Sun Oct 9 12:42:28 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+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 12:42:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 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: 0.6993420 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): -9.948000 35.99500 ymin,ymax (A): -4.009000 46.89600 zmin,zma (A): -7.127000 37.74700 x,y,z range (A): 45.94300 50.90500 44.87400 scale (grids/A): 0.6993420 object centre (A): 13.02350 21.44350 15.31000 number of atom coordinates read : 2442 total number of charged atoms : 2300 net assigned charge : 5.500007 assigned positive charge : 374.3898 centred at (gu) : 90.46024 90.31812 89.73450 assigned negative charge : -368.8904 centred at (gu) : 90.56448 90.18516 89.67618 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7785 nv = 96 ne = 84 npr = 50177 no. pairs analyzed = 50177 no. exposed pairs = 2926 no. arc points = 20253 no. surface atoms = 992 nbur = 1450 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4393 m= 0 mr = 73 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2000000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1865 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9004 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0274237E-08 6.3317266E-08 midg,1,midg; midg,igrid,midg -2.5370541E-08 1.0897092E-07 1,midg,midg; igrid,midg,midg 8.1026073E-08 -1.4366725E-08 gauss-seidel spectral radius is 0.9893755 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 12:42:29 rms-change max change #iterations 0.2108679 29.27397 at 10iterations 2.5495704E-02 3.886618 at 20iterations 3.2104694E-03 0.3908372 at 30iterations 4.3259526E-04 5.2264214E-02 at 40iterations 7.6003598E-05 1.0440826E-02 at 50iterations finished qdiffx linear iterations at : 12:42:32 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 7.6003598E-05 1.0440826E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 12:42:32 3.426u 0.175s 0:03.89 92.2% 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 Sun Oct 9 2011 at 12:42:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 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: 2.098026 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): -9.948000 35.99500 ymin,ymax (A): -4.009000 46.89600 zmin,zma (A): -7.127000 37.74700 x,y,z range (A): 45.94300 50.90500 44.87400 scale (grids/A): 2.098026 object centre (A): 13.02350 21.44350 15.31000 number of atom coordinates read : 2442 total number of charged atoms : 2300 net assigned charge : 5.500007 assigned positive charge : 374.3898 centred at (gu) : 91.37999 90.95405 89.20309 assigned negative charge : -368.8904 centred at (gu) : 91.69313 90.55499 89.02816 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20253 grid for indexing accessible points = 1.400000 m= 31285 mr = 58760 m= 5454 mr = 23350 m= 452 mr = 3494 m= 11 mr = 241 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 350 time to turn everything in is 0.4100000 number of dielectric boundary points 34739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18259 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) : 0.6993420 object centre at (A) : 13.02350 21.44350 15.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7381905E-02 5.5269077E-02 midg,1,midg; midg,igrid,midg -2.9937768E-02 3.7514549E-02 1,midg,midg; igrid,midg,midg 1.6196341E-03 1.7083363E-03 gauss-seidel spectral radius is 0.9988408 estimated iterations to convergence 232 setup time was (sec) 0.6300000 now iterating at: 12:42:33 rms-change max change #iterations 4.992698 214.4451 at 10iterations 2.474596 89.46143 at 20iterations 1.225710 39.45152 at 30iterations 0.6115093 17.73300 at 40iterations 0.3049158 8.489853 at 50iterations 0.1514703 4.626040 at 60iterations 7.5455204E-02 2.186825 at 70iterations 3.7657313E-02 1.145233 at 80iterations 1.8758027E-02 0.5231323 at 90iterations 9.3502970E-03 0.2782660 at 100iterations 4.6724179E-03 0.1421318 at 110iterations 2.3324671E-03 6.2983036E-02 at 120iterations finished qdiffx linear iterations at : 12:42:40 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.3324671E-03 6.2983036E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 12:42:41 7.959u 0.206s 0:08.44 96.5% 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 Sun Oct 9 2011 at 12:42:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2442 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: 3.147039 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): -9.948000 35.99500 ymin,ymax (A): -4.009000 46.89600 zmin,zma (A): -7.127000 37.74700 x,y,z range (A): 45.94300 50.90500 44.87400 scale (grids/A): 3.147039 object centre (A): 13.02350 21.44350 15.31000 number of atom coordinates read : 2442 total number of charged atoms : 2300 net assigned charge : 5.500007 assigned positive charge : 374.3898 centred at (gu) : 92.06983 91.43088 88.80433 assigned negative charge : -368.8904 centred at (gu) : 92.53959 90.83241 88.54214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 192224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20253 grid for indexing accessible points = 1.400000 m= 99709 mr = 141534 m= 38162 mr = 82471 m= 10218 mr = 30899 m= 1928 mr = 7820 m= 193 mr = 1396 m= 7 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1139 time to turn everything in is 1.270000 number of dielectric boundary points 78205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 18400 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) : 2.098026 object centre at (A) : 13.02350 21.44350 15.31000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3124613E-02 0.4477928 midg,1,midg; midg,igrid,midg -0.2685496 0.2482920 1,midg,midg; igrid,midg,midg -8.2662970E-02 1.5868971E-02 gauss-seidel spectral radius is 0.9993009 estimated iterations to convergence 298 setup time was (sec) 1.500000 now iterating at: 12:42:43 rms-change max change #iterations 11.10714 372.6533 at 10iterations 6.588061 126.3638 at 20iterations 3.897089 67.98256 at 30iterations 2.305843 40.49210 at 40iterations 1.358314 23.90005 at 50iterations 0.7973507 15.12932 at 60iterations 0.4688082 7.734097 at 70iterations 0.2752137 4.479146 at 80iterations 0.1615795 2.787593 at 90iterations 9.4784208E-02 1.565060 at 100iterations 5.5561926E-02 0.9093978 at 110iterations 3.2559093E-02 0.5259705 at 120iterations 1.9186715E-02 0.3266325 at 130iterations 1.1285908E-02 0.1975937 at 140iterations 6.7071700E-03 0.1146660 at 150iterations 4.0193382E-03 7.6347351E-02 at 160iterations 2.4580471E-03 4.6112061E-02 at 170iterations 1.5422909E-03 3.1158447E-02 at 180iterations finished qdiffx linear iterations at : 12:42:54 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.5422909E-03 3.1158447E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 12:42:54 12.942u 0.205s 0:13.41 97.9% 0+0k 0+0io 0pf+0w