot select more than one job controller!

== Required variables ==

SUBDOCK needs:

export EXPORT_DEST=/path/to/output
export INPUT_SOURCE=/path/to/split_database_index
export DOCKFILES=/path/to/dockfiles
export DOCKEXEC=${DOCK_INSTALL_PATH}/dock3/dock64

Use paths in your own workspace. Do not write output into the shared DOCK install, e.g. avoid:

${DOCK_INSTALL_PATH}/test/docking/output

== Run ==

Example:

mkdir -p output
export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"
export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"
bash ${DOCK_INSTALL_PATH}/SUBDOCK/subdock.bash

Successful submission looks like:

submitting N out of N jobs
Submitted batch job <jobid>

== Check jobs ==

squeue -u $USER
squeue -j <jobid>

`sacct` may not work on C7 if SLURM accounting is disabled. Check logs after completion:

ls output/logs
less output/logs/1.out

Success usually includes:

starting DOCK vers=3.8
finished!

== Related pages ==

* [[SUBDOCK_DOCK3.8]]
* [[DOCK_3.8_testing_on_C7]]
* [[DOCK 3.8]]

[[Category:DOCK_3.8]]
[[Category:Cluster 7]]

C7 SUBDOCK DOCK 3.8

2026-06-22T21:15:04Z

Buyan: Buyan moved page C7 SUBDOCK DOCK 3.8 to SUBDOCK ON C7

#REDIRECT [[SUBDOCK ON C7]]

SUBDOCK on C7

2026-06-22T21:15:04Z

Buyan: Buyan moved page C7 SUBDOCK DOCK 3.8 to SUBDOCK ON C7

DOCK 3.8

2026-06-22T21:14:02Z

Buyan:

DOCK 3.8 has been the primary version of DOCK 3 since January 2021.

DOCK 3.8 is now organized into a number of smaller repositories, each with a specialized purpose.

* dock3 : the fortran source code
* pydock3 : the scripts and executables to run docking & parameter optimization
* ligdock3 : the ligand building scripts used by ZINC-22.
* SUBDOCK : scripts for submitting docking workloads to SLURM/SGE/Native
* docktop : scripts for extracting top results from docking campaigns
* zinc22-3d-submit : scripts for submitting ligand building workloads to SLURM/SGE
* DOCK : legacy repository, still being used & updated (for now)

DOCK 3.8 has been extensively reorganized from DOCK 3.7.

How to get DOCK 3.8. Use the DOCK license server dock.compbio.ucsf.edu. If you are a developer, fork the relevant repo.

[[How to install DOCK 3.8]]

[[SUBDOCK_DOCK3.8|How to dock in DOCK3.8]]

[[Docking Analysis in DOCK3.8]]

[[DOCK_3.8:How_to_install_pydock3|Installing pydock3]]

[[Dockopt_(pydock3_script)|Running pydock3/dockopt (new blastermaster script- automatic optimization!)]]

[[Blastermaster_(pydock3_script)|Running pydock3/blastermaster (classic blastermaster script - generate grid files)]]

How to run DOCK/LSD in AWS, follow our tutorial, starting with setting up an AWS account. [[AWS:Set up account]]

[[Building_The_3D_Pipeline_ZINC22| How to build libraries for DOCK 3.8]]
Please note that you only need to build libraries if you do not want to use ZINC-22, and if you do not want to use the free 3D molecule building service in TLDR.docking.org.

[[Programming DOCK 3.8]]
DOCK 3.8.5 is the current production version of DOCK 3, as of Sept 1, 2022.
If you wish to help develop DOCK 3.8, please write to us.

[[How_to_compile_DOCK| How to compile DOCK 3.8]]

== Availability ==
DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!). It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.

== C7 Usage ==
DOCK 3.8 is available on [[Cluster 7]] through the dock module.

For a C7 smoke test of the installed DOCK 3.8 setup, see [[DOCK_3.8_testing_on_C7]].

For C7-specific SUBDOCK notes, see [[SUBDOCK_on_C7]].

== General Use ==
Mechanically, docking has the following steps.
* prepare gridfiles (dockfiles)
* select database subset to run
* move all files to the target platform
* run docking at scale
* merge the results (top_poses.py)
* move results back to your server.
* process the results (interaction fingerprint, strain filter, clustering, manual review)
* final re-extract of top poses for hit picking party.
* archive the results.

