Here we give a brief overview of the necessary commands to use iMOD, but we strongly encourage to follow the tutorials. Right now, there are three different executables:
- iMODE to obtain IC Normal Modes.
- iMOVE to animate IC Normal Modes.
- iMODVIEW to visualize Normal Modes.
- iMC to perform a Monte-Carlo simulation.
- iMORPH to perform Morphing.
This user guide describes the usage of these iMOD components.
iMODE - obtaining IC Normal Modes
To obtain the IC modes, enter the following command at the prompt.
where:
pdb | PDB input file (required) |
The default output is:
- imode.log --> Log-file.
- imode_model.pdb --> Used PDB model.
- imode_ic.evec --> IC Normal modes file.
To enable deformability computations use the −d option. In this case, additional files will be saved:
- imode_def.pdb --> PDB file with deformability data in B-factor column.
- imode_mob.pdb --> PDB file with mobility data in B-factor column.
- imode_defmob.txt --> Plain text file with deformabiliy, mobility and B-factor data.
In this section, the basic options to customize the IC modes generation are detailed. Just add them after the minimum command shown above.
−h | Displays usage information and exits. |
−m <int> | Coarse-Grained model: 0=CA, 1=C5, 2=Heavy-Atom (default=2). |
−o <string> | Output files basename (default=imode). |
-d | Turn on deformability calculations (default=disabled). |
-r <float> | Randomly fixed ratio of Dihedral Coordinates (default=disabled). Example: 0.7 = 70% of dihedrals will be randomly removed. Rotational/translational coordinates always mobile. |
-f <string> | ASCII file defining the ICs to be fixed with the format: Protein: "n phi chi psi" Where "n" is the residue index (0,1,..) and the coordinate name (phi, psi, etc...) can be set to 0(fixed) or 1(mobile). Each one of the 6 inter-chain variables should be specified on separate lines in the following order: x,y,z,Rx,Ry,Rz. Note "n" is just the sequential residue index (starting with 0) and NOT the PDB's residue index. A demo file can be generated using the --save_fixfile option. |
-P <int> | Pairwise interaction potential: (default=0) 0= Sigmoid function (= k/(1+(x/x0)^p), if x < c, else k=0). By default an extra torsional potential will be added. |
-K <string> | Force constants ASCII file with 3 cols.: Where are the corresponding atomic indices (1,2,...) A demo file can be generated using --save_Kfile option. |
-n <int/float> | Used modes range, either number [1,N] <integer>, or ratio [0,1) <float> (default=20). |
-x | Considers first CHI dihedral angle (default=disabled). |
-S <string> | All dihedral coordinates with a given secondary structure (SS) will be removed (see --ss). Example: "HE" will fix the dihedrals corresponding to alpha-helices and beta-sheets. |
Only for real expert users!
--ss <string> Secondary Structure ASCII file with 2 cols.: <n> <char> Where <n> is the corresponding residue index (0,1,...), and <char> is the single character SS identifier. By default SS will be computed internally (H=helix, E=strand, C=coil). --save_fixfile Save fixation file as <basename.fix> (to be used with -r or -S options; otherwise a fully mobile file will be generated) (default=disabled). --save_cart Save Cartesian modes as <basename_cart.evec> (default=disabled) --save_wcart Save Mass-weighted Cartesian modes as <basename_wcart.evec> (default=disabled). --save_Kfile Save atom-pairwise force constants file as <basename_Kfile.dat> (to be used with -K option) (default=disabled). --save_SSfile Save secondary structure file as <basename.ss> (to be used with -S or -P=2 options) (default=disabled). --save_covar Saves the predicted covariance matrix at selected Temperature in binary packed storage format as <basename_covar.evec>. If --save_wcart selected, then mass-weighted covariance matrix will be computed instead (default=disabled). --k0_c <float> Sigmoid function distance cutoff (default=10A). --k0_k <float> Sigmoid function stiffness constant (default=1.0). --k0_x0 <float> Sigmoid function inflexion point (default=3.8A). --k0_p <float> Sigmoid function power term (default=6). --k1_c <float> Tirion's method distance cutoff (default=10A). --k1_k <float> Tirion's method stiffness constant (default=1.0). --k2_c <float> Non-bonding distance cutoff applied to --func option (default=10A). --nomodel Disables PDB model building. Warning: introduced PDB model must match the CG selected with the -m option (default=disabled). --nomass Disables mass weighting (default=disabled). --notors Disables extra torsional potential (default=disabled). --norm Enables (norm=1) eigenvector normalization. Note this does not change vector direction (default=disabled). --func <string> ASCII file defining the force constant functions to be applied according to Topology and/or Secondary Structure. The 5 cols. format is: <SS> <t> <k> <x0> <pow> Where <SS> is the two character pairwise interaction identifier, <t> is the topology, and <k>,<x0>,<pow> are the corresponding sigmoid function parameters (see -P option). If --ss is not specified, the XX pairwise interaction identifier must be introduced. This way, only topologies will be considered. If <t> is "-1", any previously not-matched topology will be considered. --model_out <int> Output Coarse-Graining model: 0=CA, 1=C5, 2=Heavy-Atom (default=disabled). --chi_out Considers first CHI dihedral angle in output modes (default=disabled). --save_covar_out Computes and Saves the predicted covariance matrix for the output model at selected Temperature in binary packed storage format as <basename_covarf.evec>. If --save_wcart selected, then mass-weighted covariance matrix will be computed instead (default=disabled). -T <double>, --temperature <double> Temperature [K] for covariance matrix computation (default=300). --seed <unsigned> Pre-define the random number generator SEED (Mersenne Twister) (default=random-seed from /dev/urandom) --verb <int> Verbose level (0=low, 1=medium, 2=high) (default=0). --, --ignore_rest Ignores the rest of the labeled arguments following this flag. -v, --version Displays version information and exits. -h, --help Displays usage information and exits.
