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APBS - software for biomolecular electrostatics and solvation
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Investigate focus calculation #174

Closed keith923 closed 9 years ago

keith923 commented 10 years ago

From a user:

-----Original Message----- From: Marcelo Marucho [mailto:marcelo.marucho@utsa.edu] Sent: Wednesday, August 06, 2014 12:10 To: Baker, Nathan Subject: update focus calculation

Dear Nathan

I am sending you the comparison between APBS and MAPBS using focusing.

As far as all atoms in the system are inside the box (for both coarse and fine grids) we are obtaining a good comparison between APBS and MAPBS.

In the case in which some atoms of the system are outside the box (and even without using focusing), apbs is getting unusual large values for the solution of PB equation for the two systems we analyzed here. (I think this issue is generated by the multigrid approach implemented in apbs).

As far as testing focusing, I think the comparison between MAPBS and apbs looks OK.

I also realized that we were using the old version of "sdh" calculation where only a monopole was used to calculate the potential at the boundary condition. Now I included in MAPBS the multipole expansion for sdh including monopole, dipole and quadrupole contributions and it works perfect. We observed very small differences using both definitions for sdh in the examples we were testing and comparing apbs and MAPBS.

Please let me know your feedback.

Many thanks

Marcelo

keith923 commented 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
kozlac commented 9 years ago

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.