The main problem is that pdb files normally do not specify bond order and charges, and frequently do not specify hydrogens, while mol2-files do. So you might have to open your pdb file in a program that allows you to add the missing information before saving it in the mol2 format.

See instructions here: http://www.swissparam.ch/SwissParam_mol2_file.html

VEGA (http://www.ddl.unimi.it) supposedly is able to convert pdb files in mol2 format assigning the correct atom types (and, if you want, also the atomic charges).

Hey ondrej: try these for molecular docking

https://bioinfo3d.cs.tau.ac.il/PatchDock/

http://www.swissdock.ch/

and for file conversion

try this

https://cactus.nci.nih.gov/translate/

I would like to try SwissDock, but it does not accept my MOL file. I'll try that "Cactus". THANKS !!

o.

Argus Lab, Molegro virtual Docker & Schrodinger (Glide) all 3 software can be used for offline docking. Conversion of Mol to sdf, pdb file can be done using these software.

You should try DockThor: http://dockthor.lncc.br

Try SWISS DOCK!!! It is freely available online tool that is very easy to run for even a layman. http://www.swissdock.ch/

Dear Ondrej Adamovsky,

Please find the list of Docking Softwares

Autodock. Free open source EA based docking software. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla.

DOCK. Anchor-and-Grow based docking program. Free for academic usage. Flexible ligand. Flexible protein. Maintained by the Soichet group at the UCSF.

GOLD. GA based docking program. Flexible ligand. Partial flexibility for protein. Product from a collaboration between the university of Sheffield, GlaxoSmithKline plc and CCDC.

SCIGRESS. Desktop/server molecular modeling software suite employing linear scaling semiempirical quantum methods for protein optimization and ligand docking. Developed and distributed by Fujitsu, Ltd.

GlamDock. Docking program based on a Monte-Carlo with minimization (basin hopping) search in a hybrid interaction matching / internal coordinate search space. Part of the Chil2 suite. Open for general research.

FlexAID. A small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function. The pairwise energy parameters were derived from a large dataset of true positive poses and negative decoys from the PDBbind database through an iterative process using Monte Carlo simulations. Precompiled Linux, MacOS and Windows versions are made available by the University of Sherbrooke, Canada.

GEMDOCK. Generic Evolutionary Method for molecular DOCKing. Program for computing a ligand conformation and orientation relative to the active site of target protein==== Docking - Software ====

iGEMDOCK. Graphic environment for the docking, virtual screening, and post-screening analysis. Free for non commercial researches. For Windows and Linux.

HomDock. Progam for similarity-based docking, based on a combination of the ligand based GMA molecular alignment tool and the docking tool GlamDock. Part of the Chil2 suite. Open for general research.

ICM. Docking program based on pseudo-Brownian sampling and local minimization. Ligand and protein flexible. Provided by MolSoft.

FlexX, Flex-Ensemble (FlexE). Incremental build based docking program. Flexible ligand. Protein flexibility through ensemble of protein structure. Provided by BioSolveIT.

Fleksy. Program for flexible and induced fit docking using receptor ensemble (constructed using backbone-dependent rotamer library) to describe protein flexibility. Provided by the Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen.

FITTED. (Flexibility Induced Through Targeted Evolutionary Description). Suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds (covalent docking) with the protein side-chains. Part of the Molecular FORECASTER package and FITTED Suite. Free for an academic site license (excluding cluster).

VLifeDock. Multiple approaches for protein - ligand docking. Provides three docking approches: Grid based docking, GA docking and VLife's own GRIP docking program. Several scoring functions can be used: PLP score, XCscore and Steric + Electrostatic score. Available for Linux and Windows. Provided by VLife.

ParaDockS. (Parallel Docking Suite). Free, open source program, for docking small, drug-like molecules to a rigid receptor employing either the knowledge-based potential PMF04 or the empirical energy function p-Score.

