MDFF Plugin, Version 0.2
The MDFF plugin provides commands for setting up and analyzing molecular dynamics flexible fitting simulations, i.e., simulations in which an atomic structure is flexibly fitted into a density map.
Getting started
For a description of the MDFF method, required software, related publications, related updates, etc., please see the MDFF website. The following reference provides a practical guide to MDFF:
Molecular Dynamics Flexible Fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography.
Leonardo G. Trabuco*, Elizabeth Villa*, Eduard Schreiner, Christopher B. Harrison, and Klaus Schulten. Methods, 49, 174-180, 2009.
MDFF tutorial: For tutorials related to the MDFF method, click here.
Getting help: Any questions, bug reports, feature requests, suggestions or comments related to MDFF should be sent to the VMD mailing list.
Acknowledging MDFF in publications
Please cite the following reference in any work that applied MDFF:
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
Leonardo G. Trabuco*, Elizabeth Villa*, Kakoli
Mitra, Joachim Frank, and Klaus Schulten.
Structure, 16, 673-683, 2008.
MDFF developers
The MDFF plugin was written by Leonardo Trabuco and Elizabeth Villa.
MDFF commands
The current version of MDFF plugin provides text commands only. You first need to load the MDFF plugin by typing package require mdff in the VMD text console or the Tk Console. Typing mdff will print the available subcommands:
Usage: mdff <command> [args...]
Commands:
ccc -- calculates the cross-correlation coefficient
check -- monitors the fitting via RMSD and CCC
constrain -- creates a pdb file for restraining atoms
delete -- deletes volume corresponding to atomic structure
edges -- creates a map with smooth edges
fix -- creates a pdb file for fixing atoms
griddx -- creates a map for docking
gridpdb -- creates a pdb file with atomic masses in the beta field
setup -- writes a NAMD configuration file for MDFF
sim -- creates a simulated map from an atomic structure
Typing each command will print the corresponding usage information (e.g., type mdff sim to get the usage information of the sim subcommand.
mdff ccc
Usage: mdff ccc <atom selection> -i <input map> -res <map resolution in Angstroms> ?options?
Options:
-spacing <grid spacing in Angstroms> (default: 1.0)
-threshold <x sigmas>
-allframes (average over all frames)
mdff check
Usage: mdff check ?options?
Options:
-mol <molid> (default: top)
-frames <begin:end> or <begin:step:end> or all or now (default: all)
-rmsd -- calculate the RMSD with respect to the refence structure
-rmsdseltext <selection text for calculating the RMSD> (default: backbone)
-refpdb <pdb file> -- reference for RMSD calculation (default: frame 0)
-rmsdfile <file to write RMSD> (default: none)
-ccc -- calculate cross correlation coefficient
-map <input map> (required by -ccc)
-res <map resolution in Angstroms> (required by -ccc)
-spacing <grid spacing in Angstroms> (default: 1.0)
-cccseltext <selection text for calculating the cross correlation (default: protein or nucleic)
-cccfile <file to write cross correlation> (default: none)
-threshold <x sigmas>
mdff constrain
Usage: mdff constrain <atomselection> -o <pdb file> ?options?
Options:
-col <column> (default: B)
-k <force constant in kcal/mol/A^2> (default: 10.0)
mdff delete
Usage: mdff delete <atom selection> -i <input map> -o <output dx map> ?options?
Options:
-res <target resolution in Angstroms> (default: 10.0)
-spacing <grid spacing for "mask" map in Angstroms> (default: 1.0)
-allframes -- average over all frames
mdff edges
Usage: mdff edge -i <input map> -o <output dx map> ?options?
Options:
-kernel <Gaussian kernel> (default: 3.0)
mdff fix
Usage: mdff fix <atomselection> -o <pdb file> ?options?
Options:
-col <column> (default: O)
mdff griddx
Usage: mdff griddx -i <input map> -o <output dx map> ?options?
Options:
-threshold <value> (default: 0)
mdff gridpdb
Usage: mdff gridpdb -psf <input psf> -pdb <input pdb> -o <output pdb> ?options?
Options:
-seltext -- atom selection text (default: noh and (protein or nucleic))
mdff setup
Usage: mdff setup -o <output prefix> -psf <psf file> -pdb <pdb file> -griddx <griddx file> ?options?
Options:
-gridpdb -- pdb file for docking (default: -pdb)
-diel -- dielectric constant (default: 80; 1 with -pbc)
-temp -- temperature in Kelvin (default: 300)
-ftemp -- final temperature (default: 300)
-gscale -- scaling factor for the grid (default: 0.3)
-extrab -- extrabonds file (default: none)
-conspdb -- pdb file with constrained atoms (default: none)
-conscol -- force constant column in conspdb (default: beta)
-fixpdb -- pdb file with fixed atoms (default: none)
-fixcol -- column in fixpdb (default: occupancy)
-scal14 -- 1-4 scaling (default: 1.0)
-step -- docking protocol step (default: 1)
-parfiles -- parameter file list
-minsteps -- number of minimization steps (default 200)
-numsteps -- number of time steps to run (default: 500000)
-margin -- extra length in patch dimension during simulation (default: 0)
-pbc -- use periodic boundary conditions (for explicit solvent)
mdff sim
Usage: mdff sim <atomselection> -o <output map> ?options?
Options:
-res <target resolution in Angstroms> (default: 10.0)
-spacing <grid spacing in Angstroms> (default: 1.0)
-allframes (average over all frames)