The APBS module is initialized when &apbs keyword is encountered in the input file. Also, igb must be set to 6 in the &cntrl section. The &apbs keyword can be then followed by additional apbs keywords, for details see Amber/APBS keywords.
This example executes a solvation energy calculation and prints out total solvation energy for the given molecule (in energy terms EPB and ENPOLAR for polar and non-polar solvation terms, respectively).
iAPBS solvation energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_print=1
grid=0.5, 0.5, 0.5,
calc_type=0, cmeth=1,
bcfl=2, srfm=1, chgm=1,
pdie=1.0, sdie=78.54,
srad = 1.4,
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
radiopt = 3, pqr = 'my.pqr',
calcforce=0, calcnpenergy=1,
&end
|
This example executes a single point electrostatic energy calculation and prints out the calculated energy (in energy terms EPB and ENPOLAR for polar and non-polar terms, respectively).
APBS electrostatic energy example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0,
ntpr=1,
/
&apbs
apbs_print=1
grid = 0.1, 0.5, 0.5,
calc_type=0, cmeth=1,
sp_apbs=.true.,
&end
|
This examples shows how to use the Amber/APBS module for carrying out a molecular dynamics simulation in implicit solvent with APBS.
Example of APBS implicit solvent dynamics
&cntrl
ntx=1, irest=0, imin=0,
ntpr=10, ntwx=500, nscm=100, ntwr=5000,
dt=0.001, nstlim=50,
temp0=300, tempi=0, ntt=1, tautp=0.1,
igb=6, cut=12.0, ntb=0,
ntc=2, ntf=2, tol=0.000001
/
&apbs
apbs_print=0,
grid = 0.5, 0.5, 0.5,
calc_type=0,
cmeth=1,
bcfl=2, srfm=2, chgm=1,
pdie=2.0, sdie=78.54,
radiopt=2, pqr='my.pqr',
calcforce=2, calcnpenergy=1,
nion=2,
ionq = 1.0, -1.0,
ionc = 0.15, 0.15,
ionrr = 2.0, 2.0,
&end
|
When this input file is run three DX files will be created. These can be visualized using several applications (for details please see APBS visualization guide). The DX files will be iapbs-pot.dx, iapbs-smol.dx and iapbs-charge.dx which will contain electrostatic potential, solvent accessible surface and charge information, respectively.
APBS visualization example
&cntrl
maxcyc=0, imin=1,
cut=12.0,
igb=6, ntb=0
ntpr=1,
/
&apbs
apbs_print=1,
grid= 0.5, 0.5, 0.5,
calc_type = 0,
srad = 0.7,
wpot = 1, wchg = 1, wsmol =1,
sp_apbs=.true.,
&end
|
To determine the correct size of the numerical grid enveloping the studied molecule (parameters cglen and fglen) you can use psize.py tool from the APBS distribution.
Parameter sp_apbs=.true. triggers only a single APBS calculation (SP, single point energy). The calculated electrostatic energy contains self-energy terms thus it is not very useful by itself. This is however useful when, for instance, generating DX files for visualization. If the parameter sp_apbs is omitted (or set to .false., which is the default) then two APBS calculations (one for a system in solvent and then in vacuum) are performed every time solvation energy and forces are recalculated. This is used during minimization and MD simulations.