SMOG 2

A Downloadable, Portable and Versatile Software Package


We have developed a standalone software package for generating SMOG models. This is a nearly complete re-write of the original SMOG software. The original models are still provided, though the files may look a bit different. While the SMOG web-based interface will continue to be available, the standalone code is particularly useful if you want to modify the forcefield (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.

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

User's Manual
Version
2.0
Beta (and 2.1/2.2)

Download SMOG 2
Version Release Date md5sum (.tgz file)
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
Beta
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.
Version md5sum (.tgz file)
2.2 25cb56afc4cf2f5bfc6369e0d8e2573a
2.1 d61efe5b2171e81a696beda3a3f85585
2.0 (and 2.0.x) 3d8769d49eddde28911a7806ba516d4e
Beta
Git repository
Within the bundle you will find a shorter sanity test called quick-check and a very comprehensive set of tests called smog-check, which can take up to an hour to complete. You will also find a script called smog-tool-check that will test the basic functionality of the tools 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 run simply by:
>$ cd [smog-check-directory]
>$ ./quick-check
...quick-check output...
>$ ./smog-check
...smog-check output...
>$ ./smog-tool-check
...smog-tool-check output...

Forcefield repository: One of the key features of SMOG 2 is that the forcefields are portable. That is, you can share new models by simply making your template files available. Officially-supported forcefields (i.e. those tested by smog-check) are included as part of the default distribution. Other forcefields are available here. As forcefields are integrated within smog-check, they will be moved to the standard SMOG 2 bundle. Each set of templates includes a README that provides a detailed description of the model. If you would like to have your forcefield made available, please contact us.
Forcefield Name Brief description Contributor
SBM_AA+hydrogen AA model with explicit hydrogens Heiko Lammert
SBM_AA_charged AA model with charges Jeff Noel
ENM AA model with elastic network for contacts Jeff Noel

Version history for SMOG 2: SMOG 2 updates will be documented here. The version history for the Shadow Contact Map can be found elsewhere. Since new versions occasionally have bug fixes, it is highly recommended that you only use the most recent released version. If you would like to test out the newest options available, then you may be interested in trying the beta version.

  • 2.1:

    • Improved error messaging for inconsistent bif-pdb atom naming.
    • Added a fix to command line parsing in smog_adjustPDB.
    • Significant performance improvements (factor of 3-4) for "vanilla" models and large systems.
    • Extended output messaging.
    • Introduction to CPAN added to manual.
    • Description of forcefield corrected in manual.
    • smog_extract module added.
    • Increased default excluded volume in SBM_AA+gaussian, so that it is consistent with SBM_AA.
    • Added more checks for mismatched atoms in improper connections.
    • Added MIA residue to Whitford09 templates.
    • Added connection definition for nucleic to protein (e.g. in aminoacyl-tRNA).
    • Removed officially-unsupported templates from distro. Now they may be found in the force field repo.
    • Changes option -warnonly to -warn N. Rather than ignore all errors, the first N can be considered warnings. -1 indicates that all errors will be converted to warnings.
    • smog_ion module added.
    • Cleaned up a variety of routines.
    • Added more robust template checks.
  • 2.0.3:

    • Added -rescaleCD option.
    • Improved performance of error checking.
    • Minor cleanup of code.
  • 2.0.2:

    • Added error message when END is missing after ATOM lines.
    • Chain ordering in ndx file is now numerical.
    • Added free_bond routines.
    • Fix to pairType assignment. nbType was used for contact function matching. Now, pairType is used.
  • 2.0.1:

    • Updated license information.
    • Updated warning messages.
    • Added additional error checks.
  • 2.0:

    • Initial release of standalone SMOG 2 software package.

    Page created and maintained by Jeff Noel and Paul Whitford