BinAC2/Software/AMDock

Description	Content
module load	chem/amdock
License	GPL-3.0
Links	GitHub
Graphical Interface	Yes

Description

AMDock (Assisted Molecular Docking) is a user-friendly graphical tool to assist in the docking of protein-ligand complexes using Autodock-Vina or AutoDock4. This tool integrates several external programs for processing docking input files, define the search space (box) and perform docking under user’s supervision.

You can use the AMDock graphical user interface on BinAC 2 via TigerVNC. The AMDock provides an ready to use example jobscript.

Usage

VNC viewer

First, you will need an VNC viewer on your local workstation. Please refer to the TigerVNC documentation for installing the VNC viewer.

Start AMDock

The AMDock module provides a ready to use example jobscript.

# Load AMDock module
module load chem/amdock/1.6.2

# Copy the jobscript into your current working directory
cp $AMDOCK_EXA_DIR/binac2-amdock-1.6.2-example.slurm .

Adjust needed resources (cpus, memory, time) as needed. Please don't touch anything else.

#!/bin/bash

# Adjust these values as needed
#SBATCH --cpus-per-task=10
#SBATCH --mem=20gb
#SBATCH --time=6:00:00

# Don't change these settings
#SBATCH --nodes=1
#SBATCH --partition=interactive
#SBATCH --gres=display:1
#SBATCH --signal=B:SIGUSR1@60
#SBATCH --job-name=amdock-1.6.2

module load chem/amdock/1.6.2

# AMDock is used via a graphical user interface (GUI)
# We need to start a VNC server in order to work with
# AMDock
# This wrapper script will start the VNC server and prints
# connection details to the job's stdout file
amdock_wrapper

Submit the AMDock job.

jobid=$(sbatch --parsable binac2-amdock-1.6.2-example.slurm)

Create SSH tunnel

The compute node on which AMDock is running is not directly reachable from your local workstation. Therefore, you need to create an SSH tunnel from your workstation to the compute node via the BinAC 2 login node.

The job's standard output file (slurm-${jobid}.out) contains all the information you need. Please note that details such as the IP address, port number, and access URL will differ in your case.

$ cat slurm-${jobid}.out
[...]

   Paste this ssh command in a terminal on local host (i.e., laptop)
   -----------------------------------------------------------------
   ssh -N -L 5901:172.0.0.1:5901 tu_iioba01@login.binac2.uni-tuebingen.de

   Then you can connect to the session with your local vncviewer:
   -----------------------------------------------------------------
   vncviewer localhost:5901
[...]

Linux users can simply copy&paste the ssh -N -L ... command into their terminal. Windows users, please refer to this documentation. It's about JupyterLab, but the SSH-tunnel is created in a similar way.

Connect to VNC Server

Now you can use your local VNC viewer and access the VNC session. Please use the correct port you got when starting the VNC server. At some point you will need to enter the password you create earlier.

Windows

TODO

Linux

vncviewer localhost:5901

You should be greeted with the virtual desktop running AMDock.

Attention: If you close the AMDock window the VNCserver, as well as the interactive job, will be stopped.