Sat Oct 15 15:12:10 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 15 2011 at 15:12:10 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2835 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6660928 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): -11.26500 37.25200 ymin,ymax (A): -26.57200 22.69400 zmin,zma (A): -7.980000 45.46600 x,y,z range (A): 48.51700 49.26600 53.44600 scale (grids/A): 0.6660928 object centre (A): 12.99350 -1.939000 18.74300 number of atom coordinates read : 2835 total number of charged atoms : 2675 net assigned charge : 3.451019 assigned positive charge : 433.5975 centred at (gu) : 89.97450 90.38580 91.44686 assigned negative charge : -430.1471 centred at (gu) : 89.71104 90.31827 91.61678 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8362 nv = 96 ne = 84 npr = 57631 no. pairs analyzed = 57631 no. exposed pairs = 3387 no. arc points = 23661 no. surface atoms = 1126 nbur = 1709 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 4823 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 109 time to turn everything in is 0.2200000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2259 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9849 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9852072E-08 -4.5236714E-08 midg,1,midg; midg,igrid,midg -5.7273173E-09 3.0567406E-08 1,midg,midg; igrid,midg,midg -5.8380561E-08 7.6132444E-08 gauss-seidel spectral radius is 0.9883339 estimated iterations to convergence 76 setup time was (sec) 0.4100000 now iterating at: 15:12:11 rms-change max change #iterations 0.1879725 23.35155 at 10iterations 2.0883488E-02 2.905334 at 20iterations 2.5749039E-03 0.3214417 at 30iterations 5.0457567E-04 6.7853928E-02 at 40iterations 1.5298935E-04 1.9588470E-02 at 50iterations finished qdiffx linear iterations at : 15:12:14 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.5298935E-04 1.9588470E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 15:12:14 3.400u 0.160s 0:04.05 87.9% 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 15 2011 at 15:12:14 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2835 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 1.998278 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): -11.26500 37.25200 ymin,ymax (A): -26.57200 22.69400 zmin,zma (A): -7.980000 45.46600 x,y,z range (A): 48.51700 49.26600 53.44600 scale (grids/A): 1.998278 object centre (A): 12.99350 -1.939000 18.74300 number of atom coordinates read : 2835 total number of charged atoms : 2675 net assigned charge : 3.451019 assigned positive charge : 433.5975 centred at (gu) : 89.92297 91.15685 94.34007 assigned negative charge : -430.1471 centred at (gu) : 89.13277 90.95428 94.84994 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 89519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23661 grid for indexing accessible points = 1.400000 m= 34937 mr = 63581 m= 6246 mr = 26691 m= 427 mr = 4240 m= 5 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2462 time to turn everything in is 0.4300000 number of dielectric boundary points 36444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 21151 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) : 0.6660928 object centre at (A) : 12.99350 -1.939000 18.74300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0488892E-02 -9.8910090E-03 midg,1,midg; midg,igrid,midg -1.7495649E-02 -1.2770709E-02 1,midg,midg; igrid,midg,midg -1.7615631E-02 8.5712016E-02 gauss-seidel spectral radius is 0.9987753 estimated iterations to convergence 226 setup time was (sec) 0.6400000 now iterating at: 15:12:15 rms-change max change #iterations 4.966543 193.3236 at 10iterations 2.428484 71.41666 at 20iterations 1.186745 35.63939 at 30iterations 0.5810618 16.51531 at 40iterations 0.2826960 8.802250 at 50iterations 0.1382148 3.763159 at 60iterations 6.7450464E-02 1.751484 at 70iterations 3.3046447E-02 0.9462118 at 80iterations 1.6201315E-02 0.4623566 at 90iterations 7.9832040E-03 0.2125282 at 100iterations 3.9456426E-03 0.1377678 at 110iterations 1.9908426E-03 5.5801392E-02 at 120iterations finished qdiffx linear iterations at : 15:12:22 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.9908426E-03 5.5801392E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 15:12:23 7.882u 0.205s 0:08.53 94.7% 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 Sat Oct 15 2011 at 15:12:23 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2835 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.997418 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): -11.26500 37.25200 ymin,ymax (A): -26.57200 22.69400 zmin,zma (A): -7.980000 45.46600 x,y,z range (A): 48.51700 49.26600 53.44600 scale (grids/A): 2.997418 object centre (A): 12.99350 -1.939000 18.74300 number of atom coordinates read : 2835 total number of charged atoms : 2675 net assigned charge : 3.451019 assigned positive charge : 433.5975 centred at (gu) : 89.88433 91.73489 96.51001 assigned negative charge : -430.1471 centred at (gu) : 88.69905 91.43130 97.27484 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 206617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23661 grid for indexing accessible points = 1.400000 m= 110331 mr = 153157 m= 43515 mr = 92017 m= 11541 mr = 36027 m= 1860 mr = 9026 m= 136 mr = 1335 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 8453 time to turn everything in is 1.180000 number of dielectric boundary points 82359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 21396 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) : 1.998278 object centre at (A) : 12.99350 -1.939000 18.74300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5649225 0.1744233 midg,1,midg; midg,igrid,midg -0.1746765 -0.1862502 1,midg,midg; igrid,midg,midg -7.7116497E-02 0.7550040 gauss-seidel spectral radius is 0.9992914 estimated iterations to convergence 296 setup time was (sec) 1.430000 now iterating at: 15:12:25 rms-change max change #iterations 11.28162 459.5139 at 10iterations 6.616222 135.3231 at 20iterations 3.887622 68.02248 at 30iterations 2.283981 42.70932 at 40iterations 1.338238 22.58863 at 50iterations 0.7822328 13.71323 at 60iterations 0.4579310 8.857912 at 70iterations 0.2670883 4.338810 at 80iterations 0.1560549 2.556437 at 90iterations 9.1264121E-02 1.487172 at 100iterations 5.3209946E-02 0.8772850 at 110iterations 3.1120956E-02 0.4886122 at 120iterations 1.8211640E-02 0.3126984 at 130iterations 1.0723564E-02 0.1745195 at 140iterations 6.3663768E-03 0.1049538 at 150iterations 3.8329295E-03 6.2759399E-02 at 160iterations 2.3683249E-03 4.1391373E-02 at 170iterations 1.5277779E-03 2.9693604E-02 at 180iterations finished qdiffx linear iterations at : 15:12:37 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 1.5277779E-03 2.9693604E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 15:12:37 13.762u 0.236s 0:14.31 97.7% 0+0k 0+0io 0pf+0w