DAIM-SEED-FFLD. Free open source fragment-based docking suite. The docking is realized in three steps. DAIM (Decomposition And Identification of Molecules) decomposes the molecules into molecular fragments that are docked using SEED (Program for docking libraries of fragments with solvation energy evaluation). Finally, the molecules are reconstructed ''in situ'' from the docked fragments using the FFLD program (Program for fragment-based flexible ligand docking). Developed and maintained by the Computational Structural Biology of ETH, Zurich, Switzerland.

Autodock Vina. MC based docking software. Free for academic usage. Flexible ligand. Flexible protein side chains. Maintained by the Molecular Graphics Laboratory, The Scripps Research Institute, la Jolla.

VinaMPI. Massively parallel Message Passing Interface (MPI) program based on the multithreaded virtual docking program AutodockVina. Free and open source. Provided by the University of Tennessee.

FlipDock. GA based docking program using FlexTree data structures to represent a protein-ligand complex. Free for academic usage. Flexible ligand. Flexible protein. Developed by the Department of Molecular Biology at the Scripps Research Institute, la Jolla.

PharmDock. A protein pharmacophore-based docking program. PharmDock and a PyMOL plugin are made freely available by the Purdue University, West Lafayette, USA.

FRED. FRED performs a systematic, exhaustive, nonstochastic examination of all possible poses within the protein active site, filters for shape complementarity and pharmacophoric features before selecting and optimizing poses using the Chemgauss4 scoring function. Provided by OpenEye scientific software.

POSIT. POSIT uses the information from bound ligands to improve pose prediction. Using a combination of approaches, including structure generation, shape alignment and flexible fitting, a ligand of interest is compared to bound ligands and its similarity to such both guides the nature of the applied algorithm and produces an estimate. Both 2D and 3D similarity measures are used in this reliability index. Provided by OpenEye scientific software.

HYBRID. Docking program similar to FRED, except that it uses the Chemical Gaussian Overlay (CGO) ligand-based scoring function. Provided by OpenEye scientific software.

idock. Free and open source multithreaded virtual screening tool for flexible ligand docking for computational drug discovery. Developed by the Chinese university of Hong Kong.

POSIT. Ligand guided pose prediction. POSIT uses bound ligand information to improve pose prediction. Using a combination of several approaches, including structure generation, shape alignment and flexible fitting, it produces a predicted pose whose accuracy depends on similarity measures to known ligand poses. As such, it produces a reliability estimate for each predicted pose. In addition, if provided with a selection of receptors from a crystallographic series, POSIT will automatically determine which receptor is best suited for pose prediction. Provided by OpenEye scientific software.

Rosetta Ligand. Monte Carlo minimization procedure in which the rigid body position and orientation of the small molecule and the protein side-chain conformations are optimized simultaneously. Free for academic and non-profit users.

Surflex-Dock. Docking program based on an idealized active site ligand (a protomol), used as a target to generate putative poses of molecules or molecular fragments, which are scored using the Hammerhead scoring function. Distributed by Tripos.

CDocker. CHARMm based docking program. Random ligand conformations are generated by molecular dynamics and the positions of the ligands are optimized in the binding site using rigid body rotations followed by simulated annealing. Provided by Accelrys.

LigandFit. CHARMm based docking program. Ligand conformations generated using Monte-Carlo techniques are initially docked into an active site based on shape, followed by further CHARMm minimization. Provided by Accelrys.

rDock. Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. Free and open source.Developed by the University of Barcelona.

MOE. Suite of medicinal chemistry tools like Ligand-Receptor Docking, Protein/Ligand Interaction Diagrams, Contact Statistics, Electrostatic, & Interaction Maps, LigX (Ligand Optimization in Pocket), Ligand & Structure-Based Scaffold Replacement, Multiple Molecule Flexible Alignment, Conformation Generation, Analysis, & Clustering, Active Site Detection & Visualization, Multi-Fragment Search, Ligand & Structure-Based Query Editor, High-Throughput Conformation Generation, Pharmacophore Search. Distributed by Chemical Computing Group.

Lead Finder. program for molecular docking, virtual screening and quantitative evaluation of ligand binding and biological activity.Distributed by Moltech. For Windows and linux.

YASARA Structure. Adds support for small molecule docking to YASARA View/Model/Dynamics using Autodock and Fleksy. Provided by YASARA.

