SMOG 2

A Downloadable, Portable and Versatile Software Package

Manuscript   Tutorial   Manual   Download   SMOG-CHECK   Force Field Repo   Version History


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.

Manuscript: The manuscript describing SMOG 2 is available in PLOS Computational Biology. It can be found here. Since the default model in SMOG 2 differs from SMOG 1, it is highly encouraged that all SMOG 2 users read the manuscript, first.

Introductory Tutorial: In addition to consulting the user's manual, one may find a tutorial for using SMOG 2 here.

User's Manual
Version
2.3
2.0
Beta

Download SMOG 2
Version Release Date md5 (.tgz file)
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
Docker Container (v2.3) 2/18/21 Note: Container also has smog-check

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.
Version md5 (.tgz file)
2.3 7b0f2f89722d2a5bdb622d9d8f7ba6c9
2.2 25cb56afc4cf2f5bfc6369e0d8e2573a
2.1 d61efe5b2171e81a696beda3a3f85585
2.0 (and 2.0.x) 3d8769d49eddde28911a7806ba516d4e
Git repository
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
...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.

Force Field Repository: In an effort to ease the sharing of models and increase transparency, users are encouraged to make their templates publicly available through the force field repository. See the repo here.

Version History for SMOG 2: A complete version history of SMOG 2 may be found here.