Action: PARABETARMSD

Module	secondarystructure
Description	Usage
Probe the parallel beta sheet content of your protein structure.
output value	type
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet	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.

Input

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

Further details and examples

Probe the parallel beta sheet content of your protein structure.

Two protein segments containing three contiguous residues can form a parallel beta sheet. Although if the two segments are part of the same protein chain they must be separated by a minimum of 3 residues to make room for the turn. This colvar thus generates the set of all possible six residue sections that could conceivably form a parallel beta sheet and calculates the DRMSD or RMSD distance between the configuration in which the residues find themselves and an idealized parallel beta sheet 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.

This colvar is based on the reference in the bibliography below. The authors of this paper use the set of distances from the parallel beta sheet configurations to measure the number of segments whose configuration resembles a parallel beta sheet. 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 parallel beta sheet. 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 structure composed of only parallel beta sheets or the distance between the set of residues that is closest to a parallel beta sheet 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 parallel beta sheet 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 somethingpbThe PARABETARMSD action with label pb calculates the following quantities:
 Quantity   
 Type   
 Description  
pb
scalar
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to a parallel beta sheet: PARABETARMSDProbe the parallel beta sheet content of your 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 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 R_0The r_0 parameter of the switching function=0.1
pb: PARABETARMSDProbe the parallel beta sheet content of your 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 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 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 STYLE Parallel beta sheets can either form in a single chain or from a pair of chains=all TYPE the manner in which RMSD alignment is performed=DRMSD
# PLUMED interprets the command:
# pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1 R_0=0.1
# as follows (Click the red comment above to revert to the short version of the input):
pb_bothThe SECONDARY_STRUCTURE_RMSD action with label pb_both calculates the following quantities:
 Quantity   
 Type   
 Description  
pb_both.struct-1
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 1th of these quantities
pb_both.struct-2
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 2th of these quantities: 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 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59 SEGMENT5this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=1.244,-4.62,-2.127,-0.016,-4.5,-1.395,0.105,-5.089,0.024,-0.287,-3,-1.301,0.55,-2.245,-0.822,-1.445,-2.551,-1.779,-1.752,-1.13,-1.677,-2.113,-0.55,-3.059,-2.906,-0.961,-0.689,-3.867,-1.738,-0.695,-2.774,0.034,0.19,-3.788,0.331,1.201,-3.188,0.3,2.624,-4.294,1.743,0.937,-3.503,2.671,0.821,4.746,-2.363,0.188,3.427,-1.839,0.545,3.135,-1.958,2.074,3.346,-0.365,0.181,4.237,0.412,0.521,2.261,0.013,-0.487,2.024,1.401,-0.875,1.489,1.514,-2.313,0.914,1.902,0.044,-0.173,1.33,0.052,1.202,2.94,0.828,0.19,3.507,1.718,0.772,3.801,3.104,-0.229,4.791,1.038,0.523,5.771,0.996 STRUCTURE2the reference structure=-1.439,-5.122,-1.144,-0.816,-3.803,-1.013,0.099,-3.509,-2.206,-1.928,-2.77,-0.952,-2.991,-2.97,-1.551,-1.698,-1.687,-0.215,-2.681,-0.613,-0.143,-3.323,-0.477,1.267,-1.984,0.681,-0.574,-0.807,0.921,-0.273,-2.716,1.492,-1.329,-2.196,2.731,-1.883,-2.263,2.692,-3.418,-2.989,3.949,-1.433,-4.214,3.989,-1.583,2.464,-4.352,2.149,3.078,-3.17,1.541,3.398,-3.415,0.06,2.08,-2.021,1.639,0.938,-2.178,1.225,2.525,-0.886,2.183,1.692,0.303,2.346,1.541,0.665,3.842,2.42,1.41,1.608,3.567,1.733,1.937,1.758,1.976,0.6,2.373,2.987,-0.238,2.367,2.527,-1.72,1.684,4.331,-0.148,0.486,4.43,-0.415     # Action input conctinues with 5 further SEGMENTn keywords, 
pb_lowThe LOWEST action with label pb_low calculates the following quantities:
 Quantity   
 Type   
 Description  
pb_low
vector
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=pb_both.struct-1,pb_both.struct-2
pb_ltThe LESS_THAN action with label pb_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
pb_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=pb_low 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}
pbThe SUM action with label pb calculates the following quantities:
