Institute of Chemistry - University of Campinas

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Tutorial Input options

Input options

In order to obtain the optimal alignment of a fraction of the atoms of each frame of your trajectory, do:

mdlovofit -f [fraction] -t align.pdb file1.pdb file2.pdb file3.pdb ...

[fraction] is (real number) the fraction of the atoms that will be considered explicitly on the fit (that is, that will automatically be chosen by the method as the best aligned atoms). Use any real number between 0 and 1. For example: [fraction] = 0.7 for 70% of the atoms.
align.pdb This is the PDB file which will containt the aligned trajectory.
file1.pdb etc. These are the PDB files that contain the trajectory to the aligned. Each PDB file may contain more than one frame of the trajectory, and the files will be considered as a sequential trajectory in the input order. In each PDB file, the frames must be separated by "END" or "ENDMDL". These files must always be the LAST input options of the command line.
-rmsf rmsf.dat A file, in the example called 'rmsf.dat', is created containing the Root Mean Square Fluctuations (RMSF) of the selection atoms.
-atoms N CA ... By default, MDLovoFit considers only CA atoms for alignment. You can change this with this keyword, by selecting the atom names (see the -atomsfile option for more sofisticated selections).
-atomsfile file.pdb This file determines which are the atoms that will be considered for alignment (default: CA). Atoms with zero occupancy will not be considered, and atoms with 1.00 occupancy will be considered. You can create a file with sofisticated selections using VMD, for example. For more simple selections, see the -atoms option above.
-ntrial [integer] The number of different initial correspondences. Larger ntrial improves the chances that the global minimizer of the RMSD is obtained. The computational time is proportional to the number of trials. The default value is 100.
-perframe (or -pf) The fraction of best aligned atoms is computed independently for each frame. Thus, the assignment of which are the least and most mobile atoms changes from frame to frame. If this option is not set, the average best assignment is kept and the alignmnet of this set is repeated for every frame.
In order to compute the RMSD of the least flexible fractions of atoms, for all fractions, do:

mdlovofit -mapfrac file1.pdb file2.pdb file3.pdb ...

-mapfrac Using this option, the program will run varying the fraction of aligned atoms from 0. to 1. in "mapstep" intervals, and print the overall RMSDs for each fraction.
-mapstep [real] The step for mapfrac. Default step : 0.01
See also:
M3G home-page
The TANGO project