Sat Oct 8 16:47:43 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 16:47:43 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: FAD 994 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5640944 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): 16.93400 79.46799 ymin,ymax (A): 119.3900 182.5000 zmin,zma (A): -1.743000 56.01300 x,y,z range (A): 62.53400 63.11000 57.75600 scale (grids/A): 0.5640944 object centre (A): 48.20100 150.9450 27.13500 number of atom coordinates read : 4419 total number of charged atoms : 4251 net assigned charge : 4.500040 assigned positive charge : 683.2551 centred at (gu) : 92.00264 89.79805 88.08495 assigned negative charge : -678.7582 centred at (gu) : 91.98453 89.73949 88.09773 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9348 nv = 96 ne = 84 npr = 86431 no. pairs analyzed = 86431 no. exposed pairs = 5460 no. arc points = 38096 no. surface atoms = 1827 nbur = 2592 mkacc time = 0.2000000 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 = 1.540000 m= 435 mr = 5121 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3871 ## 478 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2456989E-09 1.9241050E-10 midg,1,midg; midg,igrid,midg -6.3278671E-10 1.5880608E-09 1,midg,midg; igrid,midg,midg 1.2486832E-10 1.4412309E-09 gauss-seidel spectral radius is 0.9839033 estimated iterations to convergence 65 setup time was (sec) 0.6900000 now iterating at: 16:47:44 rms-change max change #iterations 0.1084625 20.51094 at 10iterations 8.1363181E-03 1.164330 at 20iterations 9.7297318E-04 0.1299229 at 30iterations 2.5025991E-04 3.1097412E-02 at 40iterations 7.8931487E-05 1.0050774E-02 at 50iterations finished qdiffx linear iterations at : 16:47:47 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 7.8931487E-05 1.0050774E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 16:47:48 4.276u 0.237s 0:04.79 93.9% 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 16:47:48 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: FAD 994 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.692283 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): 16.93400 79.46799 ymin,ymax (A): 119.3900 182.5000 zmin,zma (A): -1.743000 56.01300 x,y,z range (A): 62.53400 63.11000 57.75600 scale (grids/A): 1.692283 object centre (A): 48.20100 150.9450 27.13500 number of atom coordinates read : 4419 total number of charged atoms : 4251 net assigned charge : 4.500040 assigned positive charge : 683.2551 centred at (gu) : 96.00658 89.39299 84.25399 assigned negative charge : -678.7582 centred at (gu) : 95.95329 89.21812 84.29311 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 104063 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38096 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 34910 mr = 73128 m= 4388 mr = 24699 m= 146 mr = 2428 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 479 time to turn everything in is 0.7300000 number of dielectric boundary points 43226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 435 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 32819 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) : 0.5640944 object centre at (A) : 48.20100 150.9450 27.13500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0448266E-03 6.9811032E-03 midg,1,midg; midg,igrid,midg 2.1111287E-02 5.2213423E-02 1,midg,midg; igrid,midg,midg -1.1534397E-02 -1.8970771E-02 gauss-seidel spectral radius is 0.9984600 estimated iterations to convergence 202 setup time was (sec) 1.070000 now iterating at: 16:47:49 rms-change max change #iterations 4.610095 226.6411 at 10iterations 2.053358 82.56488 at 20iterations 0.9174876 32.91518 at 30iterations 0.4097923 13.93197 at 40iterations 0.1830163 6.778582 at 50iterations 8.1902385E-02 2.379001 at 60iterations 3.6647141E-02 1.047557 at 70iterations 1.6435253E-02 0.4646602 at 80iterations 7.3404438E-03 0.2112031 at 90iterations 3.3104292E-03 9.4146729E-02 at 100iterations 1.4957680E-03 4.1456938E-02 at 110iterations 6.8655430E-04 2.0585060E-02 at 120iterations finished qdiffx linear iterations at : 16:47:58 total time elapsed so far: 9.680000 # loops : 120 mean,max change (kT/e) : 6.8655430E-04 2.0585060E-02 energy calculations done at 9.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 16:47:58 9.857u 0.267s 0:10.54 95.9% 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 16:47:58 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: FAD 994 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.538425 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): 16.93400 79.46799 ymin,ymax (A): 119.3900 182.5000 zmin,zma (A): -1.743000 56.01300 x,y,z range (A): 62.53400 63.11000 57.75600 scale (grids/A): 2.538425 object centre (A): 48.20100 150.9450 27.13500 number of atom coordinates read : 4419 total number of charged atoms : 4251 net assigned charge : 4.500040 assigned positive charge : 683.2551 centred at (gu) : 99.00972 89.08932 81.38083 assigned negative charge : -678.7582 centred at (gu) : 98.92998 88.82695 81.43976 start vw surface at 0.1900000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 241399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38096 grid for indexing accessible points = 1.400000 m= 118564 mr = 177837 m= 36892 mr = 95565 m= 7206 mr = 28216 m= 650 mr = 5066 m= 12 mr = 362 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 1337 time to turn everything in is 1.930000 number of dielectric boundary points 97677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 33985 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) : 1.692283 object centre at (A) : 48.20100 150.9450 27.13500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0083889E-02 0.1147426 midg,1,midg; midg,igrid,midg 0.2850531 0.8698016 1,midg,midg; igrid,midg,midg -0.1771091 -0.3120405 gauss-seidel spectral radius is 0.9992495 estimated iterations to convergence 288 setup time was (sec) 2.330000 now iterating at: 16:48:01 rms-change max change #iterations 11.64607 423.6293 at 10iterations 6.804478 145.2079 at 20iterations 3.965001 84.01860 at 30iterations 2.300000 41.55521 at 40iterations 1.326437 25.49295 at 50iterations 0.7673101 13.59439 at 60iterations 0.4405205 7.425755 at 70iterations 0.2537863 4.909347 at 80iterations 0.1454754 2.706421 at 90iterations 8.3601803E-02 1.337380 at 100iterations 4.7936503E-02 0.8107176 at 110iterations 2.7454391E-02 0.4457397 at 120iterations 1.5752876E-02 0.2681427 at 130iterations 9.0289470E-03 0.1497002 at 140iterations 5.1757386E-03 8.5731506E-02 at 150iterations 2.9614950E-03 4.8464775E-02 at 160iterations 1.6987599E-03 2.7912140E-02 at 170iterations 9.7316940E-04 1.5338898E-02 at 180iterations finished qdiffx linear iterations at : 16:48:16 total time elapsed so far: 17.34000 # loops : 180 mean,max change (kT/e) : 9.7316940E-04 1.5338898E-02 energy calculations done at 17.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.52000 DelPhi exited at 16:48:17 17.520u 0.334s 0:18.12 98.5% 0+0k 0+0io 0pf+0w