Mon Oct 10 14:11:29 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:11:30 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7011601 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -19.30700 23.05100 ymin,ymax (A): -16.14100 24.38700 zmin,zma (A): 4.222000 54.99500 x,y,z range (A): 42.35800 40.52800 50.77300 scale (grids/A): 0.7011601 object centre (A): 1.872000 4.123000 29.60850 number of atom coordinates read : 1874 total number of charged atoms : 1743 net assigned charge : -0.9999900 assigned positive charge : 272.3783 centred at (gu) : 89.78199 88.47794 88.52411 assigned negative charge : -273.3782 centred at (gu) : 89.83349 88.62009 88.52819 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6250 nv = 96 ne = 84 npr = 39162 no. pairs analyzed = 39162 no. exposed pairs = 2228 no. arc points = 16129 no. surface atoms = 741 nbur = 1133 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3551 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 162 time to turn everything in is 0.2400000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1431 ## 113 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7858689E-09 -7.3160860E-09 midg,1,midg; midg,igrid,midg 6.0571566E-08 -4.5995399E-08 1,midg,midg; igrid,midg,midg 1.1543266E-08 -2.6395234E-08 gauss-seidel spectral radius is 0.9893821 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 14:11:30 rms-change max change #iterations 0.1824507 26.03857 at 10iterations 2.1890689E-02 3.853802 at 20iterations 2.6814525E-03 0.3700740 at 30iterations 3.2601945E-04 4.3680906E-02 at 40iterations 3.8670525E-05 6.1035156E-03 at 50iterations finished qdiffx linear iterations at : 14:11:34 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 3.8670525E-05 6.1035156E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 14:11:35 4.418u 0.382s 0:05.30 90.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:11:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.103480 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -19.30700 23.05100 ymin,ymax (A): -16.14100 24.38700 zmin,zma (A): 4.222000 54.99500 x,y,z range (A): 42.35800 40.52800 50.77300 scale (grids/A): 2.103480 object centre (A): 1.872000 4.123000 29.60850 number of atom coordinates read : 1874 total number of charged atoms : 1743 net assigned charge : -0.9999900 assigned positive charge : 272.3783 centred at (gu) : 89.34618 85.43385 85.57251 assigned negative charge : -273.3782 centred at (gu) : 89.50060 85.86029 85.58464 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16129 grid for indexing accessible points = 1.400000 m= 25038 mr = 46667 m= 4643 mr = 18634 m= 484 mr = 3062 m= 14 mr = 193 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4323 time to turn everything in is 0.5500000 number of dielectric boundary points 27974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 13831 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.7011601 object centre at (A) : 1.872000 4.123000 29.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7748415E-02 -1.8144328E-02 midg,1,midg; midg,igrid,midg 1.3880868E-03 -8.9923767E-03 1,midg,midg; igrid,midg,midg 1.2971939E-02 -4.4107609E-03 gauss-seidel spectral radius is 0.9987948 estimated iterations to convergence 228 setup time was (sec) 0.8300000 now iterating at: 14:11:36 rms-change max change #iterations 4.248576 230.8052 at 10iterations 2.069888 79.83188 at 20iterations 1.016074 36.20935 at 30iterations 0.4986662 15.47593 at 40iterations 0.2450446 8.925900 at 50iterations 0.1197185 3.854864 at 60iterations 5.8697164E-02 1.983263 at 70iterations 2.8772211E-02 0.9219946 at 80iterations 1.4151565E-02 0.4200306 at 90iterations 6.9116289E-03 0.2162528 at 100iterations 3.3928475E-03 0.1017971 at 110iterations 1.6651206E-03 5.8067322E-02 at 120iterations finished qdiffx linear iterations at : 14:11:46 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 1.6651206E-03 5.8067322E-02 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 14:11:47 10.640u 0.456s 0:11.80 93.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:11:47 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 221 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.155220 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -19.30700 23.05100 ymin,ymax (A): -16.14100 24.38700 zmin,zma (A): 4.222000 54.99500 x,y,z range (A): 42.35800 40.52800 50.77300 scale (grids/A): 3.155220 object centre (A): 1.872000 4.123000 29.60850 number of atom coordinates read : 1874 total number of charged atoms : 1743 net assigned charge : -0.9999900 assigned positive charge : 272.3783 centred at (gu) : 89.01922 83.15092 83.35885 assigned negative charge : -273.3782 centred at (gu) : 89.25089 83.79047 83.37699 start vw surface at 0.1000000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 153371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16129 grid for indexing accessible points = 1.400000 m= 78763 mr = 112594 m= 30663 mr = 65074 m= 8765 mr = 24821 m= 1802 mr = 6724 m= 182 mr = 1234 m= 6 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 15138 time to turn everything in is 1.720000 number of dielectric boundary points 63033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 4.380000 number of grid points assigned charge 13944 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.103480 object centre at (A) : 1.872000 4.123000 29.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2393684 -0.1192625 midg,1,midg; midg,igrid,midg 2.0759902E-03 -0.1156251 1,midg,midg; igrid,midg,midg 9.2741802E-02 -2.1645930E-02 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 4.620000 now iterating at: 14:11:52 rms-change max change #iterations 9.392319 470.1835 at 10iterations 5.411979 122.5009 at 20iterations 3.133354 71.71329 at 30iterations 1.814119 35.09491 at 40iterations 1.047714 19.13192 at 50iterations 0.6068370 11.45681 at 60iterations 0.3506736 6.966864 at 70iterations 0.2029280 3.988564 at 80iterations 0.1170290 2.248703 at 90iterations 6.7754321E-02 1.149790 at 100iterations 3.9115991E-02 0.7171631 at 110iterations 2.2615144E-02 0.4216728 at 120iterations 1.3110665E-02 0.2517996 at 130iterations 7.5653736E-03 0.1308125 at 140iterations 4.3679634E-03 8.0311574E-02 at 150iterations 2.5278444E-03 4.5158386E-02 at 160iterations 1.4622242E-03 2.9003143E-02 at 170iterations 8.4602734E-04 1.5247345E-02 at 180iterations finished qdiffx linear iterations at : 14:12:08 total time elapsed so far: 20.62000 # loops : 180 mean,max change (kT/e) : 8.4602734E-04 1.5247345E-02 energy calculations done at 20.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.78000 DelPhi exited at 14:12:08 20.787u 0.467s 0:21.72 97.7% 0+0k 0+0io 0pf+0w