Mon Oct 10 17:03:49 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 Mon Oct 10 2011 at 17:03:49 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 = 2729 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5475659 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): 0.9060000 50.86800 ymin,ymax (A): -6.303000 45.78300 zmin,zma (A): 14.86900 79.88400 x,y,z range (A): 49.96200 52.08600 65.01500 scale (grids/A): 0.5475659 object centre (A): 25.88700 19.74000 47.37650 number of atom coordinates read : 2729 total number of charged atoms : 2589 net assigned charge : 4.000021 assigned positive charge : 405.6778 centred at (gu) : 89.88943 88.79924 90.84251 assigned negative charge : -401.6786 centred at (gu) : 89.98187 88.91330 90.84707 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5025 nv = 96 ne = 84 npr = 56119 no. pairs analyzed = 56119 no. exposed pairs = 3425 no. arc points = 24436 no. surface atoms = 1161 nbur = 1568 mkacc time = 0.1400000 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= 200 mr = 2454 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.3600000 number of dielectric boundary points 2763 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2455 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6761 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3210563E-10 2.7615410E-10 midg,1,midg; midg,igrid,midg 1.3091804E-09 -3.5368958E-10 1,midg,midg; igrid,midg,midg 8.5922119E-10 -3.3024697E-10 gauss-seidel spectral radius is 0.9827807 estimated iterations to convergence 63 setup time was (sec) 0.6000000 now iterating at: 17:03:50 rms-change max change #iterations 6.7567028E-02 12.48375 at 10iterations 4.6199341E-03 0.8132019 at 20iterations 3.0812039E-04 5.7123184E-02 at 30iterations 2.0995814E-05 3.5533905E-03 at 40iterations 1.5064902E-06 2.9087067E-04 at 50iterations finished qdiffx linear iterations at : 17:03:53 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.5064902E-06 2.9087067E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:03:54 3.405u 0.139s 0:05.07 69.6% 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 Mon Oct 10 2011 at 17:03:55 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 = 2729 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.642698 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): 0.9060000 50.86800 ymin,ymax (A): -6.303000 45.78300 zmin,zma (A): 14.86900 79.88400 x,y,z range (A): 49.96200 52.08600 65.01500 scale (grids/A): 1.642698 object centre (A): 25.88700 19.74000 47.37650 number of atom coordinates read : 2729 total number of charged atoms : 2589 net assigned charge : 4.000021 assigned positive charge : 405.6778 centred at (gu) : 89.66759 86.39722 92.52711 assigned negative charge : -401.6786 centred at (gu) : 89.94552 86.73981 92.54094 start vw surface at 0.2000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 55665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24436 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15457 mr = 36314 m= 1493 mr = 10096 m= 38 mr = 682 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 526 time to turn everything in is 0.5000000 number of dielectric boundary points 25561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19868 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) : 0.5475659 object centre at (A) : 25.88700 19.74000 47.37650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0971645E-02 -3.4481920E-02 midg,1,midg; midg,igrid,midg 2.0032695E-02 -1.8401018E-04 1,midg,midg; igrid,midg,midg 5.2089337E-03 -3.6390885E-03 gauss-seidel spectral radius is 0.9981714 estimated iterations to convergence 186 setup time was (sec) 0.7900000 now iterating at: 17:03:56 rms-change max change #iterations 3.151985 184.1376 at 10iterations 1.302170 57.79618 at 20iterations 0.5422140 22.52840 at 30iterations 0.2230187 8.730744 at 40iterations 9.3127333E-02 3.433872 at 50iterations 3.8598798E-02 1.403997 at 60iterations 1.6010610E-02 0.7101612 at 70iterations 6.6564213E-03 0.2750502 at 80iterations 2.7641810E-03 0.1233435 at 90iterations 1.1528244E-03 4.4542313E-02 at 100iterations 4.7782023E-04 1.7567158E-02 at 110iterations 1.9923871E-04 7.0056915E-03 at 120iterations finished qdiffx linear iterations at : 17:04:02 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.9923871E-04 7.0056915E-03 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 17:04:03 7.576u 0.215s 0:08.65 89.9% 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 Mon Oct 10 2011 at 17:04:03 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 = 2729 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: 2.464047 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): 0.9060000 50.86800 ymin,ymax (A): -6.303000 45.78300 zmin,zma (A): 14.86900 79.88400 x,y,z range (A): 49.96200 52.08600 65.01500 scale (grids/A): 2.464047 object centre (A): 25.88700 19.74000 47.37650 number of atom coordinates read : 2729 total number of charged atoms : 2589 net assigned charge : 4.000021 assigned positive charge : 405.6778 centred at (gu) : 89.50136 84.59567 93.79066 assigned negative charge : -401.6786 centred at (gu) : 89.91831 85.10967 93.81145 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 129477 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24436 grid for indexing accessible points = 1.400000 m= 53855 mr = 89419 m= 14458 mr = 41086 m= 2242 mr = 10607 m= 157 mr = 1398 m= 3 mr = 50 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1836 time to turn everything in is 1.020000 number of dielectric boundary points 57633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 20686 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) : 1.642698 object centre at (A) : 25.88700 19.74000 47.37650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2246075 -0.7870023 midg,1,midg; midg,igrid,midg 0.3175645 -4.6192776E-02 1,midg,midg; igrid,midg,midg 5.8067948E-02 -4.8384409E-02 gauss-seidel spectral radius is 0.9991260 estimated iterations to convergence 267 setup time was (sec) 1.350000 now iterating at: 17:04:05 rms-change max change #iterations 8.146551 286.0596 at 10iterations 4.541556 123.0371 at 20iterations 2.507345 66.44595 at 30iterations 1.389055 31.10073 at 40iterations 0.7638170 20.72080 at 50iterations 0.4198275 9.262131 at 60iterations 0.2305042 5.298530 at 70iterations 0.1262360 2.821434 at 80iterations 6.9005400E-02 1.583235 at 90iterations 3.7782647E-02 0.8280506 at 100iterations 2.0664658E-02 0.4687691 at 110iterations 1.1292542E-02 0.2461958 at 120iterations 6.1701732E-03 0.1353188 at 130iterations 3.3762604E-03 7.4308395E-02 at 140iterations 1.8441576E-03 4.3085098E-02 at 150iterations 1.0102162E-03 2.1068573E-02 at 160iterations 5.5105588E-04 1.2525082E-02 at 170iterations 3.0104929E-04 7.2154999E-03 at 180iterations finished qdiffx linear iterations at : 17:04:15 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 3.0104929E-04 7.2154999E-03 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 17:04:16 12.168u 0.198s 0:12.69 97.3% 0+0k 0+0io 0pf+0w