Command Line Interface Quickstart¶

This chapter provides a step-by-step introduction on how to use the SilcsBio Command Line Interface (CLI). Example commands assume a Bash shell is being used.

SILCS simulation¶

Set the environment variables required to access the software:
```
export GMXDIR=<gromacs/bin>
export SILCSBIODIR=<silcsbio>
```
Set up the SILCS simulations:
```
${SILCSBIODIR}/silcs/1_setup_silcs_boxes prot=<Protein PDB>
```
To determine if the setup is complete check that the 10 PDB files required for the simulations are available using the command ls 1_setup/*_silcs.*.pdb
Submit the SILCS GCMC/MD jobs to the queue:
```
${SILCSBIODIR}/silcs/2a_run_gcmd prot=<Protein PDB>
```
This will submit 10 jobs to the queue. To check the progress of the jobs, use the tail -n1 2a_run_gcmd/*/.progress command. You will see two numbers for each job. The first number is the current cycle number and the second number is the total number of cycles required to complete the simulation.
When the GCMC/MD jobs are finished, generate FragMaps:
```
${SILCSBIODIR}/silcs/2b_gen_maps prot=<Protein PDB>
```
This command will submit 10 jobs to the queue for calculating the occupancy maps from individual runs. Once they are done, use the following command to create the GFE FragMaps:
```
${SILCSBIODIR}/silcs/2c_fragmap prot=<Protein PDB>
```
This command will create a silcs_fragmap_<Protein PDB> folder, which contains final FragMap and VMD/PyMol scripts for easy visualization:
```
pymol view_maps.pml # PyMol
vmd -e view_maps.vmd # VMD
```
Additional files that are created include those needed for subsequent SILCS-MC docking and the file overlap_coefficient.dat. The overlap coefficients in this file are a measure of convergence for SILCS simulations. If the coefficients are less than 0.7, you may consider extending the SILCS simulations.

For additional details, please see SILCS: Site Identification by Ligand Competitive Saturation.

SSFEP simulation¶

Set the environment variables required to access the software:
```
export GMXDIR=<gromacs/bin>
export SILCSBIODIR=<silcsbio>
```
Set up the SSFEP simulations:
```
${SILCSBIODIR}/ssfep/1_setup_ssfep lig=<Ligand Mol2/SDF file> prot=<Protein PDB>
```
To determine if the setup is completed check that the PDB files required for the simulations are available using the command ls 1_setup/*/*_gmx_wat.pdb. The listing should show PDB files for the ligand alone and for the protein/ligand complex.
Submit the SSFEP MD simulation jobs to the queueing system:
```
${SILCSBIODIR}/ssfep/2_run_md_ssfep lig=<Ligand Mol2/SDF file> prot=<Protein PDB>
```
This will submit 10 jobs to the queue, 5 for the protein:ligand complex and 5 for the ligand. To check the progress of the jobs, use the tail -n1 2_run_md/*/.progress command. You will see two numbers for each job. The first number is the current cycle number and the second number is the total number of cycles required to complete the simulation. SSFEP MD simulations may take 6-12 hours to complete depending on the hardware and system size.
When the SSFEP MD simulation jobs are finished, use the ligand modification files to submit the $\Delta \Delta G$ calculations:
```
${SILCSBIODIR}/ssfep/3a_setup_modifications lig=<Ligand Mol2/SDF file> prot=<Protein PDB> mod=<modification file>
```
This command will submit 10 jobs, each of which processes one of the MD trajectories for all modifications in the modification file. Depending on the number and sizes of the modifications, this step may take minutes to several hours to complete.

Once completed, use the following command to collate the results for all of the modifications:
```
${SILCSBIODIR}/ssfep/3b_calc_ddG_ssfep mod=<modification file>
```
This command will create a lig_decor.csv file, which contains the free energy change for each modification relative to the parent ligand. SSFEP is designed to evaluate small modifications and results are best interpreted qualitatively. Therefore it is recommended that only the sign of the change, and not the magnitude, be used to inform decision making: values < 0 indicate a modification predicted to be favorable.

For more details, please see SSFEP: Single Step Free Energy Perturbation.