Mon Oct 10 14:14:28 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 14:14:28 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 = 2875 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: 0.5111711 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): 102.8770 172.5210 ymin,ymax (A): -11.95900 47.56600 zmin,zma (A): 34.19300 77.13100 x,y,z range (A): 69.64400 59.52500 42.93801 scale (grids/A): 0.5111711 object centre (A): 137.6990 17.80350 55.66200 number of atom coordinates read : 2875 total number of charged atoms : 2728 net assigned charge : 2.000015 assigned positive charge : 425.9355 centred at (gu) : 89.18677 93.56107 90.68520 assigned negative charge : -423.9363 centred at (gu) : 89.30424 93.54192 90.62497 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4845 nv = 96 ne = 84 npr = 56959 no. pairs analyzed = 56959 no. exposed pairs = 3695 no. arc points = 26287 no. surface atoms = 1257 nbur = 1618 mkacc time = 9.0000004E-02 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 = 1.680000 m= 167 mr = 2409 m= 0 mr = 3 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2599 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6467 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7179459E-11 1.4111599E-10 midg,1,midg; midg,igrid,midg -1.3472914E-12 1.4161153E-10 1,midg,midg; igrid,midg,midg 2.5366526E-10 -1.2833130E-10 gauss-seidel spectral radius is 0.9802950 estimated iterations to convergence 59 setup time was (sec) 0.3900000 now iterating at: 14:14:29 rms-change max change #iterations 5.2820593E-02 9.505116 at 10iterations 2.9792127E-03 0.5927963 at 20iterations 3.1601376E-04 7.7041626E-02 at 30iterations 7.8915880E-05 2.0404816E-02 at 40iterations 2.2505854E-05 5.8917999E-03 at 50iterations finished qdiffx linear iterations at : 14:14:32 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.2505854E-05 5.8917999E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:14:32 3.409u 0.176s 0:03.94 90.6% 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 14:14:32 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 = 2875 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: 1.533513 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): 102.8770 172.5210 ymin,ymax (A): -11.95900 47.56600 zmin,zma (A): 34.19300 77.13100 x,y,z range (A): 69.64400 59.52500 42.93801 scale (grids/A): 1.533513 object centre (A): 137.6990 17.80350 55.66200 number of atom coordinates read : 2875 total number of charged atoms : 2728 net assigned charge : 2.000015 assigned positive charge : 425.9355 centred at (gu) : 87.55976 100.6826 92.05488 assigned negative charge : -423.9363 centred at (gu) : 87.91264 100.6251 91.87465 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 54034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26287 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 16033 mr = 35771 m= 1473 mr = 10962 m= 20 mr = 633 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 24194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 20580 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) : 0.5111711 object centre at (A) : 137.6990 17.80350 55.66200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0274629E-03 4.9330606E-03 midg,1,midg; midg,igrid,midg 3.3275026E-03 -5.1245554E-03 1,midg,midg; igrid,midg,midg 7.0835849E-05 -9.0940371E-03 gauss-seidel spectral radius is 0.9979089 estimated iterations to convergence 174 setup time was (sec) 0.5000000 now iterating at: 14:14:33 rms-change max change #iterations 2.787245 161.4200 at 10iterations 1.080993 47.07752 at 20iterations 0.4238620 16.98226 at 30iterations 0.1649746 7.435755 at 40iterations 6.4517178E-02 2.591564 at 50iterations 2.5282420E-02 1.051140 at 60iterations 9.9335555E-03 0.3909426 at 70iterations 3.9102160E-03 0.1692810 at 80iterations 1.5753722E-03 7.1312904E-02 at 90iterations 6.5968058E-04 2.5863647E-02 at 100iterations 3.0051489E-04 1.4299393E-02 at 110iterations 1.5601772E-04 8.1100464E-03 at 120iterations finished qdiffx linear iterations at : 14:14:40 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 1.5601772E-04 8.1100464E-03 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 14:14:41 7.543u 0.182s 0:08.15 94.7% 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 Mon Oct 10 2011 at 14:14:41 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 = 2875 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: 2.300270 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): 102.8770 172.5210 ymin,ymax (A): -11.95900 47.56600 zmin,zma (A): 34.19300 77.13100 x,y,z range (A): 69.64400 59.52500 42.93801 scale (grids/A): 2.300270 object centre (A): 137.6990 17.80350 55.66200 number of atom coordinates read : 2875 total number of charged atoms : 2728 net assigned charge : 2.000015 assigned positive charge : 425.9355 centred at (gu) : 86.33953 106.0235 93.08211 assigned negative charge : -423.9363 centred at (gu) : 86.86887 105.9377 92.81181 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 125499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26287 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 56159 mr = 87972 m= 15614 mr = 43901 m= 2217 mr = 11669 m= 116 mr = 1324 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 54723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21775 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) : 1.533513 object centre at (A) : 137.6990 17.80350 55.66200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3672934E-02 8.0321737E-02 midg,1,midg; midg,igrid,midg 5.3494807E-02 -9.3648903E-02 1,midg,midg; igrid,midg,midg -5.4985717E-02 -6.5641715E-03 gauss-seidel spectral radius is 0.9990349 estimated iterations to convergence 254 setup time was (sec) 0.8800000 now iterating at: 14:14:42 rms-change max change #iterations 7.576948 264.8482 at 10iterations 4.133227 115.2173 at 20iterations 2.229002 56.20522 at 30iterations 1.196857 27.04415 at 40iterations 0.6407850 14.80570 at 50iterations 0.3420829 7.824684 at 60iterations 0.1826798 4.062107 at 70iterations 9.7287752E-02 2.347628 at 80iterations 5.1707510E-02 1.167365 at 90iterations 2.7538534E-02 0.6449693 at 100iterations 1.4646749E-02 0.3489848 at 110iterations 7.8013414E-03 0.1817570 at 120iterations 4.1573946E-03 9.4470024E-02 at 130iterations 2.2484022E-03 5.2700043E-02 at 140iterations 1.2195219E-03 3.0031204E-02 at 150iterations 6.8352977E-04 1.7433167E-02 at 160iterations 3.9712229E-04 1.2041092E-02 at 170iterations 2.4659533E-04 7.5378418E-03 at 180iterations finished qdiffx linear iterations at : 14:14:52 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 2.4659533E-04 7.5378418E-03 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 14:14:54 11.761u 0.208s 0:13.02 91.8% 0+0k 0+0io 0pf+0w