Action: FIT_TO_TEMPLATE

Module	generic
Description	Usage
This action is used to align a molecule to a template.

Further details and examples

This action is used to align a molecule to a template.

This can be used to move the coordinates stored in plumed so as to be aligned with a provided template in PDB format. Pdb should contain also weights for alignment (see the format of PDB files used e.g. for RMSD). Make sure your PDB file is correctly formatted as explained in the documentation for PDB2CONSTANT. Weights for displacement are ignored, since no displacement is computed here. Notice that all atoms (not only those in the template) are aligned. To see what effect try the DUMPATOMS directive to output the atomic positions.

Also notice that PLUMED propagate forces correctly so that you can add a bias on a CV computed after alignment. For many CVs this has no effect, but in some case the alignment can change the result. Examples are: - POSITION CV since it is affected by a rigid shift of the system. - DISTANCE CV with COMPONENTS. Since the alignment could involve a rotation (with TYPE=OPTIMAL) the actual components could be different from the original ones. - CELL components for a similar reason. - DISTANCE from a FIXEDATOM, provided the fixed atom is introduced after the FIT_TO_TEMPLATE action.

[!CAUTION] The implementation of TYPE=OPTIMAL is available but should be considered in testing phase. Please report any strange behavior.

[!CAUTION] This directive modifies the stored position at the precise moment it is executed. This means that only collective variables which are below it in the input script will see the corrected positions. As a general rule, put it at the top of the input file. Also, unless you know exactly what you are doing, leave the default stride (1), so that this action is performed at every MD step.

When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.5, by considering the ordered list of atoms and rebuilding the molecules using a procedure that is equivalent to that done in WHOLEMOLECULES . Notice that rebuilding is local to this action. This is different from WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.

In case you want to recover the old behavior you should use the NOPBC flag. In that case you need to take care that atoms are in the correct periodic image.

Examples

Align the atomic position to a template then print them. The following example is only translating the system so as to align the center of mass of a molecule to the one in the reference structure ref.pdb:

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
# dump coordinates before fitting, to see the difference:
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-before.xyz ATOMSthe atom indices whose positions you would like to print out=1-20

# fit coordinates to ref.pdb template
# this is a "TYPE=SIMPLE" fit, so that only translations are used.
The DUMPATOMS action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/basic/rt63/align.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt63/align.pdb
    
ATOM      1 HH31 ACE     1      -0.000  -0.000  00.000  1.00  0.00            
ATOM      2 HH31 ACE     1      -0.000  -0.000  00.000  0.50  0.00            
END
  
 TYPE the manner in which RMSD alignment is performed=SIMPLE

# dump coordinates after fitting, to see the difference:
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-after.xyz ATOMSthe atom indices whose positions you would like to print out=1-20

The following example instead performs a rototranslational fit.

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
# dump coordinates before fitting, to see the difference:
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-before.xyz ATOMSthe atom indices whose positions you would like to print out=1-20

# fit coordinates to ref.pdb template
# this is a "TYPE=OPTIMAL" fit, so that rototranslations are used.
The DUMPATOMS action with label  calculates somethingFIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details STRIDE the frequency with which molecules are reassembled=1 REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/basic/rt63/align.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt63/align.pdb
    
ATOM      1 HH31 ACE     1      -0.000  -0.000  00.000  1.00  0.00            
ATOM      2 HH31 ACE     1      -0.000  -0.000  00.000  0.50  0.00            
END
  
 TYPE the manner in which RMSD alignment is performed=OPTIMAL

# dump coordinates after fitting, to see the difference:
DUMPATOMSDump selected atoms on a file. More details FILEfile on which to output coordinates; extension is automatically detected=dump-after.xyz ATOMSthe atom indices whose positions you would like to print out=1-20

In the following example you see two completely equivalent way to restrain an atom close to a position that is defined in the reference frame of an aligned molecule. You could for instance use this command to calculate the position of the center of mass of a ligand after having aligned the atoms to the reference frame of the protein that is determined by aligning the atoms in the protein to the coordinates provided in the file ref.pdb

Click on the labels of the actions for more information on what each action computes

#SETTINGS INPUTFILES=regtest/basic/rt63/align.pdb
# center of the ligand:
centerThe CENTER_FAST action with label center calculates the following quantities:
 Quantity   
 Type   
 Description  
center
atoms
virtual atom calculated by CENTER_FAST action: CENTERCalculate the center for a group of atoms, with arbitrary weights. More details ATOMSthe group of atoms that you are calculating the Gyration Tensor for=100-110

FIT_TO_TEMPLATEThis action is used to align a molecule to a template. More details REFERENCEa file in pdb format containing the reference structure and the atoms involved in the CV=
regtest/basic/rt63/align.pdb
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/basic/rt63/align.pdb
    
ATOM      1 HH31 ACE     1      -0.000  -0.000  00.000  1.00  0.00            
ATOM      2 HH31 ACE     1      -0.000  -0.000  00.000  0.50  0.00            
END
  
 TYPE the manner in which RMSD alignment is performed=OPTIMAL

# place a fixed atom in the protein reference coordinates:
The FIT_TO_TEMPLATE action with label  calculates somethingfixThe FIXEDATOM action with label fix calculates the following quantities:
 Quantity   
 Type   
 Description  
fix
atoms
virtual atom calculated by FIXEDATOM action: FIXEDATOMAdd a virtual atom in a fixed position. This action has hidden defaults. More details ATcoordinates of the virtual atom=1.0,1.1,1.0
fix: FIXEDATOMAdd a virtual atom in a fixed position. This action uses the defaults shown here. More details ATcoordinates of the virtual atom=1.0,1.1,1.0  SET_MASS mass of the virtual atom=1 SET_CHARGE charge of the virtual atom=0

# take the distance between the fixed atom and the center of the ligand
dThe DISTANCE action with label d calculates the following quantities:
 Quantity   
 Type   
 Description  
d
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=center,fix

# apply a restraint
RESTRAINTAdds harmonic and/or linear restraints on one or more variables. More details ARGthe values the harmonic restraint acts upon=d ATthe position of the restraint=0.0 KAPPA specifies that the restraint is harmonic and what the values of the force constants on each of the variables are=100.0

Notice that you could have obtained an (almost) identical result by adding a fictitious atom to ref.pdb with the serial number corresponding to the atom labelled center (there is no automatic way to get it, but in this example it should be the number of atoms of the system plus one), and properly setting the weights for alignment and displacement in RMSD. There are two differences to be expected: (ab) FIT_TO_TEMPLATE might be slower since it has to rototranslate all the available atoms and (b) variables employing periodic boundary conditions (such as DISTANCE without NOPBC, as in the example above) are allowed after FIT_TO_TEMPLATE, whereas RMSD expects the issues related to the periodic boundary conditions to be already solved. The latter means that before the RMSD statement one should use WRAPAROUND or WHOLEMOLECULES to properly place the ligand.

Syntax

The following table describes the keywords and options that can be used with this action