Sat Oct 8 14:48:54 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 14:48:54 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6407257 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): -12.20900 43.35300 ymin,ymax (A): -23.86900 22.76600 zmin,zma (A): -7.726000 47.66900 x,y,z range (A): 55.56200 46.63500 55.39500 scale (grids/A): 0.6407257 object centre (A): 15.57200 -0.5515003 19.97150 number of atom coordinates read : 2975 total number of charged atoms : 2830 net assigned charge : 1.242007 assigned positive charge : 447.4657 centred at (gu) : 88.78854 89.96111 91.65064 assigned negative charge : -446.2244 centred at (gu) : 88.71112 89.80965 91.64514 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8078 nv = 96 ne = 84 npr = 61726 no. pairs analyzed = 61726 no. exposed pairs = 3410 no. arc points = 24122 no. surface atoms = 1168 nbur = 1807 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4653 m= 0 mr = 56 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2352 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9925073E-10 3.8989696E-09 midg,1,midg; midg,igrid,midg -1.9131749E-08 2.2096900E-08 1,midg,midg; igrid,midg,midg -1.1303286E-08 9.6005435E-09 gauss-seidel spectral radius is 0.9874099 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:48:54 rms-change max change #iterations 0.1617701 19.35584 at 10iterations 1.6028633E-02 1.904485 at 20iterations 1.6845262E-03 0.2300367 at 30iterations 2.1505383E-04 3.0593872E-02 at 40iterations 3.5785542E-05 4.8217773E-03 at 50iterations finished qdiffx linear iterations at : 14:48:57 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 3.5785542E-05 4.8217773E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 14:48:57 3.143u 0.146s 0:03.61 90.8% 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 14:48:57 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.922177 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): -12.20900 43.35300 ymin,ymax (A): -23.86900 22.76600 zmin,zma (A): -7.726000 47.66900 x,y,z range (A): 55.56200 46.63500 55.39500 scale (grids/A): 1.922177 object centre (A): 15.57200 -0.5515003 19.97150 number of atom coordinates read : 2975 total number of charged atoms : 2830 net assigned charge : 1.242007 assigned positive charge : 447.4657 centred at (gu) : 86.36485 89.88274 94.95123 assigned negative charge : -446.2244 centred at (gu) : 86.13332 89.42874 94.93517 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24122 grid for indexing accessible points = 1.400000 m= 31897 mr = 63402 m= 4754 mr = 23932 m= 321 mr = 2958 m= 1 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.5700000 number of dielectric boundary points 35009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 22291 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) : 0.6407257 object centre at (A) : 15.57200 -0.5515003 19.97150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7140918E-03 1.7031152E-02 midg,1,midg; midg,igrid,midg -6.4974665E-03 3.0266903E-02 1,midg,midg; igrid,midg,midg -4.4651121E-02 1.3876353E-02 gauss-seidel spectral radius is 0.9986914 estimated iterations to convergence 219 setup time was (sec) 0.8400000 now iterating at: 14:48:58 rms-change max change #iterations 4.674859 197.6451 at 10iterations 2.233708 64.51340 at 20iterations 1.064476 35.80069 at 30iterations 0.5078130 14.83690 at 40iterations 0.2412515 7.306185 at 50iterations 0.1152214 3.530905 at 60iterations 5.4709073E-02 1.475626 at 70iterations 2.6117655E-02 0.7167501 at 80iterations 1.2439717E-02 0.3520832 at 90iterations 5.9411856E-03 0.1556149 at 100iterations 2.8301331E-03 8.3762169E-02 at 110iterations 1.3504741E-03 4.1824341E-02 at 120iterations finished qdiffx linear iterations at : 14:49:04 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 1.3504741E-03 4.1824341E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 14:49:05 7.193u 0.172s 0:07.75 94.9% 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 14:49:05 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.883265 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): -12.20900 43.35300 ymin,ymax (A): -23.86900 22.76600 zmin,zma (A): -7.726000 47.66900 x,y,z range (A): 55.56200 46.63500 55.39500 scale (grids/A): 2.883265 object centre (A): 15.57200 -0.5515003 19.97150 number of atom coordinates read : 2975 total number of charged atoms : 2830 net assigned charge : 1.242007 assigned positive charge : 447.4657 centred at (gu) : 84.54726 89.82390 97.42666 assigned negative charge : -446.2244 centred at (gu) : 84.19988 89.14300 97.40276 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 205198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24122 grid for indexing accessible points = 1.400000 m= 103842 mr = 153448 m= 36523 mr = 86470 m= 8550 mr = 29444 m= 1340 mr = 6348 m= 124 mr = 923 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 1.500000 number of dielectric boundary points 78883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 22640 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) : 1.922177 object centre at (A) : 15.57200 -0.5515003 19.97150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6923376E-02 0.2910871 midg,1,midg; midg,igrid,midg -5.7682589E-02 0.3250610 1,midg,midg; igrid,midg,midg -0.4571082 0.1468148 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.770000 now iterating at: 14:49:07 rms-change max change #iterations 10.88517 478.0771 at 10iterations 6.383499 132.5514 at 20iterations 3.724151 68.11514 at 30iterations 2.167396 41.14882 at 40iterations 1.257302 25.03710 at 50iterations 0.7317845 14.79177 at 60iterations 0.4249867 7.335432 at 70iterations 0.2465064 4.868580 at 80iterations 0.1428942 2.564392 at 90iterations 8.2769625E-02 1.291214 at 100iterations 4.7975060E-02 0.8245392 at 110iterations 2.7818210E-02 0.4483795 at 120iterations 1.6110549E-02 0.2629738 at 130iterations 9.3534626E-03 0.1596203 at 140iterations 5.4099835E-03 8.7432861E-02 at 150iterations 3.1418395E-03 5.0654680E-02 at 160iterations 1.8391840E-03 3.1471252E-02 at 170iterations 1.0795476E-03 1.7591953E-02 at 180iterations finished qdiffx linear iterations at : 14:49:17 total time elapsed so far: 11.64000 # loops : 180 mean,max change (kT/e) : 1.0795476E-03 1.7591953E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 14:49:17 11.815u 0.196s 0:12.35 97.1% 0+0k 0+0io 0pf+0w