ParaDockS. ParaDockS includes algorithms for protein-ligand docking and is organized that every newly developed scoring function can be immediately implemented. Furthermore, interaction-based classifier, trained on a target-specific knowledge base can be used in a post-docking filter step. An implementation and validation of target-biased scoring methods within the open-source docking framework is implemented. developed and provided free of charge by the University of Halle-Wittenberg, Germany.

GalaxyDock. Protein-ligand docking program that allows flexibility of pre-selected side-chains of ligand. Developed by the Computational Biology Lab, Department of Chemistry, Seoul National University.

MS-Dock. Free multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening.

FINDSITE-LHM. Homology modeling approach to flexible ligand docking. It uses a collection of common molecule substructures derived from evolutionarily related templates as the reference compounds in similarity-based ligand binding pose prediction. It also provides a simple scoring function to rank the docked compounds. Freely available to all academic users and not-for-profit institutions. Provided by the Skolnick Research Group.

BetaDock. Molecular docking simulation software based on the theory of Beta-complex.

ADAM. Automated docking tool. Can be used for vHTS. Distributed by IMMD.

hint!. (Hydropathic INTeractions). Estimates LogP for modeled molecules or data files, numerically and graphically evaluates binding of drugs or inhibitors into protein structures and scores DOCK orientations, constructs hydropathic (LOCK and KEY) complementarity maps that can be used to predict a substrate from a known receptor or protein structure or to propose the hydropathic structure from known agonists or antagonists, and evaluates/predicts effects of site-directed mutagenesis on protein structure and stability.

DockVision. Docking package including Monte Carlo, Genetic Algorithm, and database screening docking algorithms.

PLANTS. (Protein-Ligand ANT System). Docking algorithm based on a class of stochastic optimization algorithms called ant colony optimization (ACO). In the case of protein-ligand docking, an artificial ant colony is employed to find a minimum energy conformation of the ligand in the binding site. These ants are used to mimic the behavior of real ants and mark low energy ligand conformations with pheromone trails. The artificial pheromone trail information is modified in subsequent iterations to generate low energy conformations with a higher probability. Developed by the Konstanz university.

ADDock. Anchor dependent molecular docking method. Distributed by Biodelight.

EADock. Hybrid evolutionary docking algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling.

EUDOC. Program for identification of drug interaction sites in macromolecules and drug leads from chemical databases.

FLOG. Rigid body docking program using databases of pregenerated conformations. Developed by the Merck Research Laboratories.

Hammerhead. Automatic, fast fragment-based docking procedure for flexible ligands, with an empirically tuned scoring function and an automatic method for identifying and characterizing the binding site on a protein.

ISE-Dock. Docking program which is based on the iterative stochastic elimination (ISE) algorithm.

ASEDock. Docking program based on a shape similarity assessment between a concave portion (i.e., concavity) on a protein and the ligand. Developed by yoka Systems.

HADDOCK. HADDOCK (High Ambiguity Driven biomolecular DOCKing) is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. First developed from protein-protein docking, it can also be applied to protein-ligand docking. Developed and maintained by the Bijvoet Center for Biomolecular Research, Netherlands.

Computer-Aided Drug-Design Platform using PyMOL. PyMOL plugins providing a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE).

Autodock Vina plugin for PyMOL. Allows defining binding sites and export to Autodock and VINA input files, doing receptor and ligand preparation automatically, starting docking runs with Autodock or VINA from within the plugin, viewing grid maps generated by autogrid in PyMOL, handling multiple ligands and set up virtual screenings, and set up docking runs with flexible sidechains.

GriDock. Virtual screening front-end for AutoDock 4. GriDock was designed to perform the molecular dockings of a large number of ligands stored in a single database (SDF or Zip format) in the lowest possible time. It take the full advantage of all local and remote CPUs through the MPICH2 technology, balancing the computational load between processors/grid nodes. Provided by the Drug Design Laboratory of the University of Milano.

DockoMatic. GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

BDT. Graphic front-end application which control the conditions of AutoGrid and AutoDock runs. Maintained by the Universitat Rovira i Virgili,

Web services

SwissDock. SwissDock, a web service to predict the molecular interactions that may occur between a target protein and a small molecule.

