Closed keith923 closed 9 years ago
Attachment from email follows.
Grid: 129 129 129
Coarse grid lenght: 96 96 96
Fine grid lenght: 57 57 57
Fine Grid spacing: 0.445
chgm: spl0
bc: mdh
ionic strength: 0 M
Grid: 129 129 129
Coarse grid lenght: 96 96 96
Fine grid lenght: 57 57 57
Fine Grid spacing: 0.445
srfm: mol
chgm: spl0
bc: mdh
ionic strength: 0.010 M
##########################################################################
### HCA/ACETAZOLAMIDE BINDING
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
##########################################################################
read
mol pqr acet.pqr # Read molecule 1
mol pqr hca.pqr # Read molecule 1
mol pqr complex.pqr # Read molecule 1
end
# ACETAZOLAMIDE POTENTIAL
elec name acet
mg-auto
dime 129 129 129
cglen 96.0 96.0 96.0
fglen 57 57 57
fgcent mol 2
cgcent mol 2
mol 1
lpbe
bcfl mdh
#ion charge 1 conc 0.000 radius 2.0
#ion charge -1 conc 0.000 radius 2.0
pdie 2.0
sdie 78.54
chgm spl0
srfm mol
srad 0.0
swin 0.3
sdens 10.0
temp 298.15
calcenergy total
calcforce no
end
# HCA POTENTIAL
elec name hca
mg-auto
dime 129 129 129
cglen 96.0 96.0 96.0
fglen 57 57 57
fgcent mol 2
cgcent mol 2
mol 2
lpbe
bcfl mdh
#ion charge 1 conc 0.000 radius 2.0
#ion charge -1 conc 0.000 radius 2.0
pdie 2.0
sdie 78.54
chgm spl0
srfm mol
srad 0.0
swin 0.3
sdens 10.0
temp 298.15
calcenergy total
calcforce no
end
# COMPLEX POTENTIAL
elec name complex
mg-auto
dime 129 129 129
cglen 96.0 96.0 96.0
fglen 57 57 57
fgcent mol 2
cgcent mol 2
mol 3
lpbe
bcfl mdh
#ion charge 1 conc 0.000 radius 2.0
#ion charge -1 conc 0.000 radius 2.0
pdie 2.0
sdie 78.54
chgm spl0
srfm mol
srad 0.0
swin 0.3
sdens 10.0
temp 298.15
calcenergy total
calcforce no
end
# CALCULATE BINDING ENERGY
print elecEnergy acet end
print elecEnergy hca end
print elecEnergy complex end
print elecEnergy complex - acet - hca end
quit
##########################################################################
### 1D7H/DMSO BINDING ENERGY
### $Id$
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
##########################################################################
read
mol pqr 1d7h-dmso-complex.pqr
mol pqr 1d7h-min.pqr
mol pqr dmso-min.pqr
end
# 1D7H -- SOLVATED STATE (FOCUSING)
elec name 1d7h
mg-auto
dime 129 129 129
cglen 96.0 96.0 96.0
fglen 57 57 57
fgcent mol 2
cgcent mol 2
mol 2
lpbe
bcfl mdh
ion charge 1 conc 0.010 radius 2.0
ion charge -1 conc 0.010 radius 2.0
pdie 2.0
sdie 78.0
srfm mol
chgm spl0
srad 0.0
swin 0.3
sdens 10.0
temp 300
calcenergy total
calcforce no
end
elec name dmso
mg-auto
dime 129 129 129
cglen 96.0 96.0 96.0
fglen 57 57 57
fgcent mol 2
cgcent mol 2
mol 3
lpbe
bcfl mdh
ion charge 1 conc 0.010 radius 2.0
ion charge -1 conc 0.010 radius 2.0
pdie 2.0
sdie 78.0
srfm mol
chgm spl0
srad 0.0
swin 0.3
sdens 10.0
temp 300
calcenergy total
calcforce no
end
elec name complex
mg-auto
dime 129 129 129
cglen 96.0 96.0 96.0
fglen 57 57 57
fgcent mol 2
cgcent mol 2
mol 1
lpbe
bcfl mdh
ion charge 1 conc 0.010 radius 2.0
ion charge -1 conc 0.010 radius 2.0
pdie 2.0
sdie 78.0
srfm mol
chgm spl0
srad 0.0
swin 0.3
sdens 10.0
temp 300
calcenergy total
calcforce no
end
quit
MAPBS acetazolamide
//acet_focus.inm
129 129 129
57.000000 57.000000 57.000000
0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000
focusname.inm
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
acet.pqr
hca.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox
1.000000 1.000000 1.000000 1.000000 1.000000
// focusname.inm
129 129 129
96.000000 96.000000 96.000000
0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000
mdh
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
acet.pqr
hca.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox
1.000000 1.000000 1.000000 1.000000 1.000000
MAPBS hca
//hca_bigbox.inm
129 129 129
57.000000 57.000000 57.000000
0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000
focusname.inm
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
hca.pqr
