Tue Oct 11 03:35:16 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+sph.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 = amb.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 Tue Oct 11 2011 at 03:35:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 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: 0.6116313 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): -15.53500 26.71600 ymin,ymax (A): -2.645000 51.87000 zmin,zma (A): 60.31000 118.5150 x,y,z range (A): 42.25100 54.51500 58.20500 scale (grids/A): 0.6116313 object centre (A): 5.590500 24.61250 89.41250 number of atom coordinates read : 2169 total number of charged atoms : 2091 net assigned charge : -5.499980 assigned positive charge : 321.6565 centred at (gu) : 89.18944 89.33237 89.12014 assigned negative charge : -327.1569 centred at (gu) : 89.04282 89.43967 89.14352 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5523 nv = 96 ne = 84 npr = 43755 no. pairs analyzed = 43755 no. exposed pairs = 2745 no. arc points = 19691 no. surface atoms = 929 nbur = 1240 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 249 mr = 2963 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1883 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8551397E-09 -3.6480883E-09 midg,1,midg; midg,igrid,midg 1.4817872E-09 -7.0215740E-09 1,midg,midg; igrid,midg,midg -1.1888821E-08 2.4010958E-09 gauss-seidel spectral radius is 0.9861278 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 03:35:17 rms-change max change #iterations 0.1088055 19.51053 at 10iterations 9.6919332E-03 1.473881 at 20iterations 8.6083187E-04 0.1450214 at 30iterations 7.5229276E-05 1.1709213E-02 at 40iterations 6.7103151E-06 1.0528564E-03 at 50iterations finished qdiffx linear iterations at : 03:35:21 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 6.7103151E-06 1.0528564E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 03:35:21 4.586u 0.374s 0:05.28 93.7% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 03:35:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 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: 1.834894 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): -15.53500 26.71600 ymin,ymax (A): -2.645000 51.87000 zmin,zma (A): 60.31000 118.5150 x,y,z range (A): 42.25100 54.51500 58.20500 scale (grids/A): 1.834894 object centre (A): 5.590500 24.61250 89.41250 number of atom coordinates read : 2169 total number of charged atoms : 2091 net assigned charge : -5.499980 assigned positive charge : 321.6565 centred at (gu) : 87.56803 87.99690 87.36042 assigned negative charge : -327.1569 centred at (gu) : 87.12843 88.31891 87.43059 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19691 grid for indexing accessible points = 1.400000 m= 20619 mr = 40717 m= 2850 mr = 15086 m= 89 mr = 1622 m= 0 mr = 17 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 25885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16364 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) : 0.6116313 object centre at (A) : 5.590500 24.61250 89.41250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3332794E-03 -1.9534519E-02 midg,1,midg; midg,igrid,midg -3.5179950E-02 -4.0626582E-02 1,midg,midg; igrid,midg,midg -8.9631528E-03 1.6302854E-02 gauss-seidel spectral radius is 0.9984900 estimated iterations to convergence 204 setup time was (sec) 0.8000000 now iterating at: 03:35:22 rms-change max change #iterations 3.535367 178.2480 at 10iterations 1.592295 62.19508 at 20iterations 0.7168148 25.92225 at 30iterations 0.3213880 12.20608 at 40iterations 0.1450944 5.235081 at 50iterations 6.5333687E-02 2.386822 at 60iterations 2.9221850E-02 0.9608822 at 70iterations 1.3199661E-02 0.4544661 at 80iterations 5.9490264E-03 0.1943463 at 90iterations 2.6743948E-03 0.1007956 at 100iterations 1.2046403E-03 4.3251038E-02 at 110iterations 5.4239255E-04 2.2216797E-02 at 120iterations finished qdiffx linear iterations at : 03:35:33 total time elapsed so far: 10.88000 # loops : 120 mean,max change (kT/e) : 5.4239255E-04 2.2216797E-02 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 03:35:34 11.071u 0.509s 0:12.85 90.0% 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 Tue Oct 11 2011 at 03:35:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 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: 2.752341 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): -15.53500 26.71600 ymin,ymax (A): -2.645000 51.87000 zmin,zma (A): 60.31000 118.5150 x,y,z range (A): 42.25100 54.51500 58.20500 scale (grids/A): 2.752341 object centre (A): 5.590500 24.61250 89.41250 number of atom coordinates read : 2169 total number of charged atoms : 2091 net assigned charge : -5.499980 assigned positive charge : 321.6565 centred at (gu) : 86.35191 86.99514 86.04047 assigned negative charge : -327.1569 centred at (gu) : 85.69254 87.47841 86.14582 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 138556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19691 grid for indexing accessible points = 1.400000 m= 67714 mr = 99298 m= 23538 mr = 54959 m= 4807 mr = 18708 m= 442 mr = 3449 m= 22 mr = 263 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 58400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 16727 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) : 1.834894 object centre at (A) : 5.590500 24.61250 89.41250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7401039E-02 -0.2557006 midg,1,midg; midg,igrid,midg -0.3343896 -0.4747715 1,midg,midg; igrid,midg,midg -6.7880228E-02 0.2339164 gauss-seidel spectral radius is 0.9992138 estimated iterations to convergence 282 setup time was (sec) 1.630000 now iterating at: 03:35:37 rms-change max change #iterations 8.405622 300.9143 at 10iterations 4.765948 114.4021 at 20iterations 2.703807 57.75783 at 30iterations 1.522491 31.54451 at 40iterations 0.8598380 19.84832 at 50iterations 0.4849041 11.86550 at 60iterations 0.2732640 5.607183 at 70iterations 0.1542419 2.964989 at 80iterations 8.6909086E-02 1.812838 at 90iterations 4.8830789E-02 1.031162 at 100iterations 2.7523600E-02 0.5184898 at 110iterations 1.5516626E-02 0.3151002 at 120iterations 8.7103248E-03 0.1746597 at 130iterations 4.9244883E-03 0.1092310 at 140iterations 2.7702930E-03 5.2980423E-02 at 150iterations 1.5627556E-03 3.1345367E-02 at 160iterations 8.8098744E-04 1.7631531E-02 at 170iterations 4.9641210E-04 1.0079384E-02 at 180iterations finished qdiffx linear iterations at : 03:35:59 total time elapsed so far: 19.26000 # loops : 180 mean,max change (kT/e) : 4.9641210E-04 1.0079384E-02 energy calculations done at 19.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.43000 DelPhi exited at 03:35:59 19.439u 0.549s 0:25.38 78.6% 0+0k 0+0io 0pf+0w