diff --git a/README.md b/README.md
index 96bc560a..3eeaf45b 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 # Meeko: preparation of small molecules for AutoDock
 
 [![API stability](https://img.shields.io/badge/stable%20API-no-orange)](https://shields.io/)
-[![PyPI version fury.io](https://img.shields.io/badge/version-0.6.0--alpha.2-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
+[![PyPI version fury.io](https://img.shields.io/badge/version-0.6.0--alpha.3-green.svg)](https://pypi.python.org/pypi/ansicolortags/)
 
 Meeko reads an RDKit molecule object and writes a PDBQT string (or file)
 for [AutoDock-Vina](https://github.com/ccsb-scripps/AutoDock-Vina)
@@ -35,7 +35,7 @@ For example, reading Mol2 files from ZINC
 [led to incorrect net charge of some molecules.](https://github.com/forlilab/Meeko/issues/63)
 
 
-## v0.6.0-alpha.2
+## v0.6.0-alpha.3
 
 This release aims to distribute an enhanced `mk_prepare_receptor.py`.
 Some features are still being developed, hence the `-alpha` suffix in the version.
diff --git a/meeko/__init__.py b/meeko/__init__.py
index 5178d1de..f2414d6d 100644
--- a/meeko/__init__.py
+++ b/meeko/__init__.py
@@ -4,7 +4,7 @@
 # Meeko
 #
 
-__version__ = "0.6.0-alpha.2"
+__version__ = "0.6.0-alpha.3"
 
 try:
     import openbabel
diff --git a/setup.py b/setup.py
index 0e895ad1..da0388b6 100644
--- a/setup.py
+++ b/setup.py
@@ -21,7 +21,7 @@ def find_files(directory):
 
 setup(
     name="meeko",
-    version='0.6.0-alpha.2',
+    version='0.6.0-alpha.3',
     author="Forli Lab",
     author_email="forli@scripps.edu",
     url="https://github.com/ccsb-scripps/meeko",