Mon Oct 10 19:32:05 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 19:32:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 0.7166871 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): 25.55500 73.92000 ymin,ymax (A): 16.66600 66.33900 zmin,zma (A): 7.633000 57.06300 x,y,z range (A): 48.36500 49.67300 49.43000 scale (grids/A): 0.7166871 object centre (A): 49.73750 41.50250 32.34800 number of atom coordinates read : 2488 total number of charged atoms : 2351 net assigned charge : 3.000010 assigned positive charge : 374.0517 centred at (gu) : 89.79045 86.77417 88.34174 assigned negative charge : -371.0525 centred at (gu) : 89.70970 86.93846 88.27467 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8484 nv = 96 ne = 84 npr = 52370 no. pairs analyzed = 52370 no. exposed pairs = 2940 no. arc points = 20113 no. surface atoms = 988 nbur = 1500 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4953 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.3100000 number of dielectric boundary points 3984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 116 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8852638E-08 5.4922818E-08 midg,1,midg; midg,igrid,midg 2.7133618E-07 -4.8014144E-08 1,midg,midg; igrid,midg,midg -3.1334199E-08 8.1556202E-08 gauss-seidel spectral radius is 0.9898868 estimated iterations to convergence 81 setup time was (sec) 0.5500000 now iterating at: 19:32:06 rms-change max change #iterations 0.2337240 30.74298 at 10iterations 3.0059073E-02 3.606903 at 20iterations 3.7969057E-03 0.4405823 at 30iterations 4.9650780E-04 6.2145233E-02 at 40iterations 6.9094654E-05 8.7509155E-03 at 50iterations finished qdiffx linear iterations at : 19:32:09 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 6.9094654E-05 8.7509155E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 19:32:10 3.396u 0.183s 0:04.60 77.6% 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 19:32:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.150061 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): 25.55500 73.92000 ymin,ymax (A): 16.66600 66.33900 zmin,zma (A): 7.633000 57.06300 x,y,z range (A): 48.36500 49.67300 49.43000 scale (grids/A): 2.150061 object centre (A): 49.73750 41.50250 32.34800 number of atom coordinates read : 2488 total number of charged atoms : 2351 net assigned charge : 3.000010 assigned positive charge : 374.0517 centred at (gu) : 89.37057 80.32194 85.02474 assigned negative charge : -371.0525 centred at (gu) : 89.12895 80.81520 84.82365 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20113 grid for indexing accessible points = 1.400000 m= 35083 mr = 63535 m= 6667 mr = 26929 m= 550 mr = 4404 m= 20 mr = 292 m= 0 mr = 3 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2625 time to turn everything in is 0.6800000 number of dielectric boundary points 36708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18693 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) : 0.7166871 object centre at (A) : 49.73750 41.50250 32.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1015679E-02 2.1973541E-02 midg,1,midg; midg,igrid,midg 6.6851340E-02 -1.5119562E-02 1,midg,midg; igrid,midg,midg 7.6142633E-03 2.9224919E-02 gauss-seidel spectral radius is 0.9988853 estimated iterations to convergence 237 setup time was (sec) 0.9800000 now iterating at: 19:32:11 rms-change max change #iterations 5.172979 205.9609 at 10iterations 2.603283 78.59870 at 20iterations 1.311099 41.88968 at 30iterations 0.6612588 18.96445 at 40iterations 0.3344974 9.610592 at 50iterations 0.1684027 4.504105 at 60iterations 8.4997885E-02 3.010985 at 70iterations 4.2830165E-02 1.165088 at 80iterations 2.1640005E-02 0.6246147 at 90iterations 1.0918803E-02 0.3125839 at 100iterations 5.5172006E-03 0.1586266 at 110iterations 2.7917242E-03 7.8874588E-02 at 120iterations finished qdiffx linear iterations at : 19:32:18 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 2.7917242E-03 7.8874588E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 19:32:19 7.810u 0.239s 0:08.74 91.9% 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 19:32:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 3.225092 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): 25.55500 73.92000 ymin,ymax (A): 16.66600 66.33900 zmin,zma (A): 7.633000 57.06300 x,y,z range (A): 48.36500 49.67300 49.43000 scale (grids/A): 3.225092 object centre (A): 49.73750 41.50250 32.34800 number of atom coordinates read : 2488 total number of charged atoms : 2351 net assigned charge : 3.000010 assigned positive charge : 374.0517 centred at (gu) : 89.05571 75.48265 82.53690 assigned negative charge : -371.0525 centred at (gu) : 88.69335 76.22273 82.23550 start vw surface at 0.1500000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 206871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20113 grid for indexing accessible points = 1.400000 m= 109374 mr = 153378 m= 45101 mr = 91333 m= 12445 mr = 37534 m= 2162 mr = 9544 m= 269 mr = 1528 m= 10 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.9599999 no. cavity mid-points inaccessible to solvent = 9102 time to turn everything in is 2.080000 number of dielectric boundary points 82713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 18808 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) : 2.150061 object centre at (A) : 49.73750 41.50250 32.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1019581 0.6337138 midg,1,midg; midg,igrid,midg 0.3492237 -9.7678363E-02 1,midg,midg; igrid,midg,midg 2.9514268E-02 0.1313655 gauss-seidel spectral radius is 0.9993240 estimated iterations to convergence 303 setup time was (sec) 2.380000 now iterating at: 19:32:22 rms-change max change #iterations 11.46755 404.2339 at 10iterations 6.819276 143.9810 at 20iterations 4.052624 89.26783 at 30iterations 2.403056 38.29998 at 40iterations 1.422738 25.09970 at 50iterations 0.8421068 16.36442 at 60iterations 0.4976568 8.115765 at 70iterations 0.2929385 5.152992 at 80iterations 0.1726720 2.604660 at 90iterations 0.1021486 1.550360 at 100iterations 6.0013670E-02 0.9233589 at 110iterations 3.5495911E-02 0.5647316 at 120iterations 2.0851564E-02 0.3177977 at 130iterations 1.2309920E-02 0.1873169 at 140iterations 7.2513777E-03 0.1178207 at 150iterations 4.2728903E-03 6.8173409E-02 at 160iterations 2.5240420E-03 4.1786194E-02 at 170iterations 1.4896105E-03 2.2312164E-02 at 180iterations finished qdiffx linear iterations at : 19:32:33 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 1.4896105E-03 2.2312164E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 19:32:33 13.442u 0.246s 0:14.41 94.9% 0+0k 0+0io 0pf+0w