Action: ALPHARMSD

Module	secondarystructure
Description	Usage
Probe the alpha helical content of a protein structure.
output value	type
if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix	scalar/vector

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Description
struct	vector	the vectors containing the rmsd distances between the residues and each of the reference structures
lessthan	scalar	the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
RESIDUES	atoms	this command is used to specify the set of residues that could conceivably form part of the secondary structure

Further details and examples

Probe the alpha helical content of a protein structure.

Any chain of six contiguous residues in a protein chain can form an alpha helix. This colvar thus generates the set of all possible six residue sections and calculates the DRMSD or RMSD distance between the configuration in which the residues find themselves and an idealized alpha helical structure. These distances can be calculated by either aligning the instantaneous structure with the reference structure and measuring each atomic displacement or by calculating differences between the set of inter-atomic distances in the reference and instantaneous structures.

In the original paper on this method (see below) the authors used the set of distances from the alpha helix configurations to measure the number of segments that have an alpha helical configuration. This is done by calculating the following sum of functions of the rmsd distances:

$s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m }$

where the sum runs over all possible segments of alpha helix. By default the NN, MM and D_0 parameters are set equal to those used in the paper cited below. The R_0 parameter must be set by the user - the value used in the paper cited below was 0.08 nm.

If you change the function in the above sum you can calculate quantities such as the average distance from a purely the alpha helical configuration or the distance between the set of residues that is closest to an alpha helix and the reference configuration. To do these sorts of calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN keyword if you would like to change the form of the switching function. If you use any of these options you no longer need to specify NN, R_0, MM and D_0.

The following input calculates the number of six residue segments of protein that are in an alpha helical configuration.

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

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=regtest/basic/rt32/helix.pdb Click here to see an extract from this file.
    ×  FILE: regtest/basic/rt32/helix.pdb
    ATOM      1 HH31 ACE     1      -9.105  -2.402  21.804  0.00  0.00            
ATOM      2  CH3 ACE     1      -8.930  -3.352  22.308  0.00  0.00            
ATOM      3 HH32 ACE     1      -9.504  -3.501  23.223  0.00  0.00            
ATOM      4 HH33 ACE     1      -9.067  -4.173  21.604  0.00  0.00            
ATOM      5  C   ACE     1      -7.450  -3.303  22.659  0.00  0.00            
...
ATOM    129  CH3 NME    14      -1.690  -7.089  20.487  0.00  0.00            
ATOM    130 HH31 NME    14      -1.873  -6.629  21.459  0.00  0.00            
ATOM    131 HH32 NME    14      -1.152  -6.284  19.986  0.00  0.00            
ATOM    132 HH33 NME    14      -1.135  -8.020  20.602  0.00  0.00            
END
  
The MOLINFO action with label  calculates somethingalphaThe ALPHARMSD action with label alpha calculates the following quantities: Quantity    Type    Description  
alpha scalar if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix.  If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and it has hidden defaults. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all R_0The r_0 parameter of the switching function=0.1
alpha: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut and uses the defaults shown here. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all R_0The r_0 parameter of the switching function=0.1  NN The n parameter of the switching function=8 D_0 The d_0 parameter of the switching function=0.0 MM The m parameter of the switching function=12 TYPE the manner in which RMSD alignment is performed=DRMSD
# PLUMED interprets the command:
# alpha: ALPHARMSD RESIDUES=all R_0=0.1
# as follows (Click the red comment above to revert to the short version of the input):
alpha_rmsdThe SECONDARY_STRUCTURE_RMSD action with label alpha_rmsd calculates the following quantities: Quantity    Type    Description  
alpha_rmsd vector a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=7,9,11,15,16,17,19,21,25,26,27,29,31,35,36,37,39,41,45,46,47,49,51,55,56,57,59,61,65,66,67,69,71,75,76,77,79,81,85,86,87,89,91,95,96,97,99,101,105,106,107,109,111,115,116,117,119,121,125,126 TYPE the manner in which RMSD alignment is performed=DRMSD SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673     # Action input conctinues with 2 further SEGMENTn keywords, 
alpha_ltThe LESS_THAN action with label alpha_lt calculates the following quantities: Quantity    Type    Description  
alpha_lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=alpha_rmsd SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 D_0=0.0 NN=8 MM=12}
alphaThe SUM action with label alpha calculates the following quantities: Quantity    Type    Description  
alpha scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=alpha FILEthe name of the file on which to output these quantities=colvar

Here the same is done use RMSD instead of DRMSD

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

#SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=regtest/basic/rt32/helix.pdb Click here to see an extract from this file.
    ×  FILE: regtest/basic/rt32/helix.pdb
    ATOM      1 HH31 ACE     1      -9.105  -2.402  21.804  0.00  0.00            
ATOM      2  CH3 ACE     1      -8.930  -3.352  22.308  0.00  0.00            
ATOM      3 HH32 ACE     1      -9.504  -3.501  23.223  0.00  0.00            
ATOM      4 HH33 ACE     1      -9.067  -4.173  21.604  0.00  0.00            
ATOM      5  C   ACE     1      -7.450  -3.303  22.659  0.00  0.00            
...
ATOM    129  CH3 NME    14      -1.690  -7.089  20.487  0.00  0.00            
ATOM    130 HH31 NME    14      -1.873  -6.629  21.459  0.00  0.00            
ATOM    131 HH32 NME    14      -1.152  -6.284  19.986  0.00  0.00            
ATOM    132 HH33 NME    14      -1.135  -8.020  20.602  0.00  0.00            
END
  
