SMOG 2

A Downloadable, Portable and Versatile Software Package

Manuscripts   Manual   Download   SMOG-CHECK   Force Field Repo   OpenSMOG


SMOG 2 is a standalone software package for generating SMOG models. Except for the contact map code, this is a complete rewrite of the original SMOG software. The original models are still provided, though a few default parameters have changed. While the SMOG web-based interface will continue to be available, the standalone code is particularly useful if you want to modify the force field (e.g. include new residues, design a new variant, etc).

We would like to express our gratitude to all of the beta testers. Based on your feedback, we have extensively tested the code and have tried to make it easy to use. Since we will continue to develop the software, your continued feedback is always appreciated.

Manuscripts

SMOG 2 was first described in Noel et al, PLOS Computational Biology, 2016. Since the default model in SMOG 2 differs from SMOG 1, it is highly encouraged that all SMOG 2 users read the manuscripts, first.

OpenSMOG was first described in Oliveira et al, Protein Science, 2022.

User's Manual

Version
2.4.5
2.4.4
2.4.2
2.4
2.3
2.0
Beta

Accessing the SMOG 2 software

To make SMOG 2 more widely available, we provide various avenues for accessing the code. By far, the simplest method is to use a container. Each container has SMOG 2, SMOG-CHECK and all SMOG-TOOLS configured. However, you can also download official releases of the code, or you can directly access the git repository.

Container-based Options

via Docker If you have Docker running, then you can retrieve SMOG 2 Docker images through Docker hub.

via Singularity If you have Singularity installed, then you can retrieve SMOG 2 images through Sylabs.

Download Options

While the containers are the simplest way to use SMOG 2, you can also download the code and install all necessary dependencies. Below we provide prepared official released versions, as well as access to the current git repository. For detailed instructions for installing/configuring, see the README file and/or SMOG 2 manual.
Version Release Date md5 (.tgz file)
2.4.5 11/4/22 1042c81186fc8d502f4eb09babcbb222
2.4.4 4/14/22 bccb2dce358518a62bf47f3bdbe14bdf
2.4.2 10/08/21 1fe34e0351b4bf38c67d20964e06e3e9
2.4.1 8/20/21 75c59d62ef19797e3ec10ef7c8781501
2.4 8/16/21 9b7338760eb91e76132723cc80933b91
2.3 2/18/21 83103bfea36dd41e5328c6c4702b0fb8
2.2 11/24/18 4a49290f2a0f681a6f7d5589350fc63e
2.1 01/24/18 bbf238c2340f6b15daf7a0b2e4e4e56c
2.0.3 03/12/16 508d36449c9527722fcb0f64fab84a99
2.0.2 10/12/15 ffab3d632c87d12b2a8bfa24b141a988
2.0.1 8/31/15 9a66f704b7e2386a2e6400e37f6c5f27
2.0 7/20/15 1ec90306129970f43b7895a999d7469e
Git repository

SMOG-CHECK (test suite)

It is strongly recommended that you verify your installation of SMOG is working properly on your machine. We have prepared a set of test scripts to verify that SMOG is generating appropriate models. These checks are version-specific. If you are using a container option, then you can find these scripts under /opt/smog2/SMOG-CHECK.
Version md5 (.tgz file)
>2.4.4 Distributed with SMOG 2
2.4.4 db36d07569ed66c6ed312d57176f4e42
2.4.2 f61efccf0a37ecf04508c1a9c1abe45b
2.4.1 f2666df4abc8cb2749435d3b78a4cfe1
2.4 7992cdd990ba94a8595cc4ee7641f2c7
2.3 7b0f2f89722d2a5bdb622d9d8f7ba6c9
2.2 25cb56afc4cf2f5bfc6369e0d8e2573a
2.1 d61efe5b2171e81a696beda3a3f85585
2.0 (and 2.0.x) 3d8769d49eddde28911a7806ba516d4e
Within the bundle you will find a script, called smog-check, that will run a very comprehensive set of tests. This set of tests may take up to an hour to complete. You will also find scripts called smog-tool-check and scm-check (v2.3 and newer) that will test the basic functionality of the tools and SCM included with SMOG 2. We are continually adding more tests to these scripts.
If your environment is configured properly for smog2 (i.e. when you type smog2 it prints the smog2 splashtext) then the checks can be performed with the command:
>$ cd [smog-check-directory] ...quick-check output...
>$ ./smog-check
...smog-check output...
>$ ./smog-tool-check
...smog-tool-check output...
There is a variety of options when using smog-check, such as only testing some tools, or some biomolecular systems. For details, see the README file.