== Step by Step instructions ==
During development, this was the script we used to explain how to dock:
[[How to dock in DOCK3.8]]

[[Category:DOCK 3.8]]

SUBDOCK on C7

2026-06-22T21:10:57Z

Buyan:

SUBDOCK on C7

2026-06-22T20:16:43Z

Buyan:

These are C7 specific notes for running [[SUBDOCK_DOCK3.8|SUBDOCK]] with [[DOCK 3.8]] on [[Cluster 7]].
For the full SUBDOCK reference, see [[SUBDOCK_DOCK3.8]].

== What SUBDOCK does ==
SUBDOCK submits many DOCK jobs to a scheduler.
On C7, the scheduler is SLURM, so SUBDOCK submits jobs with sbatch.

== Main C7 Rule ==
C7 uses SLURM. Do not use SGE on C7.

== Required variables ==
SUBDOCK needs four main paths:
EXPORT_DEST
INPUT_SOURCE
DOCKFILES
DOCKEXEC

# EXPORT_DEST is where results and logs go.
# INPUT_SOURCE is the file listing the ligand database files to dock.
# DOCKFILES is the directory containing the prepared docking files.
# DOCKEXEC is the DOCK executable.

On C7, after `module load dock`, the DOCK executable is usually:
${DOCK_INSTALL_PATH}/dock3/dock64

== C7 path warning ==
Do not write output into the shared DOCK installation.
Use a directory in your own workspace instead.

== Checking jobs ==

While jobs are running:
squeue -u $USER

For one job:
squeue -j <jobid>
After jobs finish, check the logs in the output directory.

== Related pages ==

* [[SUBDOCK_DOCK3.8]]
* [[DOCK_3.8_testing_on_C7]]
* [[DOCK 3.8]]

[[Category:Buyan]]
[[Category:DOCK_3.8]]
[[Category:Cluster 7]]

SUBDOCK on C7

2026-06-22T20:12:05Z

Buyan:

SUBDOCK on C7

2026-06-22T19:52:24Z

Buyan: Created page with "notes for c7 users: on Cluster 7, use path /nfs/software/dock/versions/dock385/DOCK3.8/"

notes for c7 users:
on [[Cluster 7]], use path /nfs/software/dock/versions/dock385/DOCK3.8/

DOCK 3.8 testing on C7

2026-06-22T19:34:57Z

Buyan:

These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]]. This is only a C7 quick test, not a full DOCK tutorial. For general DOCK 3.8 usage, see [[DOCK 3.8]] and [[SUBDOCK_DOCK3.8]].
== 1. Log in and start screen ==
Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.
Start a screen or tmux session so the job keeps running if your SSH disconnects:
Screen:
screen -S dock_test
Tmux alternative:
tmux new -s dock_test

== 2. Make a working folder ==

Use your own writable space, not the shared DOCK install directory.

Example:

cd /nfs/home/xyz/hdd02
mkdir -p docking
cd docking

== 3. Load DOCK ==

module load dock

Check the DOCK paths:

echo $DOCK_INSTALL_PATH
echo $DOCKBASE

== 4. Copy the test files ==

cp -r ${DOCK_INSTALL_PATH}/test/docking test
cd test

Remove old copied output. The shared test folder may already contain someone else's old results:

rm -rf output
rm -f split_database_index

== 5. Edit test_subdock.sh ==

The copied test_subdock.sh may still point back to the shared DOCK install. Edit it so it writes to your local test folder.

Change:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index

to:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index

Change:

export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"

to:

export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"

Keep:

export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"

== 6. Run with SLURM ==

C7 uses SLURM, not SGE.

export USE_SLURM=true
export USE_SGE=false
mkdir -p output
./test_subdock.sh

Successful submission looks like:

submitting 4 out of 4 jobs
Submitted batch job <jobid>

== 7. Check the job ==

squeue -u $USER

Check logs:

ls output/logs
less output/logs/1.out

Success looks like:

user=<your_username>
starting DOCK vers=3.8
finished!

If the log shows another user or paths under /nfs/software/dock/..., you are looking at old copied output, not your run.

[[Category:Buyan]]

DOCK 3.8 C7

2026-06-22T19:33:28Z

Buyan: Buyan moved page DOCK 3.8 C7 to DOCK 3.8 testing on C7: testing page

#REDIRECT [[DOCK 3.8 testing on C7]]

DOCK 3.8 testing on C7

2026-06-22T19:33:28Z

Buyan: Buyan moved page DOCK 3.8 C7 to DOCK 3.8 testing on C7: testing page

These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]].