iMOVE - animating IC normal modes
To show the vibrational motion of a given mode, just enter the following command at the prompt:
where:
<in_pdb> | PDB input file. (required) |
<ptraj> | Normal Modes input file name (.evec). (required) |
<out_pdb> | Output Multi-PDB file. (required) |
<int> | Mode number to be moved (1,2,...,size). (required) |
The unique output is the Multi-PDB file named <out_pdb>
In this section, the basic options to customize animations are detailed.
−h | Displays usage information and exits. |
−m <int> | Coarse-Graining model: 0=CA, 1=C5, 2=Heavy-Atom, 3=NCAC, 4=CA-only (default=2). |
−x | Considers first CHI dihedral angle (default=disabled). |
−c <int> | Number of conformations generated (default=11). It should be an odd number! |
−a <float> | Amplitude linear factor to scale motion (default=2). |
−T <float> | Temperature [K] (default=300). |
−f <string> | Input ASCII file defining the ICs that were fixed during NMA (default=disabled). If modes were computed removing arbitrary ICs, the user must introduce here the file generated by iMode's --save_fixfile option. |
Only for real expert users!
--cart Mandatory if Cartesian modes are supplied, otherwise moving in Internal Coordinates (default=disabled). --model_out <int> Output Coarse-Graining model: 0=CA, 1=C5, 2=Heavy-Atom. The default output model will be that selected with the -m option. --linear Enables linear motion instead of sinusoidal bounce (default=disabled). --mov <int> Motion Type (default=2): 0=K-matrix, 1=V/W-arrays, 2=Simple-Rotations , 3=Linear (if Cartesian modes). --chi_out Considers first CHI dihedral angle in output models (default=disabled) (DEVELOPER's). --fixIC <string> Plain-text file defining the fixed Internal Coordinates. Each line will contain the index (0,1,...) of the ICs to be removed (DEVELOPER's). --, --ignore_rest Ignores the rest of the labeled arguments following this flag. -v, --version Displays version information and exits.
iMODVIEW - normal modes visualization
An alternative way to visualize a normal mode motion is the arrow representation. To this end type at the prompt:
where:
<pdb> | PDB input file. Warning: This model must match exactly the one used in modes computation. (required) |
<ptraj/Kfile> | Input eigenvectors file (ptraj). Warning: Only Cartesian modes allowed. |
<filename> | Output VMD file. (required) |
The unique output file (<filename>) can be loaded into VMD using the following command in VMD's terminal:
source <filename>
In this section, the basic options to customize mode visualization are detailed.
−h | Displays usage information and exits. |
−n <int> | Normal Mode index (1,2,...,size) (default=1) |
Only for real expert users!
--color <string> Set color. All VMD colors available (default=white). --op <int>> Sets the operation method, 1=arrows, 2=springs (default=1). --max <float>> Maximum arrow length [A] (default=10). --thick <float> Arrow/spring thickness factor (default=0.05). --level <int> Sets the averaging level to compute arrows, 0=atoms, 1=residues, 2=segments, 3=chains (default=0). --pthr <float> Minimum percentual amplitude (from maximum) to show arrows (default=0, all arrows). --kthr <float> Only those springs with force constants above this threshold will be shown (default=disabled). --kthr2 <float> Only those springs with force constants below this threshold will be shown (default=disabled). --, --ignore_rest Ignores the rest of the labeled arguments following this flag. -v, --version Displays version information and exits.
iMC - performing Monte-Carlo simulations.
To carry out a basic Monte-Carlo simulation, enter the following command at the prompt:
where:
<pdb> | PDB input file. (required) |
<ptraj> | Normal modes input file (.evec), either from NMA or PCA. (required) |
The default output trajectory will be named imc.pdb
In this section, the basic options to customize trajectories are detailed.
−h | Displays usage information and exits |
−m <int> | Input Coarse-Graining model: 0=CA, 1=C5, 2=Heavy-Atom (default=2). |
−o <string> | Output files basename. (default=imc) |
−f <string> | Input ASCII file defining the ICs that were fixed during NMA (default=disabled). If modes were computed removing arbitrary ICs, the user must introduce here the file generated by iMode's --save_fixfile option. |
−p <int> | Finds the optimal energy/stiffness scaling factor to obtain the desired average RMSD (Å) from the initial model (default=disabled). |
−−Rg <float> | Filter models by target radius of gyration (default=disabled). |
−n <int> | Number of eigenvectors to be employed, either number [1,N] <integer>, or ratio from maximum available [0,1) <float> (default=5). |
−c <int> | Number of output conformations (default= 100). |
−E <float> | Energy/Stiffness scaling factor (mode energy will be multiplied by this value) (default=1.0). |
−i <int> | Number of MC iterations per output structure (default=1000). |
−x | Considers first CHI dihedral angle (default=disabled). |
−T <float> | Temperature [K] (default=300). |
−a <float> | Amplitude linear factor to scale motion (default=1). |
Only for real expert users!
--thr <float> Enable filtering by absolute tolerance (default=disabled). --Rmsd <float> Filter models by target RMSD (default=disabled). --otraj <int> Output trajectory format: 0-Normal-Mode, 1-Multi-PDB, 2-AMBER (default=1). --cart Mandatory if Cartesian modes are supplied, otherwise moving in Internal Coordinates (default=disabled). --seed <unsigned int> Set the random number generator SEED (Mersenne Twister) (default=random-seed from /dev/urandom). --include_first Includes input model as first frame in the Multi-PDB trajectory (default=disabled). --var Input eigenvalues will be considered as variance (pca), otherwise the will be force constants (nma) (default=false). --unweight Un-mass-weights the input vectors (default=false). The Mass-weighted modes (wcart) will be converted into Cartesian coordiantes (cart) (DEVELOPER's). --optf <float> Factor to scale the optimal energy/stiffness factor (default=disabled) (DEVELOPER's). --rfact <float> Agressivity factor (default=7.778) (DEVELOPER's). --mov <int> Motion Type (default=2): 0=K-matrix, 1=V/W-arrays, 2=Simple-Rotations , 3=Linear (if Cartesian modes) (DEVELOPER's). --fixIC <string> Plain-text file defining the fixed Internal Coordinates. Each line will contain the index (0,1,...) of the ICs to be removed (DEVELOPER's). --verb Enables verbose. --, --ignore_rest Ignores the rest of the labeled arguments following this flag. -v, --version Displays version information and exits.
To generate a plausible continuous trajectory between two given conformations enter the following command at the prompt.
where:
initial_pdb | Initial PDB file. (required) |
target_pdb | Target PDB file. (required) |
The trajectory movie will be automatically named imorph_movie.pdb
In this section, the basic options to customize your morphing are detailed. Just add them after the minimal command shown above.
−h | Displays usage information and exits |
−m <int> | Coarse-Grained model: 0=CA, 1=C5, 2=Heavy-Atom (default=2). |
−o <string> | Output files basename (default=imorph). |
−F | Enables full-atom output models (default=disabled). |
−r <float> | Randomly fixed ratio of Dihedral Coordinates (default=disabled). Example: 0.7 = 70% of dihedrals will be randomly removed. Rotational/translational coordinates always mobile. |
-f <string> | ASCII file defining the ICs to be fixed with the format: Protein: "n phi chi psi" Where "n" is the residue index (0,1,..) and the coordinate name (phi, psi, etc...) can be set to 0(fixed) or 1(mobile). Each one of the 6 inter-chain variables should be specified on separate lines in the following order: x,y,z,Rx,Ry,Rz. Note "n" is just the sequential residue index (starting with 0) and NOT the PDB's residue index. A demo file can be generated using the --save_fixfile option. |
-P <int> | Pairwise interaction potential: (default=0) 0= Sigmoid function (= k/(1+(x/x0)^p), if x < c, else k=0). By default an extra torsional potential will be added. |
−i <int> | Maximum number of iterations (default=100000). |
−n <int/float> | Used modes range, either number [1,N] <integer>, or ratio [0,1) <float> (default=0.1). In any case, the value of --addnevs option will be added. |
−x | Considers first CHI dihedral angle (default=disabled). |
−s <float> | Initial amplitude applied to the merge displacement (default=5). |
−e <int/float> | Excited modes range, either number [1,nevs] <integer>, or ratio [0,1) <float> (default=0.1). |
−R <float> | Randomly fixed ratio of Internal Coordinates (default=disabled). Example: 0.7 = 70% of IC will be randomly fixed. |
−S <string> | All dihedral coordinates with a given secondary structure (SS) will be removed (see --ss). Ex: "HE" will fix the dihedrals corresponding to alpha-helices and beta-sheets. |
Only for real expert users!
