| iAPBS Interface: Users's Guide | ||
|---|---|---|
| Prev | Chapter 5. Examples | |
The following examples demonstrate how APBS functionality can be used from within CHARMM. Using CHARMM/APBS module is very similar to using the PBEQ module so examples provided for the PBEQ module can be easily adapted for CHARMM/APBS. The example files are located in CHARMM/examples in iAPBS distribution directory.
This example executes a solvation energy calculation and prints out total solvation energy for the given molecule.
* sp_elstat.inp
* external files: top_all22_prot.inp, par_all22_prot.inp and radius.str
*
!if ?apbs .ne. 1 then stop
stream datadir.def
open read card unit 11 name @0top_all22_prot.inp
read rtf card unit 11
close unit 11
open read card unit 11 name @0par_all22_prot.inp
read para card unit 11
close unit 11
... read in or generate structure
coor orient
scalar charge show
PBEQ
stream @0radius.str
set factor 0.939
set sw 0.4
scalar wmain add @sw
scalar wmain mult @factor
scalar wmain set 0.0 sele type H* end
scalar wmain show
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
srfm 2 debug 1 -
calcene 1 calcforce 1 sforce -
sele all END
END
skip all excl pbelec pbnp
ener
set elstatenergy = ?ENPB
stop
|
This examples shows how to use the CHARMM/APBS module for performing molecular dynamics simulation in implicit solvent with APBS.
* md.inp
* external files: top_all22_prot.inp, par_all22_prot.inp and radius.str
*
if ?apbs .ne. 1 then stop
stream datadir.def
open read card unit 11 name @0top_all22_prot.inp
read rtf card unit 11
close unit 11
open read card unit 11 name @0par_all22_prot.inp
read para card unit 11
close unit 11
... read in or generate structure
coor orient
PBEQ
set factor 0.939
set sw 0.4
stream @0radius.str
scalar wmain add @sw
scalar wmain mult @factor
scalar wmain set 0.0 sele type H* end
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
swin @sw srfm 2 -
calcene 1 calcfor 1 -
sforce update 2 -
sele all END
END
skip none
dynamics leap verlet strt nstep 150 timestep 0.001 -
firstt 100.0 finalt 300.0 teminc 100.0 -
twindh 10.0
stop
|
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.
* visualization.inp
* external files: top_all22_prot.inp, par_all22_prot.inp and radius.str
*
!if ?apbs .ne. 1 then stop
stream datadir.def
open read card unit 11 name @0top_all22_prot.inp
read rtf card unit 11
close unit 11
open read card unit 11 name @0par_all22_prot.inp
read para card unit 11
close unit 11
... read in or generate structure
coor orient
PBEQ
stream @0radius.str
set factor 0.939
set sw 0.4
scalar wmain add @sw
scalar wmain mult @factor
scalar wmain set 0.0 sele type H* end
scalar wmain show
APBS mgauto lpbe dimx 65 dimy 65 dimz 65 -
cglx 30 cgly 30 cglz 30 fglx 15 fgly 15 fglz 15 -
calcene 1 calcforce 0 -
ionq1 1.0 ionc1 0.15 ionr1 2.0 ionq2 -1.0 ionc2 0.15 ionr2 2.0 -
wpot wsmol wchg -
debug 1 -
sele all END
END
set elstatenergy = ?ENPB
stop
|