== 1. Log in and start screen ==
Log in to [[Cluster 7]] first. The exact SSH command may depend on whether you are onsite, on VPN, or going through a portal/jump host. Once you are on C7, start a screen or tmux session so the job keeps running if your SSH disconnects.
Start a screen or tmux session so the job keeps running if your SSH disconnects:
Screen:
screen -S dock_test
Tmux alternative:
tmux new -s dock_test

== 2. Make a working folder ==

Use your own writable space, not the shared DOCK install directory.

Example:

cd /nfs/home/xyz/hdd02
mkdir -p docking
cd docking

== 3. Load DOCK ==

module load dock

Check the DOCK paths:

echo $DOCK_INSTALL_PATH
echo $DOCKBASE

== 4. Copy the test files ==

cp -r ${DOCK_INSTALL_PATH}/test/docking test
cd test

Remove old copied output. The shared test folder may already contain someone else's old results:

rm -rf output
rm -f split_database_index

== 5. Edit test_subdock.sh ==

The copied test_subdock.sh may still point back to the shared DOCK install. Edit it so it writes to your local test folder.

Change:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index

to:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index

Change:

export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"

to:

export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"

Keep:

export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"

== 6. Run with SLURM ==

C7 uses SLURM, not SGE.

export USE_SLURM=true
export USE_SGE=false
mkdir -p output
./test_subdock.sh

Successful submission looks like:

submitting 4 out of 4 jobs
Submitted batch job <jobid>

== 7. Check the job ==

squeue -u $USER

Check logs:

ls output/logs
less output/logs/1.out

Success looks like:

user=<your_username>
starting DOCK vers=3.8
finished!

If the log shows another user or paths under /nfs/software/dock/..., you are looking at old copied output, not your run.

[[Category:Buyan]]

DOCK 3.8

2026-06-22T18:51:39Z

Buyan:

DOCK 3.8 has been the primary version of DOCK 3 since January 2021.

DOCK 3.8 is now organized into a number of smaller repositories, each with a specialized purpose.

* dock3 : the fortran source code
* pydock3 : the scripts and executables to run docking & parameter optimization
* ligdock3 : the ligand building scripts used by ZINC-22.
* SUBDOCK : scripts for submitting docking workloads to SLURM/SGE/Native
* docktop : scripts for extracting top results from docking campaigns
* zinc22-3d-submit : scripts for submitting ligand building workloads to SLURM/SGE
* DOCK : legacy repository, still being used & updated (for now)

DOCK 3.8 has been extensively reorganized from DOCK 3.7.

How to get DOCK 3.8. Use the DOCK license server dock.compbio.ucsf.edu. If you are a developer, fork the relevant repo.

[[How to install DOCK 3.8]]

[[SUBDOCK_DOCK3.8|How to dock in DOCK3.8]]

[[Docking Analysis in DOCK3.8]]

[[DOCK_3.8:How_to_install_pydock3|Installing pydock3]]

[[Dockopt_(pydock3_script)|Running pydock3/dockopt (new blastermaster script- automatic optimization!)]]

[[Blastermaster_(pydock3_script)|Running pydock3/blastermaster (classic blastermaster script - generate grid files)]]

How to run DOCK/LSD in AWS, follow our tutorial, starting with setting up an AWS account. [[AWS:Set up account]]

[[Building_The_3D_Pipeline_ZINC22| How to build libraries for DOCK 3.8]]
Please note that you only need to build libraries if you do not want to use ZINC-22, and if you do not want to use the free 3D molecule building service in TLDR.docking.org.

[[Programming DOCK 3.8]]
DOCK 3.8.5 is the current production version of DOCK 3, as of Sept 1, 2022.
If you wish to help develop DOCK 3.8, please write to us.

[[How_to_compile_DOCK| How to compile DOCK 3.8]]

== Availability ==
DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!). It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.

== General Use ==
Mechanically, docking has the following steps.
* prepare gridfiles (dockfiles)
* select database subset to run
* move all files to the target platform
* run docking at scale
* merge the results (top_poses.py)
* move results back to your server.
* process the results (interaction fingerprint, strain filter, clustering, manual review)
* final re-extract of top poses for hit picking party.
* archive the results.