hca.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox
1.000000 1.000000 1.000000 1.000000 1.000000
//focusname.inm
129 129 129
96.000000 96.000000 96.000000
0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000
mdh
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
hca.pqr
hca.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox
1.000000 1.000000 1.000000 1.000000 1.000000
MAPBS hca-acetazolamide
//complex_bigbox2.inm
129 129 129
57.000000 57.000000 57.000000
0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000
focusname.inm
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
complex.pqr
hca.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox
1.000000 1.000000 1.000000 1.000000 1.000000
//focusname.inm
129 129 129
96.000000 96.000000 96.000000
0.000000 0.000000 78.540000 2.000000 298.150000 0.000000 10.000000 0.300000
mdh
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
complex.pqr
hca.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/hca_bigbox
1.000000 1.000000 1.000000 1.000000 1.000000
MAPBS 1d7h-dmso-complex
//1d7h-dmso-complex_bigbox
129 129 129
57.000000 57.000000 57.000000
0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000
focusname.inm
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
1d7h-dmso-complex.pqr
1d7h-min.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP
1.000000 1.000000 1.000000 1.000000 1.000000
// focusname.inm
129 129 129
96.000000 96.000000 96.000000
0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000
mdh
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
1d7h-dmso-complex.pqr
1d7h-min.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP
1.000000 1.000000 1.000000 1.000000 1.000000
MAPBS 1d7h
//1d7h.inm
129 129 129
57.000000 57.000000 57.000000
0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000
focusname.inm
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
1d7h-min.pqr
1d7h-min.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP
1.000000 1.000000 1.000000 1.000000 1.000000
//focusname.inm
129 129 129
96.000000 96.000000 96.000000
0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000
mdh
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
1d7h-min.pqr
1d7h-min.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP
1.000000 1.000000 1.000000 1.000000 1.000000
MAPBS dmso
//dmso.inm
129 129 129
57.000000 57.000000 57.000000
0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000
focusname.inm
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
dmso-min.pqr
1d7h-min.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP
1.000000 1.000000 1.000000 1.000000 1.000000
//focusname.inm
129 129 129
96.000000 96.000000 96.000000
0.010000 2.000000 78.000000 2.000000 300.000000 0.000000 10.000000 0.300000
mdh
6 biconjgrad
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
nouploadedfiles
dmso-min.pqr
1d7h-min.pqr
MOL
SPL0
calceneryes
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP/
/run/media/Guest/data2/Documents/Sandra/MAPBS/src/examples/Examples_APBS_MAPBS/FKBP
1.000000 1.000000 1.000000 1.000000 1.000000
Without having the results from MAPBS to compare results, the following could contribute to the observed differences mentioned in the email.
First, as mention in http://www.poissonboltzmann.org/docs/apbs-overview/#elec, for focusing calculations all of the boundary points should lie within the domain of the previous calculation for best accuracy. Focusing uses the previous calculations to come up with the new boundary conditions at the current level.Thus, any differences in previous calculations could change the following results.
Second, the email above mentioned running APBS without focusing. However, if run as in the attached elec's with mg-auto, the program will set the bcfl to focus for the finer levels which is where I think the variance could be accounted for. (nosh.c: line 2022)
Most focusing conditions, calculations, and settings are in the vpbe.c, routines.c, and vpmg.c files.
From a user: