Sat Oct 8 19:08:11 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 19:08:11 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 = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6245504 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): -31.98900 17.46400 ymin,ymax (A): -25.48500 21.91500 zmin,zma (A): -12.56000 44.44100 x,y,z range (A): 49.45300 47.40000 57.00100 scale (grids/A): 0.6245504 object centre (A): -7.262500 -1.785000 15.94050 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.800007 assigned positive charge : 393.3700 centred at (gu) : 88.52322 89.22853 89.92197 assigned negative charge : -388.5705 centred at (gu) : 88.40572 89.27029 89.80801 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6758 nv = 96 ne = 84 npr = 53507 no. pairs analyzed = 53507 no. exposed pairs = 3032 no. arc points = 21658 no. surface atoms = 1029 nbur = 1573 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3822 m= 0 mr = 46 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2000000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2449626E-09 1.2853659E-08 midg,1,midg; midg,igrid,midg 9.1150687E-09 1.2047643E-09 1,midg,midg; igrid,midg,midg -6.3065619E-09 9.6776294E-09 gauss-seidel spectral radius is 0.9867208 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 19:08:12 rms-change max change #iterations 0.1331559 19.06328 at 10iterations 1.2589416E-02 2.292358 at 20iterations 1.1773064E-03 0.1639080 at 30iterations 1.1286463E-04 1.6387939E-02 at 40iterations 1.0562549E-05 1.7147064E-03 at 50iterations finished qdiffx linear iterations at : 19:08:15 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 1.0562549E-05 1.7147064E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 19:08:15 3.594u 0.180s 0:04.04 93.3% 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 8 2011 at 19:08:15 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.873651 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): -31.98900 17.46400 ymin,ymax (A): -25.48500 21.91500 zmin,zma (A): -12.56000 44.44100 x,y,z range (A): 49.45300 47.40000 57.00100 scale (grids/A): 1.873651 object centre (A): -7.262500 -1.785000 15.94050 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.800007 assigned positive charge : 393.3700 centred at (gu) : 85.56935 87.68508 89.76550 assigned negative charge : -388.5705 centred at (gu) : 85.21710 87.81070 89.42369 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21658 grid for indexing accessible points = 1.400000 m= 26733 mr = 51192 m= 4250 mr = 20264 m= 217 mr = 2738 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3031 time to turn everything in is 0.3700000 number of dielectric boundary points 29963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19339 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) : 0.6245504 object centre at (A) : -7.262500 -1.785000 15.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7570637E-02 3.0242991E-02 midg,1,midg; midg,igrid,midg 1.6117109E-02 2.4139197E-03 1,midg,midg; igrid,midg,midg -6.0467734E-03 3.9733063E-02 gauss-seidel spectral radius is 0.9985893 estimated iterations to convergence 211 setup time was (sec) 0.6000000 now iterating at: 19:08:16 rms-change max change #iterations 4.052069 191.6790 at 10iterations 1.874762 72.37060 at 20iterations 0.8674471 27.89801 at 30iterations 0.4009055 13.43964 at 40iterations 0.1858945 5.922081 at 50iterations 8.6130619E-02 2.975208 at 60iterations 3.9648779E-02 1.367126 at 70iterations 1.8407980E-02 0.5846853 at 80iterations 8.5141324E-03 0.2744789 at 90iterations 3.9416831E-03 0.1227379 at 100iterations 1.8243585E-03 5.4798603E-02 at 110iterations 8.4561767E-04 2.9830933E-02 at 120iterations finished qdiffx linear iterations at : 19:08:23 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 8.4561767E-04 2.9830933E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 19:08:24 8.201u 0.218s 0:08.75 96.1% 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 19:08:24 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 = 2602 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.810477 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): -31.98900 17.46400 ymin,ymax (A): -25.48500 21.91500 zmin,zma (A): -12.56000 44.44100 x,y,z range (A): 49.45300 47.40000 57.00100 scale (grids/A): 2.810477 object centre (A): -7.262500 -1.785000 15.94050 number of atom coordinates read : 2602 total number of charged atoms : 2462 net assigned charge : 4.800007 assigned positive charge : 393.3700 centred at (gu) : 83.35377 86.52747 89.64822 assigned negative charge : -388.5705 centred at (gu) : 82.82558 86.71597 89.13554 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21658 grid for indexing accessible points = 1.400000 m= 86669 mr = 123709 m= 31643 mr = 71948 m= 7723 mr = 25973 m= 1003 mr = 5847 m= 37 mr = 660 m= 0 mr = 8 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 9879 time to turn everything in is 0.9500000 number of dielectric boundary points 67589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19695 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) : 1.873651 object centre at (A) : -7.262500 -1.785000 15.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4061871E-02 0.3879379 midg,1,midg; midg,igrid,midg 0.2113047 2.7827060E-02 1,midg,midg; igrid,midg,midg -5.0231084E-02 0.4795013 gauss-seidel spectral radius is 0.9992403 estimated iterations to convergence 286 setup time was (sec) 1.200000 now iterating at: 19:08:25 rms-change max change #iterations 9.587339 319.4393 at 10iterations 5.540729 128.3837 at 20iterations 3.179171 62.48278 at 30iterations 1.818552 36.86110 at 40iterations 1.043370 19.96776 at 50iterations 0.5952716 11.96168 at 60iterations 0.3396288 6.485702 at 70iterations 0.1947300 3.507167 at 80iterations 0.1108771 2.197948 at 90iterations 6.3137472E-02 1.282348 at 100iterations 3.6122572E-02 0.6420841 at 110iterations 2.0549444E-02 0.4276485 at 120iterations 1.1742695E-02 0.2095566 at 130iterations 6.6965749E-03 0.1173353 at 140iterations 3.8097855E-03 6.9252014E-02 at 150iterations 2.1730454E-03 4.1625977E-02 at 160iterations 1.2398552E-03 2.3687363E-02 at 170iterations 7.0855068E-04 1.6489029E-02 at 180iterations finished qdiffx linear iterations at : 19:08:37 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 7.0855068E-04 1.6489029E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 19:08:38 13.380u 0.226s 0:13.91 97.7% 0+0k 0+0io 0pf+0w