Sat Oct 8 19:46:03 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 19:46:03 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 611 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6228567 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): -31.83800 17.99000 ymin,ymax (A): -24.59000 23.35700 zmin,zma (A): -12.49700 44.65900 x,y,z range (A): 49.82800 47.94700 57.15600 scale (grids/A): 0.6228567 object centre (A): -6.924001 -0.6164999 16.08100 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.300008 assigned positive charge : 391.4040 centred at (gu) : 88.43462 89.16154 89.83875 assigned negative charge : -387.1045 centred at (gu) : 88.31479 89.20159 89.73431 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6765 nv = 96 ne = 84 npr = 52665 no. pairs analyzed = 52665 no. exposed pairs = 3074 no. arc points = 21724 no. surface atoms = 1038 nbur = 1547 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3808 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.3100000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2169 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8121981E-09 1.0925226E-08 midg,1,midg; midg,igrid,midg 8.1316545E-09 8.8228491E-10 1,midg,midg; igrid,midg,midg -6.9408630E-09 8.8130703E-09 gauss-seidel spectral radius is 0.9866487 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 19:46:04 rms-change max change #iterations 0.1306229 17.79240 at 10iterations 1.2230695E-02 1.674866 at 20iterations 1.1696947E-03 0.1531162 at 30iterations 1.1810765E-04 1.7658234E-02 at 40iterations 1.3695441E-05 2.2449493E-03 at 50iterations finished qdiffx linear iterations at : 19:46:07 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.3695441E-05 2.2449493E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 19:46:08 4.476u 0.420s 0:05.15 94.9% 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 Oct 8 2011 at 19:46:08 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 611 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.868570 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): -31.83800 17.99000 ymin,ymax (A): -24.59000 23.35700 zmin,zma (A): -12.49700 44.65900 x,y,z range (A): 49.82800 47.94700 57.15600 scale (grids/A): 1.868570 object centre (A): -6.924001 -0.6164999 16.08100 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.300008 assigned positive charge : 391.4040 centred at (gu) : 85.30365 87.48428 89.51581 assigned negative charge : -387.1045 centred at (gu) : 84.94431 87.60463 89.20274 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 73032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21724 grid for indexing accessible points = 1.400000 m= 26444 mr = 51262 m= 3917 mr = 19810 m= 222 mr = 2545 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3853 time to turn everything in is 0.5900000 number of dielectric boundary points 29915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19282 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) : 0.6228567 object centre at (A) : -6.924001 -0.6164999 16.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1150547E-02 2.3500731E-02 midg,1,midg; midg,igrid,midg 1.5088390E-02 5.2707242E-03 1,midg,midg; igrid,midg,midg -6.1979182E-03 3.6924768E-02 gauss-seidel spectral radius is 0.9985817 estimated iterations to convergence 210 setup time was (sec) 0.9000000 now iterating at: 19:46:09 rms-change max change #iterations 4.032019 168.0521 at 10iterations 1.863810 64.69051 at 20iterations 0.8579708 31.71003 at 30iterations 0.3950221 12.08818 at 40iterations 0.1826434 6.731877 at 50iterations 8.4524736E-02 2.593533 at 60iterations 3.8951430E-02 1.275711 at 70iterations 1.8075837E-02 0.5822220 at 80iterations 8.3114924E-03 0.2817535 at 90iterations 3.8300443E-03 0.1191673 at 100iterations 1.7722440E-03 6.3205719E-02 at 110iterations 8.2202017E-04 2.7646065E-02 at 120iterations finished qdiffx linear iterations at : 19:46:19 total time elapsed so far: 10.49000 # loops : 120 mean,max change (kT/e) : 8.2202017E-04 2.7646065E-02 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 19:46:19 10.671u 0.438s 0:11.36 97.7% 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 Sat Oct 8 2011 at 19:46:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 611 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.802855 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): -31.83800 17.99000 ymin,ymax (A): -24.59000 23.35700 zmin,zma (A): -12.49700 44.65900 x,y,z range (A): 49.82800 47.94700 57.15600 scale (grids/A): 2.802855 object centre (A): -6.924001 -0.6164999 16.08100 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.300008 assigned positive charge : 391.4040 centred at (gu) : 82.95541 86.22611 89.27356 assigned negative charge : -387.1045 centred at (gu) : 82.41646 86.40673 88.80411 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21724 grid for indexing accessible points = 1.400000 m= 86554 mr = 123984 m= 30514 mr = 71670 m= 7095 mr = 24765 m= 895 mr = 5496 m= 56 mr = 619 m= 0 mr = 26 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 13056 time to turn everything in is 1.500000 number of dielectric boundary points 67453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 19627 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) : 1.868570 object centre at (A) : -6.924001 -0.6164999 16.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8387251E-03 0.2227519 midg,1,midg; midg,igrid,midg 0.1923015 7.6113135E-02 1,midg,midg; igrid,midg,midg -4.2636577E-02 0.4782511 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.820000 now iterating at: 19:46:22 rms-change max change #iterations 9.582644 363.8468 at 10iterations 5.520766 128.9164 at 20iterations 3.162414 69.16116 at 30iterations 1.807502 39.13414 at 40iterations 1.033748 24.72262 at 50iterations 0.5904468 12.00618 at 60iterations 0.3377945 6.475918 at 70iterations 0.1926364 3.834630 at 80iterations 0.1097123 2.435505 at 90iterations 6.2758394E-02 1.125259 at 100iterations 3.5827674E-02 0.6785221 at 110iterations 2.0424478E-02 0.4249039 at 120iterations 1.1616774E-02 0.2277523 at 130iterations 6.6450201E-03 0.1271286 at 140iterations 3.7999833E-03 7.3759079E-02 at 150iterations 2.1694722E-03 4.1124821E-02 at 160iterations 1.2447654E-03 2.5384903E-02 at 170iterations 7.1977556E-04 1.4271736E-02 at 180iterations finished qdiffx linear iterations at : 19:46:38 total time elapsed so far: 17.89000 # loops : 180 mean,max change (kT/e) : 7.1977556E-04 1.4271736E-02 energy calculations done at 17.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.05000 DelPhi exited at 19:46:38 18.055u 0.496s 0:18.83 98.4% 0+0k 0+0io 0pf+0w