DockingServer. DockingServer offers a web-based, easy to use interface that handles all aspects of molecular docking from ligand and protein set-up.

1-Click Docking. Free online molecular docking solution. Solutions can be visualized online in 3D using the WebGL/Javascript based molecule viewer of GLmol. Provided by Mcule.

Blaster. Public access service for structure-based ligand discovery. Uses DOCK as the docking program and various ZINC Database subsets as the database.Provided by the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco (UCSF).

Pardock. All-atom energy based Monte Carlo, rigid protein ligand docking, implemented in a fully automated, parallel processing mode which predicts the binding mode of the ligand in receptor target site. Maintained by the Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi.

FlexPepDock. High-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor and an estimated conformation for a peptide.

PatchDock. Web server for structure prediction of protein-protein and protein-small molecule complexes based on shape complementarity principles.

MEDock. Maximum-Entropy based docking web server for efficient prediction of ligand binding sites.

BSP-SLIM. Web service for blind molecular docking method on low-resolution protein structures. The method first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The ligand-protein docking conformation is then constructed by local shape and chemical feature complementarities between ligand and the negative image of binding pockets. Provided by the University of Michigan.

BioDrugScreen. Computational drug design and discovery resource and server. The portal contains the DOPIN (Docked Proteome Interaction Network) database constituted by millions of pre-docked and pre-scored complexes from thousands of targets from the human proteome and thousands of drug-like small molecules from the NCI diversity set and other sources. The portal is also a server that can be used to (i) customize scoring functions and apply them to rank molecules and targets in DOPIN; (ii) dock against pre-processed targets of the PDB; and (iii) search for off-targets. Maintained by the laboratory of Samy Meroueh at the Center for Computational Biology and Bioinformatics at the Indiana University School of Medicine.

GPCRautomodel. Web service that automates the homology modeling of mammalian olfactory receptors (ORs) based on the six three-dimensional (3D) structures of G protein-coupled receptors (GPCRs) available so far and (ii) performs the docking of odorants on these models, using the concept of colony energy to score the complexes. Provided by INRA.

iScreen. Web service for docking and screening the small molecular database on traditional Chinese medicine (TCM) on user's protein. iScreen is also implemented with the de novo evolution function for the selected TCM compounds using the LEA3D genetic algorithm

idTarget. Web server for identifying biomolecular targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach. Maintained by the National Taiwan University.

MetaDock. Online docking solution and docking results analysis service. Docking is done with GNU/GPL-licensed AutoDock v.4 and Dock6 under academic license

Score. Allows to calculate some different docking scores of ligand-receptor complex that can be submitted as a whole file containing both interaction partners or as two separated files. The calculation phase is provided by VEGA. Provided by the Drug Design Laboratory of the University of Milano.

Pose & Rank. Web server for scoring protein-ligand complexes. Provided by the laboratory of Andrej Sali.

PLATINUM. Calculates hydrophobic properties of molecules and their match or mismatch in receptor–ligand complexes. These properties may help to analyze results of molecular docking.

Best tool for docking: go with Autodock

and for conversion use OpenBabel

I suggest you try Autodock Vina in case you are dealing high-throughput molecular docking since it is faster and simple to rapidly predict the binding affinity of a ligand, based on the ligand geometry using empirical functions, I have used it and the results are promising and reliable.

for protein- protein docking use Haddock and for protein -ligand docking use Autodock or Autodock Vina 

for converting use open babel it .....

Pymol, autodock vina, discovery 4.0, sybyl x.0

You may try Hex (http://hexserver.loria.fr/) or Sanjeevini (http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp), http://www.scfbio-iitd.res.in/sanjeevini/example/Tutorial.pdf; Free online tool for Molecular Docking.

For converting *.PDB into *.MOL2 you can use Open Babel (http://openbabel.org/wiki/Main_Page)

Biovia /discovery studio can be used to convert .mol into .pdb file. It can convert no. of different files with different formats like mol, into .pdb file.

use openbabel