Using SMOG2 to generate C-alpha and All-Atom Structure-Based models¶
This tutorial should take between 5 to 10 minutes to complete. Here, we will use the SMOG2 software pacakge to generate the SBM (Structure-Based Model) input files that will be used to perform a simulation with OpenSMOG. To install SMOG2, please check the installation notes in the SMOG 2 user manual, or use the guide here. Details of SMOG2 usage and options are described in the manual. It is assumed that the executable smog2 is in your path.
Preparing your PDB file¶
The following instructions will use a PDB file of CI2 protein (2ci2.pdb).
First, download the PDB file:
Then, it is necessary to clean up the file and only keep information needed to define a structure-based model. In this case, let us keep only the ATOM lines:
grep "^ATOM" 2ci2.pdb > 2ci2.atoms.pdb
Sometimes, you also want HETATMs. This is up to the user. HETATMs can be things that we don’t want to include (e.g. HOH), or things that we may want to included (e.g. posttranslational modifications). In this case, we only want ATOM lines.
Next, add an END line to the file 2ci2.atoms.pdb:
sed -i -e "\$aEND" 2ci2.atoms.pdb
Adjust the file, so that the naming convention conforms with the default SMOG models:
smog_adjustPDB -i 2ci2.atoms.pdb -o 2ci2.adj.pdb
Generate OpenSMOG input files for a C-alpha model¶
Use the adjusted file to generate your input CA model:
smog2 -i 2ci2.adj.pdb -CA -dname 2ci2.CA -OpenSMOG
Generate OpenSMOG input files for an all-atom model¶
To generate input files for the all-atom model, you only need to change the flag -CA to -AA:
smog2 -i 2ci2.adj.pdb -AA -dname 2ci2.AA -OpenSMOG
When running the simulation in OpenSMOG, there are differences in the simulation protocols and settings. For example, in the case of AA, the cutoff is typically much shorter than the values used with the CA model. However, larger timesteps can typically be used with the AA model. Please, check the C-alpha and All-Atom simulation tutorial pages.