The APBS module is initialized with keyword apbsForces. The APBS calculation set up is specified in apbsForcesConfig section. Please note that charges and radii definition for the electrostatic calculation must be read from a PQR file. See APBS documentation for PQR file format and description. APBS distribution also contains tools for generating valid PQR files (from a PDB file, for example). The order of atoms in the PQR file must be the same as in teh associated .top file. For list of APBS-related keywords see NAMD/APBS keywords table.
This is an example of single point solvation energy calculation. The electrostatic calculation is done on 0.5³ A numerical grid. The external charges and radii are read from dipeptide.pqr file. The final solvation energy is printed in the 'MISC" energy column (as a sum of electrostatic and non-polar energies).
amber on
parmfile dipeptide.top
ambercoor dipeptide.crd
temperature 300
exclude scaled1-4
1-4scaling 0.8333333
switching on
switchDist 9
cutoff 10
pairListDist 11
outputname output
outputEnergies 1
outputTiming 100
dcdFreq 500
restartFreq 500
wrapWater on
wrapNearest on
langevin on
langevinDamping 2
langevinHydrogen no
langevinTemp 300
apbsForces on
apbsPQRFile dipeptide.pqr
apbsForcesConfig {
calc_type 0 # mg-manual
grid 0.5 0.5 0.5
recalculateGrid on
srfm 2
chgm 1
bcfl 1
debug 1
verbose 5
pdie 2.0000
sdie 78.5400
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
gamma 0.105
sp_apbs off
wpot off
}
minimize 0 |
This calculation performs a MD simulation in implicit solvent (water in this case). The charges and radii definition is read from an external file (dipeptide.pqr) and the electrostatic calculation is done on 33³ points of numerical grid with the grid dimensions specified in the input file.
amber on
parmfile dipeptide.top
ambercoor dipeptide.crd
temperature 300
exclude scaled1-4
1-4scaling 0.8333333
switching on
switchDist 9
cutoff 10
pairListDist 11
outputname output
outputEnergies 1
outputTiming 100
dcdFreq 500
restartFreq 500
wrapWater on
wrapNearest on
langevin off
langevinDamping 2
langevinHydrogen no
langevinTemp 300
apbsForces on
apbsPQRFile dipeptide.pqr
apbsForcesConfig {
dime 33 33 33
cglen 17.0071 13.8706 12.3012
fglen 17.0071 13.8706 12.3012
srfm 2
chgm 1
bcfl 1
debug 0
pdie 2.0000
sdie 78.5400
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
gamma 0.105
sp_apbs off
wpot off
}
numsteps 100 |
This calculation writes out the calculated electrostatic potential to a file (iapbs-pot.dx). This potential can be visualized using vmd and pymol. The rid dimensions are 1.0³ A.
amber on
parmfile dipeptide.top
ambercoor dipeptide.crd
temperature 300
exclude scaled1-4
1-4scaling 0.8333333
switching on
switchDist 9
cutoff 10
pairListDist 11
outputname output
outputEnergies 1
outputTiming 100
dcdFreq 500
restartFreq 500
wrapWater on
wrapNearest on
langevin on
langevinDamping 2
langevinHydrogen no
langevinTemp 300
apbsForces on
apbsPQRFile dipeptide.pqr
apbsForcesConfig {
dime 0 0 0
grid 1.0 1.0 1.0
srfm 2
chgm 1
bcfl 1
debug 0
verbose 2
pdie 2.0000
sdie 78.5400
sdens 10.00
srad 1.40
swin 0.30
temp 298.15
gamma 0.105
sp_apbs on
wpot on
}
minimize 0 |