.. _ssfep_gui:

SSFEP Using the SilcsBio GUI
----------------------------

Please see :ref:`ssfep_simulations_gui` in the :doc:`../quickstart/quickstart_gui` for
instructions on running SSFEP from the SilcsBio GUI.

.. _ssfep_cli:

SSFEP Using the CLI
-------------------

The following usage details are provided for completeness. **We strongly 
recommend using the SilcsBio GUI to set up, run, and analyze SSFEP 
calculations**.

To perform the SSFEP precomputation simulations, protein coordinates in PDB 
file format and parent ligand coordinates in Mol2 file format are required.
The protein should have termini properly capped, missing loops built or the 
ends of the missing loops capped, standard atom and residue names, and 
sequential atom and residue numbering. Using these two files, run the 
following: 

::

   ${SILCSBIODIR}/ssfep/1_setup_ssfep prot=<Protein PDB> lig=<Ligand Mol2/SDF>

.. warning::

   The setup program internally use the GROMACS utility ``pdb2gmx``,
   which may have problems processing the protein PDB file. The most
   common ``pdb2gmx`` issue involves mismatches between the
   expected residue name/atom names in the input PDB and those
   defined in the CHARMM force-field.

   To fix this problem: Run the ``pdb2gmx`` command manually from
   within the ``1_setup`` directory for a detailed error message.
   Please contact support@silcsbio.com for additional assistance.

Following completion of the setup, run 10 MD jobs:

::

   ${SILCSBIODIR}/ssfep/2_run_md_ssfep prot=<Protein PDB> lig=<Ligand Mol2/SDF>

This command will submit 10 jobs to the pre-defined queue: 5 for the
ligand in water and 5 for the ligand complexed with protein.

Once the precomputation simulations are completed, the
``2_run_md/1_lig/[1-5]`` and ``2_run_md/2_prot_lig/[1-5]``
directories will contain ``*.1-10.whole.trr`` trajectory files. If
these files are not generated, then your simulations are either still
running or have stopped due to a problem. Look into the log files
within these directories for an explanation of the failure.

Ligand Modifications
--------------------

Follow the instructions in :ref:`ligand_mod_usage` to create modifications
to your parent ligand.


Evaluating Binding Affinity Changes
-----------------------------------

Once ``modifications.txt`` has been prepared and the MD simulations
involving the parent ligand are completed, run the following script 
to set up a :math:`\Delta \Delta G` calculation.

::

   ${SILCSBIODIR}/ssfep/3a_setup_modifications prot=<Protein PDB> lig=<Ligand Mol2/SDF File> mod=modifications.txt

This will submit 10 jobs to evaluate all snapshots from the completed MD 
simulations of the parent ligand in order to calculate the
change in free energy for every modification specified in your 
``modifications.txt``. Structures of these modifications in Mol2 format 
are output as ``3_analysis_<modified ligand name entry in 
modifications.txt>/mod_files/*.mol2``.

After these jobs complete, you may obtain :math:`\Delta \Delta G` for 
your full list of modifications using:

::

   ${SILCSBIODIR}/ssfep/3b_calc_ddG_ssfep mod=modifications.txt

Example output follows:

.. image:: images/ssfep-score.png