== Step by Step instructions ==
During development, this was the script we used to explain how to dock:
[[How to dock in DOCK3.8]]

[[Category:DOCK 3.8]]

DOCK 3.8 testing on C7

2026-06-22T18:48:40Z

Buyan:

DOCK 3.8 testing on C7

2026-06-22T18:48:09Z

Buyan:

DOCK 3.8 testing on C7

2026-06-22T18:44:43Z

Buyan:

These are instructions to run the [[DOCK 3.8]] test on [[Cluster 7]].

== 1. Log in and start screen ==

Start a screen session so the job keeps running if your SSH disconnects:

screen -S dock_test

Detach: Ctrl-a, then d

Reattach:

screen -r dock_test

== 2. Make a working folder ==

Use your own writable space, not the shared DOCK install directory.

Example:

cd /nfs/home/xyz/hdd02
mkdir -p docking
cd docking

== 3. Load DOCK ==

module load dock

Check the DOCK paths:

echo $DOCK_INSTALL_PATH
echo $DOCKBASE

== 4. Copy the test files ==

cp -r ${DOCK_INSTALL_PATH}/test/docking test
cd test

Remove old copied output. The shared test folder may already contain someone else's old results:

rm -rf output
rm -f split_database_index

== 5. Edit test_subdock.sh ==

The copied test_subdock.sh may still point back to the shared DOCK install. Edit it so it writes to your local test folder.

Change:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index

to:

find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index

Change:

export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"

to:

export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"

Keep:

export DOCKEXEC="${DOCK_INSTALL_PATH}/dock3/dock64"

[[Category:Buyan]]

DOCK 3.8 testing on C7

2026-06-22T18:00:17Z

Buyan:

These are instructions to follow on [[Cluster 7]] to run [[DOCK 3.8]].

* step 1. log in to C7
* cd hdd02 # find a place to work
* mkdir docking # create an area for docking
* cd docking
* pwd
/nfs/home/xyz/hdd02/docking
* screen -S john # could also be tmux
# set up a docking environment on C7
module load dock
echo $DOCK_INSTALL_PATH
echo $DOCKBASE

# copy test data to my account
cp -r ${DOCK_INSTALL_PATH}/test/docking test
cd test
# edit file to point to my own copy
./test_subdock.sh

After copying the test directory into your own workspace, edit test_subdock.sh so it uses the local copied directory.
Change this line:
find test_ligs -name '*.db2.tgz' -exec realpath {} \; > ${DOCK_INSTALL_PATH}/test/docking/split_database_index
to:
find test_ligs -name '*.db2.tgz' -exec realpath {} \; > split_database_index
Change these:
export EXPORT_DEST="${DOCK_INSTALL_PATH}/test/docking/output"
export INPUT_SOURCE="${DOCK_INSTALL_PATH}/test/docking/split_database_index"
export DOCKFILES="${DOCK_INSTALL_PATH}/test/docking/dockfiles"
to:
export EXPORT_DEST="$(pwd)/output"
export INPUT_SOURCE="$(pwd)/split_database_index"
export DOCKFILES="$(pwd)/dockfiles"

[[Category:Buyan]]

DOCK 3.8

2026-06-10T19:27:49Z

Buyan:

DOCK 3.8 has been the primary version of DOCK 3 since January 2021.

DOCK 3.8 is organized into a number of smaller repositories, each with a specialized purpose.

* dock3 : the Fortran source code
* pydock3 : Python scripts and executables to run docking, blastermaster, and parameter optimization
* ligdock3 : ligand building scripts used by ZINC-22
* SUBDOCK : scripts for submitting docking workloads to SLURM, SGE, GNU Parallel, or other job platforms
* docktop : scripts for extracting top results from docking campaigns
* zinc22-3d-submit : scripts for submitting ligand building workloads to SLURM or SGE
* DOCK : legacy repository, still being used and updated for now

DOCK 3.8 has been extensively reorganized from DOCK 3.7.

== Start here ==

Most users do not need to compile DOCK from source. A standard DOCK 3.8 installation is usually a pre-built release downloaded from the DOCK license server. Installing DOCK usually means:

# obtain access through the DOCK license server
# download the DOCK 3.8 release
# unpack the release
# set the required environment variables
# install pydock3 with a compatible Python version
# run the included tests

Use the DOCK license server to obtain the software:

dock.compbio.ucsf.edu

If you are a developer modifying DOCK source code, fork the relevant repository and see the developer/compile instructions below.

