Introduction

The molecular dynamics flexible fitting (MDFF) method can be used to flexibly fit atomic structures into density maps. The method was originally described in the manuscript:

We recommend reading the following practical guide before going through this tutorial:

Required software

The necessary capabilities for setting up and analyzing MDFF simulations are implemented in VMD (Visual Molecular Dynamics), a molecular visualization and analysis program. MDFF simulations are performed using NAMD (NAnoscale Molecular Dynamics), a molecular dynamics simulation program. Both VMD and NAMD are developed by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign.

To apply the MDFF method you need to download and install both VMD and NAMD. Download and installation instructions can be found following the links above (if you are reading the electronic version of this document). In this tutorial we assume you are familiar with VMD; thus, we recommend that you complete the VMD tutorial beforehand. Completing the NAMD tutorial is not critical for understanding this tutorial, but it is nonetheless recommended. In this tutorial, we also use the third-party software package Situs for rigid-body docking (see Section 2.5 for details).

Tutorial Topics and Files

The tutorial starts with a brief overview of MDFF commands available in VMD (Section 1). In Section 2, a simple example of MDFF in vacuo is worked out. This first example uses two atomic structures of adenylate kinase in different conformations, and a simulated map is generated from one of the conformations, which is then used as a target for MDFF. All the basic steps for setting up, running, and analyzing MDFF simulations are covered. In Section 3, a similar MDFF simulation is performed, but this time in explicit solvent. In Section 4, use of domain restraints to maintain rigid domain during MDFF simulations is discussed. Finally, in Section 5, use of symmetry restraintes for MDFF of symmetric molecules is covered. Other topics will be covered in a future version of this tutorial, including MDFF for RNA-containing systems, multi-step MDFF protocols, and interactive MDFF. The files provided with this tutorial are listed in the next table.

**Table 1:** Files provided for each section of this tutorial. All files can be found at the `mdff-tutorial-files` directory.
Section 2: A simple MDFF example
`1ake-colores.pdb`
`1ake-initial.pdb`
`4ake-target.pdb`
`adk-step1-result.dcd`
`adk-step2-result.dcd`

Section 3: MDFF with explicit solvent
`adk-solvent-step1-result.dcd`
`adk-solvent-step2-result.dcd`
Section 4: MDFF with Domain Restraints
`acoasyn-initial.pdb`
`acoasyn-initial.psf`
`acoasyn-target.dx`
`acoasyn-target.pdb`
`domain-step1-result.dcd`
`no-domain-step1-result.dcd`
`par_all27_prot_lipid_na.inp`
Section 5: MDFF with Symmetry Restraints
`helix.pdb`
`helix.psf`
`helix-target.dx`
`helix-matrices.txt`
`no-symmetry-step1-result.dcd`
`par_all27_prot_lipid_na.inp`
`set_symmetry.tcl`
`symmetry-step1-result.dcd`