Action: SASA_LCPO

Module	sasa
Description	Usage
Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it.
output value	type
the solvent accessible surface area (SASA) of the molecule	scalar

Details and examples

Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it.

The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The LCPO algorithm is used for the calculation (please, read and cite the first paper cited below). The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of the SASA is updated (the default is every 10 steps).

Different properties can be calculated and selected using the TYPE keyword:

1) the total SASA (TOTAL);

2) the free energy of transfer for the protein according to the transfer model (TRANSFER). This keyword can be used, for instance, to compute the transfer of a protein to different temperatures, as detailed in the second paper cited below, or to different pressures, as detailed in the fourth paper cited below, or to different osmolyte solutions, as detailed in the third paper cited below.

When the TRANSFER keyword is used, a file with the free energy of transfer values for the sidechains and backbone atoms should be provided (using the keyword DELTAGFILE). Such file should have the following format:

\verbatim ----------------Sample DeltaG.dat file--------------------- ALA 0.711019999999962 ARG -2.24832799999996 ASN -2.74838799999999 ASP -2.5626376 CYS 3.89864000000006 GLN -1.76192 GLU -2.38664400000002 GLY 0 HIS -3.58152799999999 ILE 2.42634399999986 LEU 1.77233599999988 LYS -1.92576400000002 MET -0.262827999999956 PHE 1.62028800000007 PRO -2.15598800000001 SER -1.60934800000004 THR -0.591559999999987 TRP 1.22936000000027 TYR 0.775547999999958 VAL 2.12779200000011 BACKBONE 1.00066920000002

\endverbatim

where the second column is the free energy of transfer for each sidechain/backbone, in kJ/mol.

A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure (according to the second, third and fourth papers cited below) is freely available here. The script automatically outputs a DeltaG.dat file compatible with this SASA module.

If the DELTAGFILE is not provided, the program computes the free energy of transfer values as if they had to take into account the effect of temperature according to approaches 2 or 3 in the paper the second paper cited below. Please read and cite this paper if using the transfer model for computing the effect of temperature in implicit solvent simulations. For this purpose, the keyword APPROACH should be added, and set to either 2 or 3.

The SASA usually makes sense when atoms used for the calculation are all part of the same molecule. When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.2, by rebuilding the broken entities 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.

The SASA may also be computed using the SASA_HASEL collective variable, which makes use of the algorithm described in the third paper cited below. SASA_HASEL is less accurate then SASA_LCPO, but the computation is faster.

Examples

The following input tells plumed to print the total SASA for atoms 10 to 20 in a protein chain.

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

SASA_LCPOCalculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. More details TYPE The type of calculation you want to perform=TOTAL ATOMSthe group of atoms that you are calculating the SASA for=10-20 NL_STRIDEThe frequency with which the neighbor list is updated=10 LABELa label for the action so that its output can be referenced in the input to other actions=sasaThe SASA_LCPO action with label sasa calculates the following quantities: Quantity    Type    Description  
sasa scalar the solvent accessible surface area (SASA) of the molecule
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sasa STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar

The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are read from a file called DeltaG.dat.

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

SASA_LCPOCalculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. More details TYPE The type of calculation you want to perform=TRANSFER ATOMSthe group of atoms that you are calculating the SASA for=10-20 NL_STRIDEThe frequency with which the neighbor list is updated=10 DELTAGFILEa file containing the free energy values for backbone and sidechains=DeltaG.dat LABELa label for the action so that its output can be referenced in the input to other actions=sasaThe SASA_LCPO action with label sasa calculates the following quantities: Quantity    Type    Description  
sasa scalar the solvent accessible surface area (SASA) of the molecule

biasThe BIASVALUE action with label bias calculates the following quantities: Quantity    Type    Description  
bias.bias scalar the instantaneous value of the bias potential
bias.sasa_bias scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named sasa: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=sasa

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sasa,bias.* STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar

The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are computed according to the second paper cited blow, and take into account the effect of temperature using approach 2 as described in the paper.

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

SASA_LCPOCalculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. More details TYPE The type of calculation you want to perform=TRANSFER ATOMSthe group of atoms that you are calculating the SASA for=10-20 NL_STRIDEThe frequency with which the neighbor list is updated=10 APPROACHeither approach 2 or 3=2 LABELa label for the action so that its output can be referenced in the input to other actions=sasaThe SASA_LCPO action with label sasa calculates the following quantities: Quantity    Type    Description  
sasa scalar the solvent accessible surface area (SASA) of the molecule

biasThe BIASVALUE action with label bias calculates the following quantities: Quantity    Type    Description  
bias.bias scalar the instantaneous value of the bias potential
bias.sasa_bias scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named sasa: BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=sasa

PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=sasa,bias.* STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=colvar

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
ATOMS	atoms	the group of atoms that you are calculating the SASA for

Full list of keywords

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

Keyword	Type	Default	Description
ATOMS	input	none	the group of atoms that you are calculating the SASA for
TYPE	compulsory	TOTAL	The type of calculation you want to perform
NL_STRIDE	compulsory	none	The frequency with which the neighbor list is updated
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
DELTAGFILE	optional	not used	a file containing the free energy values for backbone and sidechains
APPROACH	optional	not used	either approach 2 or 3

References

More information about how this action can be used is available in the following articles:

Quantity	Type	Description
sasa	scalar	the solvent accessible surface area (SASA) of the molecule