== Main documentation ==

* [[How to install DOCK 3.8]] — start here for installation
* [[SUBDOCK_DOCK3.8|How to dock in DOCK3.8]] — submit docking jobs with SUBDOCK
* [[Docking Analysis in DOCK3.8]] — analyze docking results
* [[DOCK_3.8:How_to_install_pydock3|Installing pydock3]] — install the Python tools
* [[Dockopt_(pydock3_script)|Running pydock3/dockopt]] — automatic parameter optimization
* [[Blastermaster_(pydock3_script)|Running pydock3/blastermaster]] — generate grid files for docking
* [[Building_The_3D_Pipeline_ZINC22|How to build libraries for DOCK 3.8]] — ligand/library building
* [[Programming DOCK 3.8]] — developer information
* [[How_to_compile_DOCK|How to compile DOCK 3.8]] — developer-only source compilation

To run DOCK/LSD in AWS, follow the AWS tutorial starting with [[AWS:Set up account]].

== Which path should I follow? ==

=== Most users ===

Use the pre-built DOCK 3.8 release from the license server. You should not need to compile DOCK.

Expected basic workflow:

tar -xzf dock-[version].tgz
export DOCK_INSTALL_PATH=/absolute/path/to/DOCK3.8

Many older scripts and tutorials also expect:

export DOCKBASE=/absolute/path/to/DOCK3.8/legacy3

Then install pydock3 using Python >=3.8.1 and <3.11. Python 3.10 is recommended.

=== BKS / cluster users ===

If DOCK is already installed as a module on your cluster, load the module and check the environment variables instead of downloading or compiling DOCK yourself.

module load dock
echo $DOCK_INSTALL_PATH
echo $DOCKBASE

If these variables are not set, ask your cluster administrator or see [[How to install DOCK 3.8]].

=== Developers ===

Only compile DOCK from source if you are developing DOCK or making a new release. Normal users should not need the NVIDIA HPC SDK, Docker build environment, PGI/NVHPC compiler setup, or source compilation workflow.

See [[How_to_compile_DOCK|How to compile DOCK 3.8]].

== Requirements ==

The DOCK 3.8 release expects:

* GLIBC >= 2.17
* Python >= 3.8.1 and < 3.11 for pydock3
* One supported job platform for running jobs at scale:
** SLURM
** SGE
** GNU Parallel

Python 3.10 is a safe choice for pydock3. Newer Python versions, such as Python 3.13, may not work with pydock3.

== Availability ==

DOCK 3.8 is installed on the BKS cluster and on Wynton. It is also available on AWS and OCI as a Docker/container image.

The software should be runnable on modern HPC platforms. We recommend using an operating system where a compatible Python version is available by default, or creating a separate Python environment with Python 3.10.

== General Use ==

Mechanically, docking has the following steps:

# prepare grid files / dockfiles for the target
# select the database subset to run
# move all required files to the target platform
# run docking at scale, often using SUBDOCK
# merge the results, for example with top_poses.py
# move results back to your server
# process the results, such as interaction fingerprints, strain filters, clustering, and manual review
# re-extract final top poses for hit picking
# archive the results

== Testing your installation ==

After installation, run the included tests before starting a real docking campaign.

=== Test DOCK / SUBDOCK ===

Choose one job platform:

export USE_SLURM=true

or

export USE_SGE=true

or

export USE_PARALLEL=true

Then run:

cd ${DOCK_INSTALL_PATH}/test/docking
./test_subdock.sh

If the test works, you should see an output directory containing numbered result folders, one for each test ligand package. Each result folder should contain an OUTDOCK file and a test.mol2.gz.0 pose file.

If the test fails, check the logs directory for stdout/stderr from the submitted jobs.

=== Test pydock3 / blastermaster ===

Activate the pydock3 Python environment first. Then run:

cd ${DOCK_INSTALL_PATH}/test/pydock
pydock3 blastermaster - new
cd blastermaster_job
pydock3 blastermaster - run

If this works, the job should produce dockfiles and visualization directories.

== Step by step docking instructions ==

For a full docking workflow, see:

[[SUBDOCK_DOCK3.8|How to dock in DOCK3.8]]

== Notes on building libraries ==

You only need to build libraries if you do not want to use ZINC-22 and do not want to use the free 3D molecule building service in TLDR.docking.org.

For library building, see:

[[Building_The_3D_Pipeline_ZINC22|How to build libraries for DOCK 3.8]]

== Developer notes ==

DOCK 3.8.5 is the current production version of DOCK 3, as of Sept 1, 2022. If you wish to help develop DOCK 3.8, please write to us.

[[Category:DOCK 3.8]]