This page provides how to preprocess your inputs for setting up GALigandDock runs. Note that many of current preprocessing stages require running external softwares, since GALigandDock is still a new application and not many effort has been made to improve its user interface. Many of preprocessing stages listed below will be simplified or unified into our own script in the future so that users can easily setup docking runs.
Prepare a "proper" mol2 file starting from either SMILES string or a mol2 file. (see below NOTES:HOW-TO-MAKE-PROPER-MOL2 if you are not sure with yours)
Add AM1-BCC partial charge to your mol2file. You can skip this stage if you are going to run partial charge calculation through mol2genparams.py in stage3 below, although it is still unstable and for now we recommend running external softwares listed below.
$ROSETTA/source/scripts/python/public/generic_potential/mol2genparams.py -s [your.mol2]
Expected outputs are:
Usage: python mol2genparams.py [-s mol2file or -l mol2filelist] [options] Options: -h, --help show this help message and exit -s INPUTS, --inputs=INPUTS -l L --nm=RESNAME, --resname=RESNAME Residue name --auto_nm=AUTO_RESPREFIX Automatically rename resname starting with argument; default L[00-99] --am1bcc Calculate am1bcc charge (currently am1 part only; bcc will be added soon) --prefix=PREFIX Prefix of output names (prefix.params,prefix_0001.pdb), default as the prefix of input mol2 file --debug Report verbose output for debugging --no_output Do not report params or pdb --funcgrp Report functional group assignment to stdout --elec_cp_rep Report elec-countpair info to [prefix].elec_cp_ref --elec_grpdef Report elec-grp-definition info to [prefix].grpref --puckering_chi Define ring puckering torsions as rotatable CHI --amide_chi Define amide as rotatable CHI --freeze_ringring Define as rotatable CHI
Skip conformer generation! You don't need it anymore. Any single conformation is enough as input and docking tool will take care of rest of conformer sampling even beyond what could be generated by typical conformer generation tools.
1. If your input is in pdb or mol2 format Requires installation of OpenBabel (http://openbabel.org/wiki/Main_Page). If it is pdb format, first strip ligand part in your pdb file as "ligand.pdb", then run:
obabel -i pdb ligand.pdb -o mol2 -O ligand.mol2
Attaching missing hydrogens starting from mol2 format (still careful visual inspection recommend afterwards):
obabel -i mol2 ligand.mol2 -o mol2 -O ligandH.mol2 -p [pH of your interest; usually 7.0]
2. If your input is in SMILES string There are multiple ways of converting SMILES to mol2 file, you can use Openbable as well. We recommend online demo version of Corina: https://www.mn-am.com/online_demos/corina_demo