Mon Oct 10 17:01:30 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 17:01:30 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: HIZ 230 has a net charge of 0.2000 !!! WARNING: HIZ 245 has a net charge of 0.2000 !!! WARNING: ZN6 647 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 has a net charge of 1.4000 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: 0.6719770 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): -18.14600 28.39100 ymin,ymax (A): 2.243000 55.22100 zmin,zma (A): 111.7510 161.3650 x,y,z range (A): 46.53700 52.97800 49.61401 scale (grids/A): 0.6719770 object centre (A): 5.122499 28.73200 136.5580 number of atom coordinates read : 1966 total number of charged atoms : 1835 net assigned charge : -8.699987 assigned positive charge : 281.8951 centred at (gu) : 88.29171 91.42250 90.58353 assigned negative charge : -290.5950 centred at (gu) : 88.42120 91.14201 90.47115 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6006 nv = 96 ne = 84 npr = 41512 no. pairs analyzed = 41512 no. exposed pairs = 2670 no. arc points = 19017 no. surface atoms = 894 nbur = 1072 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 360 mr = 3043 m= 0 mr = 47 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3400000 number of dielectric boundary points 3276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1760 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6896 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8304180E-08 -1.0507141E-08 midg,1,midg; midg,igrid,midg -6.6844393E-08 3.1273249E-08 1,midg,midg; igrid,midg,midg -7.9867144E-09 -4.1044199E-08 gauss-seidel spectral radius is 0.9884690 estimated iterations to convergence 76 setup time was (sec) 0.6500000 now iterating at: 17:01:32 rms-change max change #iterations 0.1638239 26.62668 at 10iterations 1.7892925E-02 3.621366 at 20iterations 1.9818405E-03 0.2785797 at 30iterations 2.1716341E-04 3.5308838E-02 at 40iterations 2.3887122E-05 3.5095215E-03 at 50iterations finished qdiffx linear iterations at : 17:01:35 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 2.3887122E-05 3.5095215E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 17:01:38 4.322u 0.267s 0:07.87 58.1% 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 17:01:38 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: HIZ 230 has a net charge of 0.2000 !!! WARNING: HIZ 245 has a net charge of 0.2000 !!! WARNING: ZN6 647 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 has a net charge of 1.4000 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: 2.015931 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): -18.14600 28.39100 ymin,ymax (A): 2.243000 55.22100 zmin,zma (A): 111.7510 161.3650 x,y,z range (A): 46.53700 52.97800 49.61401 scale (grids/A): 2.015931 object centre (A): 5.122499 28.73200 136.5580 number of atom coordinates read : 1966 total number of charged atoms : 1835 net assigned charge : -8.699987 assigned positive charge : 281.8951 centred at (gu) : 84.87518 94.26750 91.75091 assigned negative charge : -290.5950 centred at (gu) : 85.26372 93.42601 91.41348 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 63639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19017 grid for indexing accessible points = 1.400000 m= 22198 mr = 41377 m= 3658 mr = 15846 m= 205 mr = 2204 m= 4 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.6300000 number of dielectric boundary points 30190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14545 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) : 0.6719770 object centre at (A) : 5.122499 28.73200 136.5580 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5244064E-02 -2.7024526E-02 midg,1,midg; midg,igrid,midg -5.5925459E-02 -1.2061384E-02 1,midg,midg; igrid,midg,midg 2.6640058E-02 -1.9630417E-02 gauss-seidel spectral radius is 0.9987136 estimated iterations to convergence 221 setup time was (sec) 1.000000 now iterating at: 17:01:39 rms-change max change #iterations 4.081597 202.1111 at 10iterations 1.931692 70.00693 at 20iterations 0.9261688 33.66328 at 30iterations 0.4431865 15.77526 at 40iterations 0.2108176 7.050630 at 50iterations 0.1008667 3.373172 at 60iterations 4.8036400E-02 1.548828 at 70iterations 2.3013882E-02 0.7778740 at 80iterations 1.0984840E-02 0.3534832 at 90iterations 5.2423924E-03 0.1657043 at 100iterations 2.5158580E-03 8.0669403E-02 at 110iterations 1.1978643E-03 3.7519455E-02 at 120iterations finished qdiffx linear iterations at : 17:01:47 total time elapsed so far: 9.460000 # loops : 120 mean,max change (kT/e) : 1.1978643E-03 3.7519455E-02 energy calculations done at 9.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 17:01:48 9.693u 0.275s 0:10.62 93.7% 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 17:01:49 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! WARNING: HIZ 69 has a net charge of 0.2000 !!! WARNING: HIZ 84 has a net charge of 0.2000 !!! WARNING: HIY 97 has a net charge of 0.2000 !!! WARNING: HIZ 119 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 129 has a net charge of 0.2000 !!! WARNING: HIZ 230 has a net charge of 0.2000 !!! WARNING: HIZ 245 has a net charge of 0.2000 !!! WARNING: ZN6 647 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 has a net charge of 1.4000 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: 3.023897 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): -18.14600 28.39100 ymin,ymax (A): 2.243000 55.22100 zmin,zma (A): 111.7510 161.3650 x,y,z range (A): 46.53700 52.97800 49.61401 scale (grids/A): 3.023897 object centre (A): 5.122499 28.73200 136.5580 number of atom coordinates read : 1966 total number of charged atoms : 1835 net assigned charge : -8.699987 assigned positive charge : 281.8951 centred at (gu) : 82.31271 96.40127 92.62642 assigned negative charge : -290.5950 centred at (gu) : 82.89551 95.13901 92.12025 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 146858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19017 grid for indexing accessible points = 1.400000 m= 70927 mr = 100813 m= 25976 mr = 56451 m= 6359 mr = 20448 m= 979 mr = 4758 m= 78 mr = 670 m= 0 mr = 37 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 1.600000 number of dielectric boundary points 68000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 14680 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) : 2.015931 object centre at (A) : 5.122499 28.73200 136.5580 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4686236 -0.2528004 midg,1,midg; midg,igrid,midg -0.4421347 -0.2004117 1,midg,midg; igrid,midg,midg 0.4104313 -0.1719598 gauss-seidel spectral radius is 0.9992748 estimated iterations to convergence 293 setup time was (sec) 1.990000 now iterating at: 17:01:51 rms-change max change #iterations 9.301487 317.3104 at 10iterations 5.442859 147.8245 at 20iterations 3.168608 74.80811 at 30iterations 1.839551 40.09566 at 40iterations 1.065645 24.72865 at 50iterations 0.6186684 13.77668 at 60iterations 0.3563207 6.763220 at 70iterations 0.2058224 3.804424 at 80iterations 0.1189804 2.556549 at 90iterations 6.8413317E-02 1.416209 at 100iterations 3.9529338E-02 0.7667923 at 110iterations 2.2778027E-02 0.4592519 at 120iterations 1.3157559E-02 0.2571697 at 130iterations 7.5827921E-03 0.1567947 at 140iterations 4.3737483E-03 8.0388069E-02 at 150iterations 2.5286505E-03 5.2254677E-02 at 160iterations 1.4613499E-03 2.6012421E-02 at 170iterations 8.4676407E-04 1.5769958E-02 at 180iterations finished qdiffx linear iterations at : 17:02:04 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 8.4676407E-04 1.5769958E-02 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 17:02:05 15.778u 0.311s 0:16.78 95.8% 0+0k 0+0io 0pf+0w