Mon Oct 10 11:33:02 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+sph.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 = amb.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 11:33:03 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6647248 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): 6.513000 55.51600 ymin,ymax (A): -69.34200 -21.06200 zmin,zma (A): 33.13200 86.68800 x,y,z range (A): 49.00300 48.28000 53.55600 scale (grids/A): 0.6647248 object centre (A): 31.01450 -45.20200 59.91000 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -7.999972 assigned positive charge : 320.1319 centred at (gu) : 91.57980 88.21197 91.74895 assigned negative charge : -328.1320 centred at (gu) : 91.71432 88.12693 91.51102 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6310 nv = 96 ne = 84 npr = 43587 no. pairs analyzed = 43587 no. exposed pairs = 2724 no. arc points = 19270 no. surface atoms = 912 nbur = 1224 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3384 m= 0 mr = 63 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 121 time to turn everything in is 0.2700000 number of dielectric boundary points 3219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1793 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7851422E-08 3.0373226E-08 midg,1,midg; midg,igrid,midg -5.6301289E-08 -5.2527258E-09 1,midg,midg; igrid,midg,midg 1.0511872E-09 -6.7164251E-08 gauss-seidel spectral radius is 0.9882280 estimated iterations to convergence 75 setup time was (sec) 0.5100000 now iterating at: 11:33:03 rms-change max change #iterations 0.1594557 26.02648 at 10iterations 1.6925395E-02 2.557526 at 20iterations 1.8311205E-03 0.2488499 at 30iterations 1.9309507E-04 2.8825760E-02 at 40iterations 2.1018290E-05 3.7002563E-03 at 50iterations finished qdiffx linear iterations at : 11:33:06 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.1018290E-05 3.7002563E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 11:33:06 3.341u 0.195s 0:03.90 90.5% 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 11:33:06 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.994174 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): 6.513000 55.51600 ymin,ymax (A): -69.34200 -21.06200 zmin,zma (A): 33.13200 86.68800 x,y,z range (A): 49.00300 48.28000 53.55600 scale (grids/A): 1.994174 object centre (A): 31.01450 -45.20200 59.91000 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -7.999972 assigned positive charge : 320.1319 centred at (gu) : 94.73931 84.63583 95.24674 assigned negative charge : -328.1320 centred at (gu) : 95.14288 84.38078 94.53298 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 67709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19270 grid for indexing accessible points = 1.400000 m= 24562 mr = 46036 m= 4029 mr = 17969 m= 280 mr = 2503 m= 1 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3276 time to turn everything in is 0.4900000 number of dielectric boundary points 29965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 15754 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) : 0.6647248 object centre at (A) : 31.01450 -45.20200 59.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3800510E-02 -1.3783963E-02 midg,1,midg; midg,igrid,midg -1.3839230E-02 3.4261360E-03 1,midg,midg; igrid,midg,midg -3.8901253E-03 -4.7849938E-02 gauss-seidel spectral radius is 0.9987003 estimated iterations to convergence 220 setup time was (sec) 0.7700000 now iterating at: 11:33:07 rms-change max change #iterations 4.199758 167.0993 at 10iterations 2.002924 79.85905 at 20iterations 0.9512652 34.02893 at 30iterations 0.4542187 15.49582 at 40iterations 0.2164107 7.348919 at 50iterations 0.1030166 3.398341 at 60iterations 4.9127117E-02 1.541586 at 70iterations 2.3391321E-02 0.7388991 at 80iterations 1.1142837E-02 0.3399315 at 90iterations 5.3024897E-03 0.1677971 at 100iterations 2.5333550E-03 8.2313538E-02 at 110iterations 1.2051455E-03 3.8121700E-02 at 120iterations finished qdiffx linear iterations at : 11:33:14 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.2051455E-03 3.8121700E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 11:33:14 7.444u 0.242s 0:07.98 96.2% 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 11:33:14 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 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: 2.991262 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): 6.513000 55.51600 ymin,ymax (A): -69.34200 -21.06200 zmin,zma (A): 33.13200 86.68800 x,y,z range (A): 49.00300 48.28000 53.55600 scale (grids/A): 2.991262 object centre (A): 31.01450 -45.20200 59.91000 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -7.999972 assigned positive charge : 320.1319 centred at (gu) : 97.10889 81.95368 97.87010 assigned negative charge : -328.1320 centred at (gu) : 97.71419 81.57110 96.79933 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 156209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19270 grid for indexing accessible points = 1.400000 m= 78761 mr = 111510 m= 29152 mr = 64115 m= 7395 mr = 23267 m= 1255 mr = 5591 m= 102 mr = 848 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 11014 time to turn everything in is 1.230000 number of dielectric boundary points 67496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 15960 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) : 1.994174 object centre at (A) : 31.01450 -45.20200 59.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3179379 -5.0945237E-02 midg,1,midg; midg,igrid,midg -6.6338234E-02 8.5379127E-03 1,midg,midg; igrid,midg,midg -4.5248859E-02 -0.4211646 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.540000 now iterating at: 11:33:16 rms-change max change #iterations 9.759167 377.2327 at 10iterations 5.684746 141.9396 at 20iterations 3.298727 75.21973 at 30iterations 1.910391 36.11459 at 40iterations 1.102928 21.35154 at 50iterations 0.6366668 11.93670 at 60iterations 0.3671384 6.675348 at 70iterations 0.2120939 4.093621 at 80iterations 0.1222758 2.295914 at 90iterations 7.0481941E-02 1.498234 at 100iterations 4.0620342E-02 0.7157192 at 110iterations 2.3353051E-02 0.4383698 at 120iterations 1.3486326E-02 0.2543077 at 130iterations 7.7558099E-03 0.1427402 at 140iterations 4.4656307E-03 8.6947441E-02 at 150iterations 2.5753137E-03 4.8374176E-02 at 160iterations 1.4818606E-03 2.6200116E-02 at 170iterations 8.5341354E-04 1.6353369E-02 at 180iterations finished qdiffx linear iterations at : 11:33:27 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 8.5341354E-04 1.6353369E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 11:33:27 12.126u 0.241s 0:12.74 97.0% 0+0k 0+0io 0pf+0w