The MOLINFO action with label  calculates somethingWHOLEMOLECULESThis action is used to rebuild molecules that can become split by the periodic boundary conditions. More details ENTITY0the atoms that make up a molecule that you wish to align=1-100
alphaThe ALPHARMSD action with label alpha calculates the following quantities: Quantity    Type    Description  
alpha vector if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix.  If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix
alpha_lessthan scalar the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold: ALPHARMSDProbe the alpha helical content of a protein structure. This action is a shortcut. More details RESIDUESthis command is used to specify the set of residues that could conceivably form part of the secondary structure=all TYPE the manner in which RMSD alignment is performed=OPTIMAL LESS_THANcalculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.={RATIONAL R_0=0.1 NN=8 MM=12}
# PLUMED interprets the command:
# alpha: ALPHARMSD RESIDUES=all TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12}
# as follows (Click the red comment above to revert to the short version of the input):
alphaThe SECONDARY_STRUCTURE_RMSD action with label alpha calculates the following quantities: Quantity    Type    Description  
alpha vector a vector containing the rmsd distance between each of the residue segments and the reference structure: SECONDARY_STRUCTURE_RMSDCalclulate the distance between segments of a protein and a reference structure of interest More details BONDLENGTHthe length to use for bonds=0.17 ATOMSthis is the full list of atoms that we are investigating=7,9,11,15,16,17,19,21,25,26,27,29,31,35,36,37,39,41,45,46,47,49,51,55,56,57,59,61,65,66,67,69,71,75,76,77,79,81,85,86,87,89,91,95,96,97,99,101,105,106,107,109,111,115,116,117,119,121,125,126 TYPE the manner in which RMSD alignment is performed=OPTIMAL SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29 SEGMENT2this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34 SEGMENT3this is the lists of atoms in the segment that are being considered=10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT4this is the lists of atoms in the segment that are being considered=15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT5this is the lists of atoms in the segment that are being considered=20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=0.733,0.519,5.298,1.763,0.81,4.301,3.166,0.543,4.881,1.527,-0.045,3.053,1.646,0.436,1.928,1.18,-1.312,3.254,0.924,-2.203,2.126,0.65,-3.626,2.626,-0.239,-1.711,1.261,-0.19,-1.815,0.032,-1.28,-1.172,1.891,-2.416,-0.661,1.127,-3.548,-0.217,2.056,-1.964,0.529,0.276,-2.364,0.659,-0.88,-1.13,1.391,0.856,-0.62,2.565,0.148,0.228,3.439,1.077,0.231,2.129,-1.032,0.179,2.733,-2.099,1.028,1.084,-0.833,1.872,0.593,-1.919,2.85,-0.462,-1.397,1.02,0.02,-3.049,1.317,0.227,-4.224,-0.051,-0.684,-2.696,-0.927,-1.261,-3.713,-1.933,-2.219,-3.074,-1.663,-0.171,-4.475,-1.916,-0.296,-5.673     # Action input conctinues with 2 further SEGMENTn keywords, 
alpha_ltThe LESS_THAN action with label alpha_lt calculates the following quantities: Quantity    Type    Description  
alpha_lt vector the vector obtained by doing an element-wise application of a function that is one if the input is less than a threshold to the input vectors: LESS_THANUse a switching function to determine how many of the input variables are less than a certain cutoff. More details ARGthe values input to this function=alpha SWITCHThis keyword is used if you want to employ an alternative to the continuous swiching function defined above={RATIONAL R_0=0.1 NN=8 MM=12}
alpha_lessthanThe SUM action with label alpha_lessthan calculates the following quantities: Quantity    Type    Description  
alpha_lessthan scalar the sum of all the elements in the input vector: SUMCalculate the sum of the arguments More details ARGthe values input to this function=alpha_lt PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
# --- End of included input --- PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=alpha.lessthan FILEthe name of the file on which to output these quantities=colvar

References

More information about how this action can be used is available in the following articles: - F. Pietrucci, A. Laio, A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1. Journal of Chemical Theory and Computation. 5, 2197–2201 (2009)

Syntax

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

Keyword	Type	Default	Description
RESIDUES	input	none	this command is used to specify the set of residues that could conceivably form part of the secondary structure
TYPE	compulsory	DRMSD	the manner in which RMSD alignment is performed
D_0	compulsory	0.0	The d_0 parameter of the switching function
NN	compulsory	8	The n parameter of the switching function
MM	compulsory	12	The m parameter of the switching function
SERIAL	optional	false	do the calculation in serial
NOPBC	optional	false	ignore the periodic boundary conditions
VERBOSE	optional	false	write a more detailed output
LESS_THAN	optional	not used	calculate the number of a residue segments that are within a certain target distance of this secondary structure type. Options for this keyword are explained in the documentation for LESS_THAN.
R_0	optional	not used	The r_0 parameter of the switching function

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Quantity	Type	Description
alpha	scalar	if LESS_THAN is present the RMSD distance between each residue and the ideal alpha helix. If LESS_THAN is not present the number of residue segments where the structure is similar to an alpha helix