Mon Oct 10 14:40:37 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 14:40:37 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 = 5010 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5145476 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): -20.15300 49.03400 ymin,ymax (A): 10.36400 73.14500 zmin,zma (A): 33.63400 95.21400 x,y,z range (A): 69.18700 62.78100 61.58000 scale (grids/A): 0.5145476 object centre (A): 14.44050 41.75450 64.42400 number of atom coordinates read : 5010 total number of charged atoms : 4850 net assigned charge : 1.000021 assigned positive charge : 750.6442 centred at (gu) : 90.23046 90.81275 90.16951 assigned negative charge : -749.6490 centred at (gu) : 90.23354 90.76742 90.18192 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8155 nv = 96 ne = 84 npr = 103980 no. pairs analyzed = 103980 no. exposed pairs = 6020 no. arc points = 39937 no. surface atoms = 2050 nbur = 2960 mkacc time = 0.2400000 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 = 1.652000 m= 303 mr = 4386 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3958 ## 513 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3094411E-11 -2.5538830E-11 midg,1,midg; midg,igrid,midg -1.0570630E-10 1.9949925E-10 1,midg,midg; igrid,midg,midg 2.4054696E-11 6.0380594E-12 gauss-seidel spectral radius is 0.9806883 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 14:40:38 rms-change max change #iterations 7.2517708E-02 10.69832 at 10iterations 4.9701533E-03 0.7895966 at 20iterations 1.1260496E-03 0.1794491 at 30iterations 4.6024169E-04 6.1367035E-02 at 40iterations 2.0216638E-04 2.6725769E-02 at 50iterations finished qdiffx linear iterations at : 14:40:41 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 2.0216638E-04 2.6725769E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 14:40:42 3.851u 0.199s 0:04.51 89.5% 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 14:40:42 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 = 5010 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.543643 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): -20.15300 49.03400 ymin,ymax (A): 10.36400 73.14500 zmin,zma (A): 33.63400 95.21400 x,y,z range (A): 69.18700 62.78100 61.58000 scale (grids/A): 1.543643 object centre (A): 14.44050 41.75450 64.42400 number of atom coordinates read : 5010 total number of charged atoms : 4850 net assigned charge : 1.000021 assigned positive charge : 750.6442 centred at (gu) : 90.68980 92.43626 90.50716 assigned negative charge : -749.6490 centred at (gu) : 90.69989 92.30188 90.54519 start vw surface at 0.2300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 93118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39937 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27605 mr = 65720 m= 2504 mr = 18667 m= 41 mr = 1139 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.7300000 number of dielectric boundary points 37742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 480 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 36546 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) : 0.5145476 object centre at (A) : 14.44050 41.75450 64.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2776355E-03 7.9136528E-03 midg,1,midg; midg,igrid,midg -7.3852097E-03 2.7437537E-04 1,midg,midg; igrid,midg,midg -2.5809618E-02 -5.2161897E-03 gauss-seidel spectral radius is 0.9981548 estimated iterations to convergence 185 setup time was (sec) 1.050000 now iterating at: 14:40:43 rms-change max change #iterations 3.943177 157.5959 at 10iterations 1.624529 53.08477 at 20iterations 0.6756192 21.05650 at 30iterations 0.2797954 8.553619 at 40iterations 0.1163180 3.428041 at 50iterations 4.8283607E-02 1.451706 at 60iterations 2.0297315E-02 0.5996695 at 70iterations 8.6700860E-03 0.2762699 at 80iterations 3.9102901E-03 0.1424494 at 90iterations 1.9382931E-03 5.7800293E-02 at 100iterations 1.1238635E-03 3.2985687E-02 at 110iterations 7.4756687E-04 1.9950867E-02 at 120iterations finished qdiffx linear iterations at : 14:40:51 total time elapsed so far: 8.930000 # loops : 120 mean,max change (kT/e) : 7.4756687E-04 1.9950867E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.120000 DelPhi exited at 14:40:52 9.122u 0.239s 0:09.77 95.7% 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 14:40:52 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 = 5010 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.315464 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): -20.15300 49.03400 ymin,ymax (A): 10.36400 73.14500 zmin,zma (A): 33.63400 95.21400 x,y,z range (A): 69.18700 62.78100 61.58000 scale (grids/A): 2.315464 object centre (A): 14.44050 41.75450 64.42400 number of atom coordinates read : 5010 total number of charged atoms : 4850 net assigned charge : 1.000021 assigned positive charge : 750.6442 centred at (gu) : 91.03423 93.65398 90.76028 assigned negative charge : -749.6490 centred at (gu) : 91.04969 93.45261 90.81785 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 217745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39937 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 98600 mr = 161547 m= 25622 mr = 77567 m= 3524 mr = 18935 m= 178 mr = 2257 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 374 time to turn everything in is 1.710000 number of dielectric boundary points 85302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 38706 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) : 1.543643 object centre at (A) : 14.44050 41.75450 64.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0881043E-02 0.1440182 midg,1,midg; midg,igrid,midg -0.1567014 -1.1523963E-02 1,midg,midg; igrid,midg,midg -0.5403103 -1.9475805E-02 gauss-seidel spectral radius is 0.9991733 estimated iterations to convergence 275 setup time was (sec) 2.040000 now iterating at: 14:40:54 rms-change max change #iterations 10.64280 286.9137 at 10iterations 6.126418 149.0744 at 20iterations 3.507530 86.73798 at 30iterations 1.996545 45.23605 at 40iterations 1.133386 22.31390 at 50iterations 0.6401260 12.16907 at 60iterations 0.3615302 6.475595 at 70iterations 0.2031373 3.592848 at 80iterations 0.1141385 2.036371 at 90iterations 6.4038098E-02 1.123140 at 100iterations 3.5876390E-02 0.6316690 at 110iterations 2.0175654E-02 0.4338472 at 120iterations 1.1323561E-02 0.2067137 at 130iterations 6.4249309E-03 0.1148357 at 140iterations 3.6926176E-03 6.7787170E-02 at 150iterations 2.1757528E-03 4.0473938E-02 at 160iterations 1.3409358E-03 2.4950027E-02 at 170iterations 8.8270247E-04 1.5472412E-02 at 180iterations finished qdiffx linear iterations at : 14:41:06 total time elapsed so far: 13.68000 # loops : 180 mean,max change (kT/e) : 8.8270247E-04 1.5472412E-02 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 14:41:06 13.870u 0.257s 0:14.45 97.7% 0+0k 0+0io 0pf+0w