Sat Oct 8 20:29:21 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 Sat Oct 8 2011 at 20:29:21 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6344567 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): -31.70700 17.39300 ymin,ymax (A): -23.11500 22.70400 zmin,zma (A): -11.90900 44.20200 x,y,z range (A): 49.10000 45.81900 56.11100 scale (grids/A): 0.6344567 object centre (A): -7.157001 -0.2054996 16.14650 number of atom coordinates read : 2570 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 88.59496 89.15108 89.78796 assigned negative charge : -389.5226 centred at (gu) : 88.49187 89.20348 89.67744 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 53396 no. pairs analyzed = 53396 no. exposed pairs = 3008 no. arc points = 21441 no. surface atoms = 1010 nbur = 1560 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3735 m= 0 mr = 46 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.3900000 number of dielectric boundary points 3283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2090 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8259 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1331816E-09 1.4672227E-08 midg,1,midg; midg,igrid,midg 1.1577641E-08 -6.8356693E-10 1,midg,midg; igrid,midg,midg -8.3435161E-09 1.0824479E-08 gauss-seidel spectral radius is 0.9871237 estimated iterations to convergence 72 setup time was (sec) 0.7100000 now iterating at: 20:29:22 rms-change max change #iterations 0.1419408 20.23981 at 10iterations 1.3811888E-02 1.822891 at 20iterations 1.3761112E-03 0.1939812 at 30iterations 1.4958688E-04 2.1734238E-02 at 40iterations 2.1502310E-05 4.0578842E-03 at 50iterations finished qdiffx linear iterations at : 20:29:26 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 2.1502310E-05 4.0578842E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 20:29:26 4.482u 0.396s 0:05.15 94.5% 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 Sat Oct 8 2011 at 20:29:26 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.903370 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): -31.70700 17.39300 ymin,ymax (A): -23.11500 22.70400 zmin,zma (A): -11.90900 44.20200 x,y,z range (A): 49.10000 45.81900 56.11100 scale (grids/A): 1.903370 object centre (A): -7.157001 -0.2054996 16.14650 number of atom coordinates read : 2570 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 85.78431 87.45274 89.36370 assigned negative charge : -389.5226 centred at (gu) : 85.47540 87.61016 89.03217 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 73073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21441 grid for indexing accessible points = 1.400000 m= 25819 mr = 51164 m= 3851 mr = 19002 m= 207 mr = 2386 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3361 time to turn everything in is 0.7400000 number of dielectric boundary points 30344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 19240 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) : 0.6344567 object centre at (A) : -7.157001 -0.2054996 16.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8837539E-02 2.5911542E-02 midg,1,midg; midg,igrid,midg 1.4707978E-02 -2.7108483E-04 1,midg,midg; igrid,midg,midg -7.3161442E-03 3.4339834E-02 gauss-seidel spectral radius is 0.9986280 estimated iterations to convergence 214 setup time was (sec) 1.060000 now iterating at: 20:29:28 rms-change max change #iterations 4.247380 170.8972 at 10iterations 1.984611 62.14093 at 20iterations 0.9289143 30.86921 at 30iterations 0.4337701 15.25726 at 40iterations 0.2021717 6.304012 at 50iterations 9.4727762E-02 2.932173 at 60iterations 4.4376493E-02 1.589830 at 70iterations 2.0703260E-02 0.6486139 at 80iterations 9.7043589E-03 0.3060951 at 90iterations 4.5289118E-03 0.1427488 at 100iterations 2.1200695E-03 6.5322876E-02 at 110iterations 9.9715253E-04 3.2533646E-02 at 120iterations finished qdiffx linear iterations at : 20:29:37 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 9.9715253E-04 3.2533646E-02 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.61000 DelPhi exited at 20:29:38 10.615u 0.449s 0:11.39 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 Sat Oct 8 2011 at 20:29:38 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.855055 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): -31.70700 17.39300 ymin,ymax (A): -23.11500 22.70400 zmin,zma (A): -11.90900 44.20200 x,y,z range (A): 49.10000 45.81900 56.11100 scale (grids/A): 2.855055 object centre (A): -7.157001 -0.2054996 16.14650 number of atom coordinates read : 2570 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 83.67641 86.17908 89.04553 assigned negative charge : -389.5226 centred at (gu) : 83.21296 86.41524 88.54821 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 169377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21441 grid for indexing accessible points = 1.400000 m= 84500 mr = 123593 m= 29060 mr = 69615 m= 6700 mr = 23277 m= 791 mr = 4999 m= 34 mr = 484 m= 0 mr = 14 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 11031 time to turn everything in is 1.920000 number of dielectric boundary points 68480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 19589 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) : 1.903370 object centre at (A) : -7.157001 -0.2054996 16.14650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4991915E-02 0.2842017 midg,1,midg; midg,igrid,midg 0.1722103 -3.6045838E-02 1,midg,midg; igrid,midg,midg -6.8413191E-02 0.4264997 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 2.260000 now iterating at: 20:29:40 rms-change max change #iterations 9.872025 381.8627 at 10iterations 5.708579 127.7291 at 20iterations 3.290579 63.50719 at 30iterations 1.891391 37.72025 at 40iterations 1.086359 20.69531 at 50iterations 0.6249760 11.91643 at 60iterations 0.3582172 6.443313 at 70iterations 0.2054282 3.972518 at 80iterations 0.1178092 2.318970 at 90iterations 6.7407958E-02 1.214310 at 100iterations 3.8604673E-02 0.7028694 at 110iterations 2.2197282E-02 0.3910127 at 120iterations 1.2672039E-02 0.2462597 at 130iterations 7.2617428E-03 0.1353035 at 140iterations 4.1625639E-03 7.8357697E-02 at 150iterations 2.3872764E-03 4.8147202E-02 at 160iterations 1.3712947E-03 2.5728226E-02 at 170iterations 7.8599324E-04 1.5205383E-02 at 180iterations finished qdiffx linear iterations at : 20:29:56 total time elapsed so far: 17.42000 # loops : 180 mean,max change (kT/e) : 7.8599324E-04 1.5205383E-02 energy calculations done at 17.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.63000 DelPhi exited at 20:29:56 17.631u 0.501s 0:18.44 98.3% 0+0k 0+0io 0pf+0w