Sat Oct 15 12:08:27 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 15 2011 at 12:08:27 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 = 2428 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5983294 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): -7.8999996E-02 53.12500 ymin,ymax (A): -15.63200 27.52100 zmin,zma (A): 24.55600 84.05500 x,y,z range (A): 53.20400 43.15300 59.49900 scale (grids/A): 0.5983294 object centre (A): 26.52300 5.944500 54.30550 number of atom coordinates read : 2428 total number of charged atoms : 2292 net assigned charge : 10.50003 assigned positive charge : 351.7012 centred at (gu) : 90.51234 89.33959 90.36673 assigned negative charge : -341.2020 centred at (gu) : 90.51833 89.45563 90.34136 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5851 nv = 96 ne = 84 npr = 48377 no. pairs analyzed = 48377 no. exposed pairs = 3282 no. arc points = 23510 no. surface atoms = 1094 nbur = 1334 mkacc time = 7.9999998E-02 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= 282 mr = 2907 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2328 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7231 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1923000E-09 5.4268794E-09 midg,1,midg; midg,igrid,midg 8.9624681E-09 5.8626748E-10 1,midg,midg; igrid,midg,midg 3.9436796E-09 4.5324571E-09 gauss-seidel spectral radius is 0.9855382 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 12:08:28 rms-change max change #iterations 9.7359434E-02 17.08084 at 10iterations 8.1872903E-03 1.281811 at 20iterations 7.2299526E-04 0.1150246 at 30iterations 6.8928646E-05 1.0232925E-02 at 40iterations 8.8112838E-06 1.2588501E-03 at 50iterations finished qdiffx linear iterations at : 12:08:31 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 8.8112838E-06 1.2588501E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 12:08:32 3.934u 0.243s 0:04.55 91.6% 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 Sat Oct 15 2011 at 12:08:32 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 = 2428 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.794988 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): -7.8999996E-02 53.12500 ymin,ymax (A): -15.63200 27.52100 zmin,zma (A): 24.55600 84.05500 x,y,z range (A): 53.20400 43.15300 59.49900 scale (grids/A): 1.794988 object centre (A): 26.52300 5.944500 54.30550 number of atom coordinates read : 2428 total number of charged atoms : 2292 net assigned charge : 10.50003 assigned positive charge : 351.7012 centred at (gu) : 91.53680 88.01839 91.09962 assigned negative charge : -341.2020 centred at (gu) : 91.55495 88.36671 91.02407 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23510 grid for indexing accessible points = 1.400000 m= 20885 mr = 41581 m= 3022 mr = 14387 m= 142 mr = 1738 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 29659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 233 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 17905 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) : 0.5983294 object centre at (A) : 26.52300 5.944500 54.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5347697E-02 4.8899859E-02 midg,1,midg; midg,igrid,midg 1.9615833E-02 -5.5865790E-03 1,midg,midg; igrid,midg,midg 3.0938817E-02 3.1687748E-02 gauss-seidel spectral radius is 0.9984622 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 12:08:33 rms-change max change #iterations 3.525157 186.0964 at 10iterations 1.563195 60.41341 at 20iterations 0.6954051 25.56393 at 30iterations 0.3111727 11.80066 at 40iterations 0.1385081 4.813731 at 50iterations 6.1991017E-02 2.352180 at 60iterations 2.7713519E-02 1.038900 at 70iterations 1.2385602E-02 0.4263687 at 80iterations 5.5508828E-03 0.2031269 at 90iterations 2.4733108E-03 9.2493057E-02 at 100iterations 1.1063355E-03 3.9045334E-02 at 110iterations 4.9622526E-04 1.7822266E-02 at 120iterations finished qdiffx linear iterations at : 12:08:41 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 4.9622526E-04 1.7822266E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 12:08:41 8.347u 0.229s 0:08.98 95.3% 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 15 2011 at 12:08:41 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 = 2428 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.692482 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): -7.8999996E-02 53.12500 ymin,ymax (A): -15.63200 27.52100 zmin,zma (A): 24.55600 84.05500 x,y,z range (A): 53.20400 43.15300 59.49900 scale (grids/A): 2.692482 object centre (A): 26.52300 5.944500 54.30550 number of atom coordinates read : 2428 total number of charged atoms : 2292 net assigned charge : 10.50003 assigned positive charge : 351.7012 centred at (gu) : 92.30513 87.02758 91.64941 assigned negative charge : -341.2020 centred at (gu) : 92.33239 87.55024 91.53628 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 146610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23510 grid for indexing accessible points = 1.400000 m= 68699 mr = 101855 m= 23086 mr = 53796 m= 5286 mr = 17697 m= 694 mr = 3827 m= 34 mr = 393 m= 0 mr = 18 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 66823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 18330 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) : 1.794988 object centre at (A) : 26.52300 5.944500 54.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3142688 0.7712501 midg,1,midg; midg,igrid,midg 0.2332107 -8.2467437E-02 1,midg,midg; igrid,midg,midg 0.3905568 0.3652773 gauss-seidel spectral radius is 0.9992181 estimated iterations to convergence 282 setup time was (sec) 1.080000 now iterating at: 12:08:42 rms-change max change #iterations 8.628522 336.5216 at 10iterations 4.982224 141.0993 at 20iterations 2.870967 64.85090 at 30iterations 1.642189 36.97076 at 40iterations 0.9377864 19.44172 at 50iterations 0.5343120 12.34540 at 60iterations 0.3036309 6.360458 at 70iterations 0.1724079 3.692795 at 80iterations 9.7887143E-02 1.984051 at 90iterations 5.5469424E-02 1.137081 at 100iterations 3.1454168E-02 0.6388702 at 110iterations 1.7868344E-02 0.3779540 at 120iterations 1.0076118E-02 0.2120910 at 130iterations 5.7156780E-03 0.1121483 at 140iterations 3.2350759E-03 6.4156532E-02 at 150iterations 1.8339349E-03 3.8618088E-02 at 160iterations 1.0390686E-03 2.1585464E-02 at 170iterations 5.9085933E-04 1.1415482E-02 at 180iterations finished qdiffx linear iterations at : 12:08:54 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 5.9085933E-04 1.1415482E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 12:08:55 13.002u 0.249s 0:13.53 97.8% 0+0k 0+0io 0pf+0w