Mon Oct 10 18:53:04 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 18:53:05 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 !!! WARNING: SEP 31 has a net charge of -0.4750 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 249 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5753257 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): 40.13600 95.35600 ymin,ymax (A): -71.04500 -9.167001 zmin,zma (A): 68.03500 112.7040 x,y,z range (A): 55.22001 61.87800 44.66900 scale (grids/A): 0.5753257 object centre (A): 67.74600 -40.10600 90.36949 number of atom coordinates read : 2572 total number of charged atoms : 2430 net assigned charge : 5.3008214E-02 assigned positive charge : 394.7124 centred at (gu) : 89.71805 91.82152 90.48771 assigned negative charge : -394.6604 centred at (gu) : 89.77016 91.71427 90.62183 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 50742 no. pairs analyzed = 50742 no. exposed pairs = 3316 no. arc points = 23072 no. surface atoms = 1105 nbur = 1467 mkacc time = 0.1300000 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 = 1.484000 m= 289 mr = 2998 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2341 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7165 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9438917E-09 -2.5705755E-09 midg,1,midg; midg,igrid,midg -1.1830786E-09 2.7220921E-09 1,midg,midg; igrid,midg,midg 9.0774510E-10 -8.2991197E-10 gauss-seidel spectral radius is 0.9843746 estimated iterations to convergence 66 setup time was (sec) 0.5900000 now iterating at: 18:53:05 rms-change max change #iterations 9.0164527E-02 15.80452 at 10iterations 7.0584929E-03 1.108223 at 20iterations 7.3506439E-04 0.1226449 at 30iterations 1.5106918E-04 2.5950432E-02 at 40iterations 4.2476579E-05 7.1430206E-03 at 50iterations finished qdiffx linear iterations at : 18:53:09 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 4.2476579E-05 7.1430206E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 18:53:10 4.564u 0.386s 0:05.24 94.2% 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 18:53:10 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 !!! WARNING: SEP 31 has a net charge of -0.4750 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 249 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.725977 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): 40.13600 95.35600 ymin,ymax (A): -71.04500 -9.167001 zmin,zma (A): 68.03500 112.7040 x,y,z range (A): 55.22001 61.87800 44.66900 scale (grids/A): 1.725977 object centre (A): 67.74600 -40.10600 90.36949 number of atom coordinates read : 2572 total number of charged atoms : 2430 net assigned charge : 5.3008214E-02 assigned positive charge : 394.7124 centred at (gu) : 89.15343 95.46391 91.46247 assigned negative charge : -394.6604 centred at (gu) : 89.31026 95.14253 91.86518 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61667 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23072 grid for indexing accessible points = 1.400000 m= 20940 mr = 42182 m= 2725 mr = 15021 m= 104 mr = 1490 m= 0 mr = 17 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 554 time to turn everything in is 0.5500000 number of dielectric boundary points 26726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18822 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) : 0.5753257 object centre at (A) : 67.74600 -40.10600 90.36949 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4320968E-03 -6.5906607E-03 midg,1,midg; midg,igrid,midg -1.0559293E-02 1.4196973E-02 1,midg,midg; igrid,midg,midg 2.0443119E-02 -6.2621771E-03 gauss-seidel spectral radius is 0.9983380 estimated iterations to convergence 195 setup time was (sec) 0.8300000 now iterating at: 18:53:11 rms-change max change #iterations 3.521268 184.2707 at 10iterations 1.512990 62.74240 at 20iterations 0.6530514 23.97789 at 30iterations 0.2842194 10.87894 at 40iterations 0.1224983 4.617470 at 50iterations 5.3210672E-02 2.043598 at 60iterations 2.3104502E-02 0.7876806 at 70iterations 1.0072882E-02 0.3945596 at 80iterations 4.4427807E-03 0.1504593 at 90iterations 1.9808067E-03 7.3150635E-02 at 100iterations 9.2049758E-04 3.4096718E-02 at 110iterations 4.5833469E-04 1.6629219E-02 at 120iterations finished qdiffx linear iterations at : 18:53:21 total time elapsed so far: 10.61000 # loops : 120 mean,max change (kT/e) : 4.5833469E-04 1.6629219E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.78000 DelPhi exited at 18:53:21 10.781u 0.454s 0:11.50 97.6% 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 18:53:21 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2572 !!! WARNING: SEP 31 has a net charge of -0.4750 !!! WARNING: HIR 78 has a net charge of 0.5140 !!! WARNING: HIR 249 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.588965 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): 40.13600 95.35600 ymin,ymax (A): -71.04500 -9.167001 zmin,zma (A): 68.03500 112.7040 x,y,z range (A): 55.22001 61.87800 44.66900 scale (grids/A): 2.588965 object centre (A): 67.74600 -40.10600 90.36949 number of atom coordinates read : 2572 total number of charged atoms : 2430 net assigned charge : 5.3008214E-02 assigned positive charge : 394.7124 centred at (gu) : 88.72986 98.19559 92.19354 assigned negative charge : -394.6604 centred at (gu) : 88.96534 97.71361 92.79771 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 142871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23072 grid for indexing accessible points = 1.400000 m= 69578 mr = 103003 m= 23031 mr = 55911 m= 4438 mr = 17875 m= 426 mr = 3108 m= 11 mr = 228 m= 0 mr = 2 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1681 time to turn everything in is 1.300000 number of dielectric boundary points 60228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19430 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) : 1.725977 object centre at (A) : 67.74600 -40.10600 90.36949 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0777779E-02 -6.5055981E-02 midg,1,midg; midg,igrid,midg 8.5362181E-02 0.3492687 1,midg,midg; igrid,midg,midg 0.3831441 -0.1293038 gauss-seidel spectral radius is 0.9991736 estimated iterations to convergence 275 setup time was (sec) 1.610000 now iterating at: 18:53:23 rms-change max change #iterations 8.872026 326.0264 at 10iterations 5.091267 131.5497 at 20iterations 2.889463 77.08180 at 30iterations 1.634140 40.54131 at 40iterations 0.9234271 20.50140 at 50iterations 0.5180767 11.16583 at 60iterations 0.2915656 6.903975 at 70iterations 0.1630609 3.667305 at 80iterations 9.1367550E-02 1.838037 at 90iterations 5.1038850E-02 1.064904 at 100iterations 2.8559746E-02 0.6260643 at 110iterations 1.5964726E-02 0.3760209 at 120iterations 8.9511210E-03 0.1807718 at 130iterations 5.0159767E-03 0.1014175 at 140iterations 2.8353622E-03 6.0609818E-02 at 150iterations 1.6190193E-03 3.4218788E-02 at 160iterations 9.3912333E-04 2.0048141E-02 at 170iterations 5.6590972E-04 1.1961937E-02 at 180iterations finished qdiffx linear iterations at : 18:53:40 total time elapsed so far: 18.03000 # loops : 180 mean,max change (kT/e) : 5.6590972E-04 1.1961937E-02 energy calculations done at 18.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.20000 DelPhi exited at 18:53:40 18.201u 0.470s 0:18.93 98.6% 0+0k 0+0io 0pf+0w