Sun Oct 9 11:31:06 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 Sun Oct 9 2011 at 11:31:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2866 !!! WARNING: HIR 216 has a net charge of 0.5140 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: 0.5790877 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): -22.52800 38.94800 ymin,ymax (A): -25.92000 27.16300 zmin,zma (A): -27.87500 26.66100 x,y,z range (A): 61.47600 53.08300 54.53600 scale (grids/A): 0.5790877 object centre (A): 8.210001 0.6215000 -0.6070004 number of atom coordinates read : 2866 total number of charged atoms : 2765 net assigned charge : 1.4026731E-02 assigned positive charge : 424.4440 centred at (gu) : 89.65702 90.15971 91.13094 assigned negative charge : -424.4317 centred at (gu) : 89.65668 90.13895 91.06187 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6597 nv = 96 ne = 84 npr = 55927 no. pairs analyzed = 55927 no. exposed pairs = 3956 no. arc points = 28430 no. surface atoms = 1305 nbur = 1561 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 = 1.512000 m= 351 mr = 3297 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2200000 number of dielectric boundary points 3624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2730 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8239 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0971068E-09 1.8120474E-09 midg,1,midg; midg,igrid,midg -4.2311737E-10 4.2239745E-10 1,midg,midg; igrid,midg,midg -2.4185867E-11 -7.8986947E-12 gauss-seidel spectral radius is 0.9846143 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 11:31:06 rms-change max change #iterations 9.5053047E-02 12.71368 at 10iterations 7.5600166E-03 1.275940 at 20iterations 7.1162212E-04 0.1211014 at 30iterations 1.2816205E-04 2.9727936E-02 at 40iterations 3.5329442E-05 8.6450577E-03 at 50iterations finished qdiffx linear iterations at : 11:31:09 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.5329442E-05 8.6450577E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 11:31:09 3.427u 0.173s 0:03.93 91.3% 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 11:31:10 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2866 !!! WARNING: HIR 216 has a net charge of 0.5140 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: 1.737263 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): -22.52800 38.94800 ymin,ymax (A): -25.92000 27.16300 zmin,zma (A): -27.87500 26.66100 x,y,z range (A): 61.47600 53.08300 54.53600 scale (grids/A): 1.737263 object centre (A): 8.210001 0.6215000 -0.6070004 number of atom coordinates read : 2866 total number of charged atoms : 2765 net assigned charge : 1.4026731E-02 assigned positive charge : 424.4440 centred at (gu) : 88.97004 90.47825 93.39174 assigned negative charge : -424.4317 centred at (gu) : 88.96998 90.41660 93.18547 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28430 grid for indexing accessible points = 1.400000 m= 24444 mr = 47573 m= 3671 mr = 16740 m= 181 mr = 1963 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1149 time to turn everything in is 0.3500000 number of dielectric boundary points 33682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21524 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) : 0.5790877 object centre at (A) : 8.210001 0.6215000 -0.6070004 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4393154E-02 4.4415928E-03 midg,1,midg; midg,igrid,midg 5.5263382E-03 2.0963443E-02 1,midg,midg; igrid,midg,midg 1.2987413E-02 -1.2844393E-02 gauss-seidel spectral radius is 0.9984202 estimated iterations to convergence 200 setup time was (sec) 0.5600000 now iterating at: 11:31:10 rms-change max change #iterations 3.709452 168.6577 at 10iterations 1.633760 61.51113 at 20iterations 0.7215250 26.22951 at 30iterations 0.3177725 11.58485 at 40iterations 0.1405424 5.261614 at 50iterations 6.2154979E-02 2.185993 at 60iterations 2.7390787E-02 1.186852 at 70iterations 1.2142236E-02 0.4620018 at 80iterations 5.3665303E-03 0.1897221 at 90iterations 2.3928424E-03 8.2290649E-02 at 100iterations 1.0696785E-03 3.6872864E-02 at 110iterations 4.8031041E-04 1.7768860E-02 at 120iterations finished qdiffx linear iterations at : 11:31:17 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 4.8031041E-04 1.7768860E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 11:31:18 7.809u 0.225s 0:08.29 96.7% 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 11:31:18 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2866 !!! WARNING: HIR 216 has a net charge of 0.5140 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: 2.605895 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): -22.52800 38.94800 ymin,ymax (A): -25.92000 27.16300 zmin,zma (A): -27.87500 26.66100 x,y,z range (A): 61.47600 53.08300 54.53600 scale (grids/A): 2.605895 object centre (A): 8.210001 0.6215000 -0.6070004 number of atom coordinates read : 2866 total number of charged atoms : 2765 net assigned charge : 1.4026731E-02 assigned positive charge : 424.4440 centred at (gu) : 88.45488 90.71738 95.08723 assigned negative charge : -424.4317 centred at (gu) : 88.45500 90.62496 94.77826 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 165892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28430 grid for indexing accessible points = 1.400000 m= 79761 mr = 116532 m= 27495 mr = 62262 m= 6215 mr = 20779 m= 702 mr = 4217 m= 16 mr = 341 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 3857 time to turn everything in is 0.8900000 number of dielectric boundary points 75950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 22115 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) : 1.737263 object centre at (A) : 8.210001 0.6215000 -0.6070004 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1577225 9.2591994E-02 midg,1,midg; midg,igrid,midg 0.1971907 0.3359588 1,midg,midg; igrid,midg,midg 0.1928196 -0.2285801 gauss-seidel spectral radius is 0.9992166 estimated iterations to convergence 282 setup time was (sec) 1.140000 now iterating at: 11:31:19 rms-change max change #iterations 9.371141 259.0222 at 10iterations 5.481125 135.4344 at 20iterations 3.166945 72.48097 at 30iterations 1.829615 40.85003 at 40iterations 1.052800 22.67927 at 50iterations 0.6021597 13.57680 at 60iterations 0.3432321 6.539314 at 70iterations 0.1954293 4.462981 at 80iterations 0.1111863 2.250829 at 90iterations 6.3174315E-02 1.258733 at 100iterations 3.5937916E-02 0.7643433 at 110iterations 2.0308087E-02 0.4529610 at 120iterations 1.1522835E-02 0.2061024 at 130iterations 6.5460685E-03 0.1349888 at 140iterations 3.7085819E-03 7.4977875E-02 at 150iterations 2.1088885E-03 3.9636612E-02 at 160iterations 1.1976399E-03 2.2636414E-02 at 170iterations 6.8428868E-04 1.4713868E-02 at 180iterations finished qdiffx linear iterations at : 11:31:30 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 6.8428868E-04 1.4713868E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 11:31:31 12.536u 0.224s 0:13.03 97.8% 0+0k 0+0io 0pf+0w