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.
imode <pdb>
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:
imove <in_pdb> <ptraj> <out_pdb> <int>
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:
imodview <pdb> <ptraj/Kfile> <filename>
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:
imc <pdb> <ptraj>
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.
imorph <initial_pdb> <final_pdb>
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.