Sat Oct 8 15:53:22 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 Sat Oct 8 2011 at 15:53:22 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 = 2346 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: 0.6638942 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): -2.370000 46.83500 ymin,ymax (A): -16.83400 30.04400 zmin,zma (A): -18.75900 34.86400 x,y,z range (A): 49.20500 46.87800 53.62300 scale (grids/A): 0.6638942 object centre (A): 22.23250 6.605000 8.052502 number of atom coordinates read : 2346 total number of charged atoms : 2286 net assigned charge : 4.000002 assigned positive charge : 351.0070 centred at (gu) : 90.68346 88.99067 90.63930 assigned negative charge : -347.0078 centred at (gu) : 90.76961 89.12121 90.68301 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7087 nv = 96 ne = 84 npr = 46420 no. pairs analyzed = 46420 no. exposed pairs = 3042 no. arc points = 21020 no. surface atoms = 1037 nbur = 1309 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3898 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2800000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8475 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7283959E-08 2.9198735E-09 midg,1,midg; midg,igrid,midg 4.4838494E-08 -1.1713285E-08 1,midg,midg; igrid,midg,midg 2.4202118E-08 -6.7628565E-09 gauss-seidel spectral radius is 0.9882200 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 15:53:23 rms-change max change #iterations 0.1578483 22.60807 at 10iterations 1.6853072E-02 2.366539 at 20iterations 1.9110327E-03 0.2865334 at 30iterations 2.6562760E-04 3.5734177E-02 at 40iterations 5.6757246E-05 8.2330704E-03 at 50iterations finished qdiffx linear iterations at : 15:53:27 total time elapsed so far: 4.730000 # loops : 50 mean,max change (kT/e) : 5.6757246E-05 8.2330704E-03 energy calculations done at 4.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.910000 DelPhi exited at 15:53:27 4.911u 0.410s 0:05.61 94.8% 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 15:53:27 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 = 2346 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: 1.991683 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): -2.370000 46.83500 ymin,ymax (A): -16.83400 30.04400 zmin,zma (A): -18.75900 34.86400 x,y,z range (A): 49.20500 46.87800 53.62300 scale (grids/A): 1.991683 object centre (A): 22.23250 6.605000 8.052502 number of atom coordinates read : 2346 total number of charged atoms : 2286 net assigned charge : 4.000002 assigned positive charge : 351.0070 centred at (gu) : 92.04976 86.97144 91.91748 assigned negative charge : -347.0078 centred at (gu) : 92.30863 87.36349 92.04918 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21020 grid for indexing accessible points = 1.400000 m= 28517 mr = 53401 m= 5278 mr = 21161 m= 348 mr = 3493 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 666 time to turn everything in is 0.6500000 number of dielectric boundary points 32368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 18098 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) : 0.6638942 object centre at (A) : 22.23250 6.605000 8.052502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7943982E-02 4.9601682E-03 midg,1,midg; midg,igrid,midg 2.4739459E-02 -4.4648685E-03 1,midg,midg; igrid,midg,midg 1.2321884E-02 -5.2330989E-02 gauss-seidel spectral radius is 0.9987265 estimated iterations to convergence 222 setup time was (sec) 1.010000 now iterating at: 15:53:29 rms-change max change #iterations 4.372422 218.0374 at 10iterations 2.101206 65.12400 at 20iterations 1.009631 33.52158 at 30iterations 0.4859725 14.97130 at 40iterations 0.2336641 7.372931 at 50iterations 0.1124879 3.873615 at 60iterations 5.4103494E-02 1.634574 at 70iterations 2.6005913E-02 0.8440094 at 80iterations 1.2546306E-02 0.3688705 at 90iterations 6.0372711E-03 0.2004538 at 100iterations 2.9204369E-03 9.2454910E-02 at 110iterations 1.4191464E-03 4.7924042E-02 at 120iterations finished qdiffx linear iterations at : 15:53:41 total time elapsed so far: 12.98000 # loops : 120 mean,max change (kT/e) : 1.4191464E-03 4.7924042E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 15:53:41 13.156u 0.476s 0:13.91 97.9% 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 15:53:41 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 = 2346 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: 2.987524 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): -2.370000 46.83500 ymin,ymax (A): -16.83400 30.04400 zmin,zma (A): -18.75900 34.86400 x,y,z range (A): 49.20500 46.87800 53.62300 scale (grids/A): 2.987524 object centre (A): 22.23250 6.605000 8.052502 number of atom coordinates read : 2346 total number of charged atoms : 2286 net assigned charge : 4.000002 assigned positive charge : 351.0070 centred at (gu) : 93.07465 85.45692 92.87614 assigned negative charge : -347.0078 centred at (gu) : 93.46286 86.04533 93.07378 start vw surface at 0.1100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 176849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21020 grid for indexing accessible points = 1.400000 m= 90873 mr = 129540 m= 35279 mr = 74414 m= 9715 mr = 28601 m= 1529 mr = 7598 m= 84 mr = 1049 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 2027 time to turn everything in is 1.690000 number of dielectric boundary points 73093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 18288 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) : 1.991683 object centre at (A) : 22.23250 6.605000 8.052502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2381470 -3.4722923E-03 midg,1,midg; midg,igrid,midg 0.1379632 -4.9626015E-02 1,midg,midg; igrid,midg,midg 9.6250087E-02 -0.7533258 gauss-seidel spectral radius is 0.9992840 estimated iterations to convergence 295 setup time was (sec) 2.060000 now iterating at: 15:53:44 rms-change max change #iterations 10.07719 386.9729 at 10iterations 5.953099 136.2043 at 20iterations 3.522593 67.29726 at 30iterations 2.074741 42.29516 at 40iterations 1.217023 24.96642 at 50iterations 0.7117375 12.77884 at 60iterations 0.4173366 9.510349 at 70iterations 0.2425385 4.366465 at 80iterations 0.1419388 2.662697 at 90iterations 8.2514547E-02 1.475215 at 100iterations 4.8041981E-02 0.8497548 at 110iterations 2.7931966E-02 0.4714527 at 120iterations 1.6283827E-02 0.2933426 at 130iterations 9.4380984E-03 0.2098503 at 140iterations 5.4840902E-03 9.7928286E-02 at 150iterations 3.2047185E-03 5.5541992E-02 at 160iterations 1.8695421E-03 3.4679413E-02 at 170iterations 1.1010374E-03 1.9557953E-02 at 180iterations finished qdiffx linear iterations at : 15:54:03 total time elapsed so far: 21.58000 # loops : 180 mean,max change (kT/e) : 1.1010374E-03 1.9557953E-02 energy calculations done at 21.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.75000 DelPhi exited at 15:54:04 21.751u 0.506s 0:22.61 98.4% 0+0k 0+0io 0pf+0w