Mon Oct 10 22:02:24 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 22:02:24 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 !!! WARNING: GLM 42 has a net charge of -0.0940 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: 0.5535687 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): -24.98500 31.79400 ymin,ymax (A): -33.84100 22.97600 zmin,zma (A): -6.946000 57.36400 x,y,z range (A): 56.77900 56.81700 64.31000 scale (grids/A): 0.5535687 object centre (A): 3.404499 -5.432500 25.20900 number of atom coordinates read : 2893 total number of charged atoms : 2795 net assigned charge : 2.406003 assigned positive charge : 429.3171 centred at (gu) : 89.87179 89.14240 90.98871 assigned negative charge : -426.9125 centred at (gu) : 89.72204 89.22328 90.92548 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5921 nv = 96 ne = 84 npr = 56548 no. pairs analyzed = 56548 no. exposed pairs = 3994 no. arc points = 28460 no. surface atoms = 1341 nbur = 1552 mkacc time = 0.1500000 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 = 1.568000 m= 223 mr = 2813 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 390 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6927988E-10 9.1961244E-10 midg,1,midg; midg,igrid,midg 1.0713685E-09 -4.0094797E-10 1,midg,midg; igrid,midg,midg -1.1313986E-09 1.3865118E-09 gauss-seidel spectral radius is 0.9831781 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 22:02:25 rms-change max change #iterations 7.4902140E-02 13.97804 at 10iterations 5.2786130E-03 0.9056416 at 20iterations 3.9805940E-04 6.8580627E-02 at 30iterations 4.4377073E-05 6.0462952E-03 at 40iterations 8.1592643E-06 1.0309219E-03 at 50iterations finished qdiffx linear iterations at : 22:02:29 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 8.1592643E-06 1.0309219E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 22:02:29 4.533u 0.387s 0:05.36 91.6% 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 22:02:29 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 !!! WARNING: GLM 42 has a net charge of -0.0940 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: 1.660706 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): -24.98500 31.79400 ymin,ymax (A): -33.84100 22.97600 zmin,zma (A): -6.946000 57.36400 x,y,z range (A): 56.77900 56.81700 64.31000 scale (grids/A): 1.660706 object centre (A): 3.404499 -5.432500 25.20900 number of atom coordinates read : 2893 total number of charged atoms : 2795 net assigned charge : 2.406003 assigned positive charge : 429.3171 centred at (gu) : 89.61462 87.42664 92.96494 assigned negative charge : -426.9125 centred at (gu) : 89.16608 87.66956 92.77619 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19615 mr = 42440 m= 2165 mr = 12785 m= 65 mr = 965 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 226 time to turn everything in is 0.5400000 number of dielectric boundary points 31035 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 304 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21515 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) : 0.5535687 object centre at (A) : 3.404499 -5.432500 25.20900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0387764E-03 4.8727067E-03 midg,1,midg; midg,igrid,midg 5.7077332E-04 -1.0210426E-02 1,midg,midg; igrid,midg,midg -1.0826728E-02 2.0429788E-02 gauss-seidel spectral radius is 0.9982570 estimated iterations to convergence 190 setup time was (sec) 0.8700000 now iterating at: 22:02:31 rms-change max change #iterations 3.350953 214.9658 at 10iterations 1.412915 59.91432 at 20iterations 0.6005871 27.38915 at 30iterations 0.2525984 10.60571 at 40iterations 0.1072941 3.661922 at 50iterations 4.5569312E-02 1.666481 at 60iterations 1.9310027E-02 0.7913051 at 70iterations 8.1797969E-03 0.2736778 at 80iterations 3.4654154E-03 0.1256323 at 90iterations 1.4741322E-03 5.4153442E-02 at 100iterations 6.2726450E-04 2.2048950E-02 at 110iterations 2.6769858E-04 1.0126114E-02 at 120iterations finished qdiffx linear iterations at : 22:02:41 total time elapsed so far: 11.22000 # loops : 120 mean,max change (kT/e) : 2.6769858E-04 1.0126114E-02 energy calculations done at 11.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 22:02:42 11.392u 0.449s 0:12.19 97.0% 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 22:02:42 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 !!! WARNING: GLM 42 has a net charge of -0.0940 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: 2.491059 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): -24.98500 31.79400 ymin,ymax (A): -33.84100 22.97600 zmin,zma (A): -6.946000 57.36400 x,y,z range (A): 56.77900 56.81700 64.31000 scale (grids/A): 2.491059 object centre (A): 3.404499 -5.432500 25.20900 number of atom coordinates read : 2893 total number of charged atoms : 2795 net assigned charge : 2.406003 assigned positive charge : 429.3171 centred at (gu) : 89.42173 86.13972 94.44734 assigned negative charge : -426.9125 centred at (gu) : 88.74909 86.50428 94.16440 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 151724 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67208 mr = 104536 m= 19433 mr = 51399 m= 3254 mr = 13937 m= 228 mr = 2009 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 1.330000 number of dielectric boundary points 69889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 22341 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) : 1.660706 object centre at (A) : 3.404499 -5.432500 25.20900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2096431 0.1843941 midg,1,midg; midg,igrid,midg -1.6751736E-02 -0.1284473 1,midg,midg; igrid,midg,midg -0.2681387 0.2765091 gauss-seidel spectral radius is 0.9991687 estimated iterations to convergence 274 setup time was (sec) 1.670000 now iterating at: 22:02:44 rms-change max change #iterations 8.766212 319.1510 at 10iterations 4.986093 132.8595 at 20iterations 2.829442 67.54389 at 30iterations 1.594897 37.20952 at 40iterations 0.8987122 19.51764 at 50iterations 0.5034844 10.59859 at 60iterations 0.2804561 6.069584 at 70iterations 0.1565904 3.635952 at 80iterations 8.7404132E-02 1.791783 at 90iterations 4.8563864E-02 1.086472 at 100iterations 2.7040275E-02 0.5530338 at 110iterations 1.5040816E-02 0.3239784 at 120iterations 8.3611682E-03 0.1950512 at 130iterations 4.6430072E-03 9.5246315E-02 at 140iterations 2.5802788E-03 5.1656723E-02 at 150iterations 1.4333944E-03 3.2043457E-02 at 160iterations 7.9704658E-04 1.7498970E-02 at 170iterations 4.4154533E-04 8.6426735E-03 at 180iterations finished qdiffx linear iterations at : 22:03:00 total time elapsed so far: 17.54000 # loops : 180 mean,max change (kT/e) : 4.4154533E-04 8.6426735E-03 energy calculations done at 17.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 22:03:00 17.711u 0.448s 0:18.45 98.3% 0+0k 0+0io 0pf+0w