Sun Oct 9 08:34:20 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 Sun Oct 9 2011 at 08:34:20 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6255 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4559134 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): -2.624000 75.46100 ymin,ymax (A): -27.58200 36.71800 zmin,zma (A): 28.12400 92.79900 x,y,z range (A): 78.08500 64.30000 64.67500 scale (grids/A): 0.4559134 object centre (A): 36.41850 4.568002 60.46150 number of atom coordinates read : 6255 total number of charged atoms : 6084 net assigned charge : -3.985961 assigned positive charge : 948.1676 centred at (gu) : 89.56028 90.18404 90.85655 assigned negative charge : -952.1617 centred at (gu) : 89.50089 90.16805 90.94003 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7830 nv = 96 ne = 84 npr = 126680 no. pairs analyzed = 126680 no. exposed pairs = 7655 no. arc points = 53021 no. surface atoms = 2574 nbur = 3681 mkacc time = 0.2700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 192 mr = 3913 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4785 ## 941 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 10768 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3459570E-11 -3.1910599E-11 midg,1,midg; midg,igrid,midg -7.0790413E-12 6.4011876E-13 1,midg,midg; igrid,midg,midg -2.1111659E-11 1.0012141E-11 gauss-seidel spectral radius is 0.9755321 estimated iterations to convergence 53 setup time was (sec) 0.8200000 now iterating at: 08:34:21 rms-change max change #iterations 4.3191459E-02 6.097733 at 10iterations 2.4285552E-03 0.5035324 at 20iterations 4.5249221E-04 0.1183510 at 30iterations 1.2278496E-04 3.0540466E-02 at 40iterations 3.5110155E-05 8.2435608E-03 at 50iterations finished qdiffx linear iterations at : 08:34:24 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 3.5110155E-05 8.2435608E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 08:34:25 3.681u 0.232s 0:04.30 90.9% 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 Sun Oct 9 2011 at 08:34:25 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6255 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.367740 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): -2.624000 75.46100 ymin,ymax (A): -27.58200 36.71800 zmin,zma (A): 28.12400 92.79900 x,y,z range (A): 78.08500 64.30000 64.67500 scale (grids/A): 1.367740 object centre (A): 36.41850 4.568002 60.46150 number of atom coordinates read : 6255 total number of charged atoms : 6084 net assigned charge : -3.985961 assigned positive charge : 948.1676 centred at (gu) : 88.67912 90.54993 92.56774 assigned negative charge : -952.1617 centred at (gu) : 88.50220 90.50378 92.81923 start vw surface at 0.2400000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90859 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53021 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 22343 mr = 61784 m= 1284 mr = 13710 m= 17 mr = 357 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.6800000 number of dielectric boundary points 38652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 921 ## 29 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 43497 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) : 0.4559134 object centre at (A) : 36.41850 4.568002 60.46150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3848377E-03 -3.1120123E-03 midg,1,midg; midg,igrid,midg -1.9602634E-03 -1.4184430E-03 1,midg,midg; igrid,midg,midg -5.4277931E-03 1.6162530E-04 gauss-seidel spectral radius is 0.9976947 estimated iterations to convergence 166 setup time was (sec) 0.9800000 now iterating at: 08:34:26 rms-change max change #iterations 3.395877 143.7355 at 10iterations 1.262775 43.32538 at 20iterations 0.4730566 14.94575 at 30iterations 0.1770567 6.557042 at 40iterations 6.6377483E-02 2.151046 at 50iterations 2.4923010E-02 0.8839221 at 60iterations 9.4689922E-03 0.3295790 at 70iterations 3.6323180E-03 0.1303177 at 80iterations 1.4582265E-03 5.3989410E-02 at 90iterations 6.3700677E-04 2.6817322E-02 at 100iterations 3.1018152E-04 1.4114380E-02 at 110iterations 1.7143952E-04 7.6141357E-03 at 120iterations finished qdiffx linear iterations at : 08:34:33 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.7143952E-04 7.6141357E-03 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 08:34:33 7.738u 0.226s 0:08.25 96.3% 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 Sun Oct 9 2011 at 08:34:33 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6255 !!! WARNING: HIR 1428 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.051610 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): -2.624000 75.46100 ymin,ymax (A): -27.58200 36.71800 zmin,zma (A): 28.12400 92.79900 x,y,z range (A): 78.08500 64.30000 64.67500 scale (grids/A): 2.051610 object centre (A): 36.41850 4.568002 60.46150 number of atom coordinates read : 6255 total number of charged atoms : 6084 net assigned charge : -3.985961 assigned positive charge : 948.1676 centred at (gu) : 88.01819 90.82461 93.85104 assigned negative charge : -952.1617 centred at (gu) : 87.75327 90.75550 94.22874 start vw surface at 0.2600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 212650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53021 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 85469 mr = 152810 m= 16520 mr = 64292 m= 1437 mr = 10965 m= 35 mr = 644 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 825 time to turn everything in is 1.550000 number of dielectric boundary points 87400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 48256 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) : 1.367740 object centre at (A) : 36.41850 4.568002 60.46150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1170949 -6.9559790E-02 midg,1,midg; midg,igrid,midg -3.4276307E-02 -3.8294952E-02 1,midg,midg; igrid,midg,midg -5.1319203E-03 -0.1598076 gauss-seidel spectral radius is 0.9990672 estimated iterations to convergence 259 setup time was (sec) 1.880000 now iterating at: 08:34:35 rms-change max change #iterations 9.927444 273.4580 at 10iterations 5.549052 137.1341 at 20iterations 3.073551 76.38557 at 30iterations 1.691247 38.64143 at 40iterations 0.9279995 23.67919 at 50iterations 0.5078373 10.51414 at 60iterations 0.2772838 5.307261 at 70iterations 0.1508671 3.140432 at 80iterations 8.2044512E-02 1.660652 at 90iterations 4.4547118E-02 0.8259773 at 100iterations 2.4120834E-02 0.5492563 at 110iterations 1.3057010E-02 0.2594347 at 120iterations 7.0704855E-03 0.1423388 at 130iterations 3.8264331E-03 7.1982384E-02 at 140iterations 2.0691939E-03 3.8448334E-02 at 150iterations 1.1235446E-03 2.2964478E-02 at 160iterations 6.0960016E-04 1.3123751E-02 at 170iterations 3.3259048E-04 6.4096451E-03 at 180iterations finished qdiffx linear iterations at : 08:34:46 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 3.3259048E-04 6.4096451E-03 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 08:34:46 12.825u 0.242s 0:13.33 97.9% 0+0k 0+0io 0pf+0w