 Quantity   
 Type   
 Description  
pb
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=pb_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=pb 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
hhThe PARABETARMSD action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
vector
if LESS_THAN is present the RMSD distance between each residue and the ideal parallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to a parallel beta sheet
hh_lessthan
scalar
the number blocks of residues that have an RMSD from the secondary structure that is less than the threshold: PARABETARMSDProbe the parallel beta sheet content of your 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 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}  STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1
hh: PARABETARMSDProbe the parallel beta sheet content of your 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 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}  STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1  STYLE Parallel beta sheets can either form in a single chain or from a pair of chains=all
# PLUMED interprets the command:
# hh: PARABETARMSD RESIDUES=all TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.1 NN=8 MM=12}  STRANDS_CUTOFF=1
# as follows (Click the red comment above to revert to the short version of the input):
hh_bothThe SECONDARY_STRUCTURE_RMSD action with label hh_both calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_both.struct-1
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 1th of these quantities
hh_both.struct-2
vector
the vectors containing the rmsd distances between the residues and each of the reference structures  This is the 2th of these quantities: 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 STRANDS_CUTOFFIf in a segment of protein the two strands are further apart then the calculation of the actual RMSD is skipped as the structure is very far from being beta-sheet like=1 SEGMENT1this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59 SEGMENT5this is the lists of atoms in the segment that are being considered=5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 STRUCTURE1the reference structure=1.244,-4.62,-2.127,-0.016,-4.5,-1.395,0.105,-5.089,0.024,-0.287,-3,-1.301,0.55,-2.245,-0.822,-1.445,-2.551,-1.779,-1.752,-1.13,-1.677,-2.113,-0.55,-3.059,-2.906,-0.961,-0.689,-3.867,-1.738,-0.695,-2.774,0.034,0.19,-3.788,0.331,1.201,-3.188,0.3,2.624,-4.294,1.743,0.937,-3.503,2.671,0.821,4.746,-2.363,0.188,3.427,-1.839,0.545,3.135,-1.958,2.074,3.346,-0.365,0.181,4.237,0.412,0.521,2.261,0.013,-0.487,2.024,1.401,-0.875,1.489,1.514,-2.313,0.914,1.902,0.044,-0.173,1.33,0.052,1.202,2.94,0.828,0.19,3.507,1.718,0.772,3.801,3.104,-0.229,4.791,1.038,0.523,5.771,0.996 STRUCTURE2the reference structure=-1.439,-5.122,-1.144,-0.816,-3.803,-1.013,0.099,-3.509,-2.206,-1.928,-2.77,-0.952,-2.991,-2.97,-1.551,-1.698,-1.687,-0.215,-2.681,-0.613,-0.143,-3.323,-0.477,1.267,-1.984,0.681,-0.574,-0.807,0.921,-0.273,-2.716,1.492,-1.329,-2.196,2.731,-1.883,-2.263,2.692,-3.418,-2.989,3.949,-1.433,-4.214,3.989,-1.583,2.464,-4.352,2.149,3.078,-3.17,1.541,3.398,-3.415,0.06,2.08,-2.021,1.639,0.938,-2.178,1.225,2.525,-0.886,2.183,1.692,0.303,2.346,1.541,0.665,3.842,2.42,1.41,1.608,3.567,1.733,1.937,1.758,1.976,0.6,2.373,2.987,-0.238,2.367,2.527,-1.72,1.684,4.331,-0.148,0.486,4.43,-0.415     # Action input conctinues with 5 further SEGMENTn keywords, 
hhThe LOWEST action with label hh calculates the following quantities:
 Quantity   
 Type   
 Description  
hh
vector
the smallest element in the input vector if one vector specified.  If multiple vectors of the same size specified the largest elements of these vector computed elementwise.: LOWESTThis function can be used to find the lowest colvar by magnitude in a set. More details ARGthe values input to this function=hh_both.struct-1,hh_both.struct-2
hh_ltThe LESS_THAN action with label hh_lt calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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=hh 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}
hh_lessthanThe SUM action with label hh_lessthan calculates the following quantities:
 Quantity   
 Type   
 Description  
hh_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=hh_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=hh.lessthan FILEthe name of the file on which to output these quantities=colvar

YOUR CALCULATION WILL BE MUCH FASTER IF YOU USE THE STRANDS_CUTOFF KEYWORD. As you can see from the expanded version of the inputs above this keyword reduces the computational cost of the calculation by avoiding calculations of the RMSD values for segments that have the two strands of the beta sheet further apart than a cutoff.

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