Action: ANTIBETARMSD

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

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 antiparallel beta sheet content of your protein structure.

Two protein segments containing three contiguous residues can form an antiparallel beta sheet. Although if the two segments are part of the same protein chain they must be separated by a minimum of 2 residues to make room for the turn. This colvar thus generates the set of all possible six residue sections that could conceivably form an antiparallel beta sheet and calculates the DRMSD or RMSD distance between the configuration in which the residues find themselves and an idealized antiparallel 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 ideas from the paper cited below. The authors of this paper use the set of distances from the anti parallel beta sheet configurations to measure the number of segments that have an configuration that resembles an anti 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 antiparallel 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 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 configuration composed of pure anti-parallel beta sheets or the distance between the set of residues that is closest to an anti-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 antiparallel 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 somethingabThe ANTIBETARMSD action with label ab calculates the following quantities: Quantity    Type    Description  
ab scalar if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet: ANTIBETARMSDProbe the antiparallel 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
ab: ANTIBETARMSDProbe the antiparallel 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 Antiparallel 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:
# ab: ANTIBETARMSD 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):
ab_rmsdThe SECONDARY_STRUCTURE_RMSD action with label ab_rmsd calculates the following quantities: Quantity    Type    Description  
ab_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 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=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT5this 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 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102     # Action input conctinues with 10 further SEGMENTn keywords, 
ab_ltThe LESS_THAN action with label ab_lt calculates the following quantities: Quantity    Type    Description  
ab_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=ab_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}
abThe SUM action with label ab calculates the following quantities: Quantity    Type    Description  
ab 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=ab_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=ab 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 ANTIBETARMSD 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 antiparallel beta sheet.  If LESS_THAN is not present the number of residue segments where the structure is similar to an anti 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: ANTIBETARMSDProbe the antiparallel 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: ANTIBETARMSDProbe the antiparallel 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 Antiparallel beta sheets can either form in a single chain or from a pair of chains=all
# PLUMED interprets the command:
# hh: ANTIBETARMSD 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):
hhThe SECONDARY_STRUCTURE_RMSD action with label hh calculates the following quantities: Quantity    Type    Description  
hh 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 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=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 SEGMENT2this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44 SEGMENT3this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49 SEGMENT4this is the lists of atoms in the segment that are being considered=0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54 SEGMENT5this 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 STRUCTURE1the reference structure=2.263,-3.795,1.722,2.493,-2.426,2.263,3.847,-1.838,1.761,1.301,-1.517,1.921,0.852,-1.504,0.739,0.818,-0.738,2.917,-0.299,0.243,2.748,-1.421,-0.076,3.757,0.273,1.68,2.854,0.902,1.993,3.888,0.119,2.532,1.813,0.683,3.916,1.68,1.58,3.94,0.395,-0.394,5.011,1.63,-1.459,4.814,0.982,-2.962,3.559,-1.359,-2.439,2.526,-2.287,-1.189,3.006,-3.087,-2.081,1.231,-1.52,-1.524,1.324,-0.409,-2.326,0.037,-2.095,-1.858,-1.269,-1.554,-3.053,-2.199,-1.291,-0.869,-1.949,-2.512,-1.255,-2.07,-3.71,0.326,-2.363,-2.072,1.405,-2.992,-2.872,2.699,-2.129,-2.917,1.745,-4.399,-2.33,1.899,-4.545,-1.102     # Action input conctinues with 10 further SEGMENTn keywords, 
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

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
STYLE	compulsory	all	Antiparallel beta sheets can either form in a single chain or from a pair of chains
SERIAL	optional	false	do the calculation in serial
NOPBC	optional	false	ignore the periodic boundary conditions
STRANDS_CUTOFF	optional	not used	If 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
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

Keys	Action
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Quantity	Type	Description
ab	scalar	if LESS_THAN is present the RMSD distance between each residue and the ideal antiparallel beta sheet. If LESS_THAN is not present the number of residue segments where the structure is similar to an anti parallel beta sheet