Sat Mar 3 15:39:10 PST 2012 #!/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_thinner.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 Mar 3 2012 at 15:39:10 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3529 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: 0.5932345 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 0.5932345 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3529 total number of charged atoms : 3381 net assigned charge : 2.000014 assigned positive charge : 539.1123 centred at (gu) : 88.73666 87.73935 89.97157 assigned negative charge : -537.1141 centred at (gu) : 88.74350 87.68259 89.93954 start vw surface at 0.1900000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7899 nv = 96 ne = 84 npr = 73172 no. pairs analyzed = 73172 no. exposed pairs = 3942 no. arc points = 27720 no. surface atoms = 1335 nbur = 2194 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 = 1.456000 m= 350 mr = 4472 m= 0 mr = 27 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.4500000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2875 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10262 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7090732E-10 2.0153550E-09 midg,1,midg; midg,igrid,midg -2.7309839E-09 1.8049799E-09 1,midg,midg; igrid,midg,midg 1.3495138E-09 3.4962472E-10 gauss-seidel spectral radius is 0.9853637 estimated iterations to convergence 68 setup time was (sec) 0.7300000 now iterating at: 15:39:11 rms-change max change #iterations 0.1209379 17.58260 at 10iterations 1.0018865E-02 1.523119 at 20iterations 8.4904244E-04 0.1107216 at 30iterations 7.2491333E-05 9.7312927E-03 at 40iterations 7.5025846E-06 1.1672974E-03 at 50iterations finished qdiffx linear iterations at : 15:39:14 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 7.5025846E-06 1.1672974E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 15:39:15 4.175u 0.253s 0:04.77 92.6% 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 Sat Mar 3 2012 at 15:39:15 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3529 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.779703 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 1.779703 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3529 total number of charged atoms : 3381 net assigned charge : 2.000014 assigned positive charge : 539.1123 centred at (gu) : 86.20938 83.21725 89.91400 assigned negative charge : -537.1141 centred at (gu) : 86.23016 83.04733 89.81847 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27720 grid for indexing accessible points = 1.400000 m= 29667 mr = 63184 m= 3791 mr = 21844 m= 144 mr = 2241 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3678 time to turn everything in is 0.7500000 number of dielectric boundary points 34627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 26342 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) : 0.5932345 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2218069E-02 -5.5826926E-03 midg,1,midg; midg,igrid,midg -4.5155426E-03 1.2191945E-02 1,midg,midg; igrid,midg,midg 2.9789053E-02 2.9788593E-02 gauss-seidel spectral radius is 0.9985180 estimated iterations to convergence 206 setup time was (sec) 1.060000 now iterating at: 15:39:16 rms-change max change #iterations 4.450974 151.9881 at 10iterations 2.023124 64.51665 at 20iterations 0.9147508 28.18954 at 30iterations 0.4163010 12.46504 at 40iterations 0.1887086 5.929241 at 50iterations 8.5914910E-02 2.575455 at 60iterations 3.8996570E-02 1.103439 at 70iterations 1.7703677E-02 0.6275654 at 80iterations 8.0665378E-03 0.2500632 at 90iterations 3.6696352E-03 0.1107216 at 100iterations 1.6631493E-03 5.2055359E-02 at 110iterations 7.5992406E-04 2.7098656E-02 at 120iterations finished qdiffx linear iterations at : 15:39:25 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 7.5992406E-04 2.7098656E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 15:39:25 9.604u 0.294s 0:10.19 97.0% 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 Sat Mar 3 2012 at 15:39:25 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3529 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.669555 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): 45.05900 103.8280 ymin,ymax (A): -27.25800 32.75200 zmin,zma (A): 1.826000 52.96600 x,y,z range (A): 58.76900 60.01000 51.14000 scale (grids/A): 2.669555 object centre (A): 74.44350 2.747000 27.39600 number of atom coordinates read : 3529 total number of charged atoms : 3381 net assigned charge : 2.000014 assigned positive charge : 539.1123 centred at (gu) : 84.31381 79.82551 89.87084 assigned negative charge : -537.1141 centred at (gu) : 84.34526 79.57085 89.72746 start vw surface at 0.1700000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 204634 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27720 grid for indexing accessible points = 1.400000 m= 100185 mr = 152814 m= 32114 mr = 82531 m= 6358 mr = 25486 m= 642 mr = 4728 m= 11 mr = 381 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 12484 time to turn everything in is 1.910000 number of dielectric boundary points 78004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 27038 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) : 1.779703 object centre at (A) : 74.44350 2.747000 27.39600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2951532 -6.0935427E-02 midg,1,midg; midg,igrid,midg -0.2513036 5.9356213E-02 1,midg,midg; igrid,midg,midg 0.3710629 0.3835672 gauss-seidel spectral radius is 0.9992373 estimated iterations to convergence 286 setup time was (sec) 2.240000 now iterating at: 15:39:28 rms-change max change #iterations 10.66718 305.9780 at 10iterations 6.143030 119.2513 at 20iterations 3.516225 65.72559 at 30iterations 2.012791 34.66502 at 40iterations 1.149499 23.68556 at 50iterations 0.6568983 11.35034 at 60iterations 0.3746158 6.748029 at 70iterations 0.2143565 3.933655 at 80iterations 0.1218997 2.187689 at 90iterations 6.9528066E-02 1.322041 at 100iterations 3.9583549E-02 0.7206402 at 110iterations 2.2587854E-02 0.4088757 at 120iterations 1.2892911E-02 0.2368479 at 130iterations 7.3469258E-03 0.1476135 at 140iterations 4.1925739E-03 7.5678110E-02 at 150iterations 2.3921344E-03 4.1470528E-02 at 160iterations 1.3670208E-03 2.4496078E-02 at 170iterations 7.8506127E-04 1.3473511E-02 at 180iterations finished qdiffx linear iterations at : 15:39:42 total time elapsed so far: 16.04000 # loops : 180 mean,max change (kT/e) : 7.8506127E-04 1.3473511E-02 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.20000 DelPhi exited at 15:39:42 16.202u 0.344s 0:16.81 98.3% 0+0k 0+0io 0pf+0w