UHBD protocol

setting the grid

The right size of the grid for UHBD calculations was determined by superposition of sample structures of the relevant serine proteases and align them to 1o5a. Used sample structures:

uPA	1lmw
thrombin	1a2c
factor Xa	1fax
trypsin	2ptn
plasmin	1bui
tPA	1a5h

final UHBD input files:

desolv1_35.inp
desolv2_35.inp

best compiled UHBD version: /sw/mcm/app/uhbd/uhbd_linux_pp/uhbd110_PGFathlon

uhbd

read mol 1 file protein.qcd qcard end
read mol 2 file ligand.qcd qcard end

write grid binary file focus_bin.grd end

Comparing different grid sizes

desolv1_110.inp
Main stop
UHBD termination
date/time : 14-Oct-05 19:07:13
total CPU seconds : 522.760
total usr/sys CPU seconds : 516.290/ 6.470

desolv1_35.inp
large:
elec calc mol 1
pdie 2.00 ! internal dielectric=2
sdie 78.00 ! solvent dielectric=78
temp 298.00 ! temperature in K
ions 150.00 ! ionic strength
rion 1.5 ! ionic radius
nmap 1.4 ! use probe-accessible surface
nsph 400 ! use 400 sphere points for surface cal.
bcfl 2 ! boundary condition - each atom
! is a Debye-Huckel sphere
efld .00 ! external electric field
grid 1.00 ! grid spacing
dime 65 81 71 ! grid dimension
gcenter 15.0 -2.0 15.0
maxit 400 ! maximum # of iteration for FDPBE
end

print elec phizero mol1 end ! zero out the phisite accumulator
print elec phisave mol1 end ! compute and store phi at atoms on grid

focus:
elec calc mol 1
pdie 2.00 ! internal dielectric=2
sdie 78.00 ! solvent dielectric=78
temp 298.00 ! temperature in K
ions 150.00 ! ionic strength
rion 1.5 ! ionic radius
nmap 1.4 ! use probe-accessible surface
nsph 400 ! use 400 sphere points for surface cal.
bcfl 4 ! focusing - use the coarse grid to
! set the boundary potential of this
! focused grid.
efld .00 ! external electric field
grid 0.25 ! spacing for focused grid
dime 109 109 109 ! grid dimension
gcenter 9.0 5.0 26.0
maxit 400 ! maximum # of iteration for FDPBE
end

print elec phisave mol1 end
print elec phinrg mol1 end ! compute and save to a user variable the

date/time : 17-Nov-05 13:48:13
UHBD termination
date/time : 17-Nov-05 13:59:58
total CPU seconds : 293.030
total usr/sys CPU seconds : 290.080/ 2.950

UHBD=/sw/mcm/app/uhbd/uhbd-6.1.expMSI_linux/bin.linux/uhbd_110_100000_65_wang

priamos
grid 109, 133.020
grid 100, 110.150
grid 109, !nmap !nsph, 133.370
grid 109, !nmap !nsph,ions=50, 136.470

epimetheus
grid 109, 142.830

prepare uhbd
uhbd

/sw/mcm/app/uhbd/uhbd_linux_pp/uhbd110_PGFathlon
step1.inp
read mol 1 file A20.3.protein.qcd qcard end
read mol 2 file A20.3.ligand.qcd qcard end
! read in the coords., charges, and radii in CHARMM qcard
! format
!step 1
! Regular Runs:
! compute the potential on a coarse grid for
! molecule 1
elec calc mol 1
pdie 2.00 ! internal dielectric=2
sdie 78.00 ! solvent dielectric=78
temp 298.00 ! temperature in K
ions 150.00 ! ionic strength
rion 1.5 ! ionic radius
bcfl 2 ! boundary condition - each atom
! is a Debye-Huckel sphere
efld .00 ! external electric field
grid 1.00 ! grid spacing
dime 81 81 81 ! grid dimension
gcenter 9.0 5.0 26.0 !11
maxit 400 ! maximum # of iteration for FDPBE
end
print elec phizero mol1 end ! zero out the phisite accumulator
print elec phisave mol1 end ! compute and store phi at atoms on grid
! compute the potential on a fine grid
! molecule 1 using the coarse grid to set the
! boundary potentials for this grid.
elec calc mol 1
pdie 2.00 ! internal dielectric=2
sdie 78.00 ! solvent dielectric=78
temp 298.00 ! temperature in K
ions 150.00 ! ionic strength
rion 1.5 ! ionic radius
bcfl 4 ! focusing - use the coarse grid to
efld .00 ! external electric field
grid 0.25 ! spacing for focused grid
dime 109 109 109 ! grid dimension
gcenter 9.0 5.0 26.0 !11
maxit 400 ! maximum # of iteration for FDPBE
end
print elec phisave mol1 end
print elec phinrg mol1 end ! compute and save to a user variable the
! phi energy
assign e1 = $phinrg end ! assign the phi energy to a local variable
! for later use
stop

priamos 95.960
epimetheus 67.980

/sw/mcm/app/uhbd/bin.linux/uhbd_110_100000_65_65_fast
step1.inp

calc_inter_model.sh
/sw/mcm/app/uhbd/uhbd_linux_pp/uhbd110_PGFathlon
step1-3: 269.010
step4: 266.230

Visualization of the grid in PyMol

pymol

converting grid:
/sw/mcm/app/vmd/aux/grid2i
grid2i B grid_uhbd.grd A grid_i.grd

draw x,y,z axis at origin
axes_cyl.py Draw X, Y, and Z reference axes as CGO cylinders, colored red, green and blue, respectively

load grid.grd, grid
isomesh msh, grid ,1.0,(model5),0.0,0

Loading binary UHBD grid, which was converted by grid2i had wrong grid spacing and a shift in the position!

Visualization of the grid in chimera

chimera

prepare chimera
prepare chimera_121
chimera_send

Chimera was used for visualzation of the grids and electrostatic potentials.

example grids:
/home/henricsn/combine2go/data/urokinase/prep-anal/model/model5_xray_medium/anal/
focus_109.grd large_81.grd

large grid (grid points 81, 81, 81; 1 A)
focus grid (grid points 109, 109, 109; 0.25 A)
surface of urokinase with benzamidine: blue=4, red=-4

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