Sun Oct 9 13:46:17 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 Sun Oct 9 2011 at 13:46:17 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 = 2365 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7030849 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): -5.673000 44.39400 ymin,ymax (A): -14.31200 36.32200 zmin,zma (A): 1.944000 45.21600 x,y,z range (A): 50.06700 50.63400 43.27200 scale (grids/A): 0.7030849 object centre (A): 19.36050 11.00500 23.58000 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 89.22314 91.34448 90.69912 assigned negative charge : -354.8976 centred at (gu) : 89.22817 91.47034 90.73544 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8108 nv = 96 ne = 84 npr = 46810 no. pairs analyzed = 46810 no. exposed pairs = 3019 no. arc points = 21080 no. surface atoms = 1017 nbur = 1348 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 516 mr = 4481 m= 1 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.1900000 number of dielectric boundary points 4042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2027 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6916313E-08 1.8946933E-08 midg,1,midg; midg,igrid,midg 7.5763083E-08 -3.9531248E-08 1,midg,midg; igrid,midg,midg 4.3885500E-08 2.8276531E-08 gauss-seidel spectral radius is 0.9894904 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 13:46:18 rms-change max change #iterations 0.2067926 28.28992 at 10iterations 2.5612380E-02 3.532974 at 20iterations 3.6217289E-03 0.5083408 at 30iterations 7.6908892E-04 0.1194649 at 40iterations 2.4053140E-04 3.9482117E-02 at 50iterations finished qdiffx linear iterations at : 13:46:21 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.4053140E-04 3.9482117E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:46:21 3.393u 0.184s 0:03.85 92.7% 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 13:46:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 2.109255 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): -5.673000 44.39400 ymin,ymax (A): -14.31200 36.32200 zmin,zma (A): 1.944000 45.21600 x,y,z range (A): 50.06700 50.63400 43.27200 scale (grids/A): 2.109255 object centre (A): 19.36050 11.00500 23.58000 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 87.66917 94.03287 92.09677 assigned negative charge : -354.8976 centred at (gu) : 87.68413 94.41096 92.20621 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 33880 mr = 59264 m= 6506 mr = 25651 m= 643 mr = 4214 m= 19 mr = 378 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 284 time to turn everything in is 0.4300000 number of dielectric boundary points 36847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17683 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) : 0.7030849 object centre at (A) : 19.36050 11.00500 23.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6134133E-02 1.3334387E-02 midg,1,midg; midg,igrid,midg 1.5244638E-02 -3.1061323E-02 1,midg,midg; igrid,midg,midg 6.1580218E-02 -1.2183324E-02 gauss-seidel spectral radius is 0.9988570 estimated iterations to convergence 234 setup time was (sec) 0.6500000 now iterating at: 13:46:22 rms-change max change #iterations 4.947369 211.3798 at 10iterations 2.454034 81.68288 at 20iterations 1.224518 36.77341 at 30iterations 0.6103265 17.29161 at 40iterations 0.3053559 9.495666 at 50iterations 0.1534006 4.417281 at 60iterations 7.6822452E-02 2.314297 at 70iterations 3.8381465E-02 1.161698 at 80iterations 1.9388610E-02 0.5555725 at 90iterations 9.8676002E-03 0.2887688 at 100iterations 5.0915666E-03 0.1559372 at 110iterations 2.7202431E-03 8.1668854E-02 at 120iterations finished qdiffx linear iterations at : 13:46:29 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.7202431E-03 8.1668854E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 13:46:30 7.872u 0.185s 0:08.33 96.6% 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 Sun Oct 9 2011 at 13:46:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 3.163882 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): -5.673000 44.39400 ymin,ymax (A): -14.31200 36.32200 zmin,zma (A): 1.944000 45.21600 x,y,z range (A): 50.06700 50.63400 43.27200 scale (grids/A): 3.163882 object centre (A): 19.36050 11.00500 23.58000 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 86.50349 96.04923 93.14506 assigned negative charge : -354.8976 centred at (gu) : 86.52625 96.61632 93.30917 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 196326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21080 grid for indexing accessible points = 1.400000 m= 105302 mr = 142789 m= 42918 mr = 86939 m= 12164 mr = 35402 m= 2524 mr = 9293 m= 397 mr = 1905 m= 11 mr = 272 m= 0 mr = 6 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 1014 time to turn everything in is 1.310000 number of dielectric boundary points 83036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 17800 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) : 2.109255 object centre at (A) : 19.36050 11.00500 23.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4342564 -8.6365966E-03 midg,1,midg; midg,igrid,midg 0.3037672 -0.3316494 1,midg,midg; igrid,midg,midg 0.6460418 -0.4549585 gauss-seidel spectral radius is 0.9993075 estimated iterations to convergence 300 setup time was (sec) 1.550000 now iterating at: 13:46:31 rms-change max change #iterations 11.01692 468.1241 at 10iterations 6.568485 139.1613 at 20iterations 3.893133 85.86977 at 30iterations 2.307022 43.95949 at 40iterations 1.364839 24.35819 at 50iterations 0.8060471 13.92753 at 60iterations 0.4748701 8.999118 at 70iterations 0.2796257 4.458122 at 80iterations 0.1646294 2.668930 at 90iterations 9.7042546E-02 1.695475 at 100iterations 5.7104517E-02 0.9192514 at 110iterations 3.3717461E-02 0.6498566 at 120iterations 2.0189483E-02 0.3866282 at 130iterations 1.2189244E-02 0.2047071 at 140iterations 7.5898506E-03 0.1477814 at 150iterations 4.9302266E-03 9.7885132E-02 at 160iterations 3.4042667E-03 6.9919586E-02 at 170iterations 2.5077239E-03 5.2860260E-02 at 180iterations finished qdiffx linear iterations at : 13:46:43 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 2.5077239E-03 5.2860260E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 13:46:43 13.220u 0.209s 0:13.70 97.9% 0+0k 0+0io 0pf+0w