--ss <string> Secondary Structure ASCII file with 2 cols.: <n> <char> Where <n> is the corresponding residue index (0,1,...), and <char> is the single character SS identifier. By default SS will be computed internally (H=helix, E=strand, C=coil). --conv <double> Convergence RMSD threshold (default=0.01Å). --conv_win <int> Window length (number of iterations) to estimate convergence (default=1000). --delta_save <float> RMSD increment to save a new trajectory frame (default=0.5Å). If a negative integer value is introduced, a new frame will be saved each --delta_save iterations. --k0_c <float> Sigmoid function distance cutoff (default=10Å). --k0_k <float> Sigmoid function stiffness constant (default=1.0). --k0_x0 <float> Sigmoid function inflexion point (default=3.8Å). --k0_p <float> Sigmoid function power term (default=6). --k1_c <float> Tirion's method distance cutoff (default=10Å). --k1_k <float> Tirion's method stiffness constant (default=1.0). --k2_c <float> Non-bonding distance cutoff applied to --func option (default=10Å). --func <string> ASCII file defining the force constant functions to be applied according to Topology and/or Secondary Structure. The 5 cols. format is: <SS> <t> <k> <x0> <pow> Where <SS> is the two character pairwise interaction identifier, <t> is the topology, and <k>,<x0>,<pow> are the corresponding sigmoid function parameters. If --ss is not specified, the XX pairwise interaction identifier must be introduced. This way, only topologies will be considered. If <t> is "-1", any previously not-matched topology will be considered. --rediag <float> RMSD to trigger NMA (default=0.1Å). --morepdbs Saves initial (basename_model.pdb) and final (basename_fitted.pdb) models. If the -F option is enabled, the fitted CG-model (basename_fitCG.pdb) will be saved (default=disabled). --morermsds Enables C-alpha RMSD computation (default=disabled). --notraj Disables Multi-PDB trajectory movie output (default=disabled). --nomodel Disables PDB model building. Warning: introduced PDB model must match the CG selected with the -m option (default=disabled). --nomass Disables mass weighting (default=disabled). --notors Disables extra torsional potential (default=disabled). --nowrmsd Disables Gaussian weighted RMSD (default=disabled). --prob <string> Normal mode selection probabitity. Each one of the --nex modes will be selected and merged from the --nevs subset according to the following probabilities (p): (default=var) plain: constant probability var: proportional to the i-th mode variance, p(i)= 1/eigenvalue(i) line: lineally decreasing probability, p(i)= 1-i/nevs --addnevs <int> Increases --nevs value by --addnevs (default=10). --step2 <float> Final amplitude applied to excited modes (amplitude will decrease linearly from --step to --step2) (default=step/10). --rand_step Random amplitude selection between --step and --step2 (default=disabled). --nex2 <int> Final number of excited eigenvectors, either number [1,nevs] <integer>, or ratio [0,1) <float>. Number of excited modes will change linearly from --nevs to --nevs2 (default=disabled). --rand_excited Random number of excited modes between --nex and --nex2 (default=disabled). --noscv Disable the Scaling Collective Variable method (default=disabled). --norand_weight Disables random excited modes weighting (default=disabled). --wrmsd <float> Sets the RMSD weighting factor for model alignment. The range is [0:1], 0=maximum-weighting 1=no-weighting (default=0). --seed <unsigned int> Set the random number generator seed (Mersenne Twister) (default=random-seed from /dev/urandom). --time Enable clocks (default=disabled). --verb <int> Verbose level (0=low, 1=medium, 2=high) (default=0). --, --ignore_rest Ignores the rest of the labeled arguments following this flag. -v, --version Displays version information and exits.