################ DESCRIPTION ############### Example for generating and running a simulation with the All-atom model using SMOG 2 and OpenSMOG In this example, we will add a Coulomb potential between charges, and we will add a +1 charge to each N in LYS. THIS MODEL IS FOR DEMONSTRATIVE PURPOSES ONLY. THE SINGLE-CHARGE LYS MODEL SHOULD NOT BE USED FOR PRODUCTION. We will also add some lines to the templates, so that the model may be used with OpenSMOG. ############### PREREQUISITES ############## - SMOG 2 must be configured and all SMOG tools must be in your PATH. If you are using a SMOG container, this will be satisfied. - the alias "python" must map to a version for which the OpenSMOG libraries are available. Conda environments can be helpful to set this up. ############## PRE-SMOG2 STEPS ############# Copy the default AA model templates from /share/templates/SBM_AA To avoid confusion, rename all files SBM_AA+coulomb In the .bif file, find the residue entry for LYS. Under LYS, replace the following line: NZ with NZ In the .sif file, under the element, list the following child element: and Explainer: For convenience, we defined constants that could be used in our force field definition. We then defined a generic Coulomb+1/r^12 term (truncated) for all nonbonded interactions. This is not the only way one could go about introducing this potential, but it will work. It also places all parameters in a single location, as opposed to having to specify each at various stages of simulation preparation. ######### USING SMOG2 AND SMOG-TOOLS ####### Begin with the file 2ci2.pdb, obtained directly from RCSB. For your convenience, it is in the current directory. Preprocess the PDB file: smog_adjustPDB will remove water molecules and recognize all valid PDB keywords. smog_adjustPDB may be applied directly to the downloaded PDB file. Since this example set of templates uses naming conventions that are consistent with the default SMOG model, we do not need to specify the mapping file. The default mapping rules will be applied. >smog_adjustPDB -i 2ci2.pdb -o 2ci2.adjusted.pdb -removewater Generate your force field with smog2: - The -t flag indicates that the template directory SBM_AA+coulomb should be used to define the force field. - The -OpenSMOG flag indicates that the input files should be prepared for use with OpenSMOG/OpenMM >smog2 -i 2ci2.adjusted.pdb -t SBM_AA+coulomb -OpenSMOG -dname 2ci2.OpenSMOG.AA+coulomb #### RUNNING A SIMULATION WITH OPENSMOG #### At this point, you have all files needed to start your calculations in OpenSMOG. Using the script run.ci2.OpenSMOG.AA+coulomb.py (in this directory), you can load, energy minimize and simulate the system. See comments in .py file for explanation of settings. >python run.ci2.OpenSMOG.AA+coulomb.py