Mon Oct 10 14:05:22 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 14:05:22 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: HIZ 44 has a net charge of 0.2000 !!! WARNING: GLM 424 has a net charge of -0.6000 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4983133 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): 25.80700 97.24800 ymin,ymax (A): -0.7270000 63.88400 zmin,zma (A): 15.54700 72.05900 x,y,z range (A): 71.44100 64.61100 56.51200 scale (grids/A): 0.4983133 object centre (A): 61.52750 31.57850 43.80300 number of atom coordinates read : 4556 total number of charged atoms : 4395 net assigned charge : 11.30004 assigned positive charge : 693.7935 centred at (gu) : 89.87784 89.17402 89.59662 assigned negative charge : -682.4985 centred at (gu) : 89.79929 89.01846 89.50528 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7162 nv = 96 ne = 84 npr = 89343 no. pairs analyzed = 89343 no. exposed pairs = 5949 no. arc points = 42264 no. surface atoms = 1992 nbur = 2564 mkacc time = 0.2300000 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 = 1.736000 m= 260 mr = 3511 m= 0 mr = 5 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4143 ## 708 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4283313E-11 2.0195769E-10 midg,1,midg; midg,igrid,midg -1.7097961E-10 2.5214875E-10 1,midg,midg; igrid,midg,midg -2.1089326E-11 2.0027902E-10 gauss-seidel spectral radius is 0.9794023 estimated iterations to convergence 58 setup time was (sec) 0.7600000 now iterating at: 14:05:23 rms-change max change #iterations 5.5914696E-02 10.51461 at 10iterations 2.9791666E-03 0.5128534 at 20iterations 2.2975600E-04 4.3176770E-02 at 30iterations 5.5551805E-05 1.3916969E-02 at 40iterations 1.8154740E-05 4.7893524E-03 at 50iterations finished qdiffx linear iterations at : 14:05:27 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 1.8154740E-05 4.7893524E-03 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 14:05:27 4.696u 0.388s 0:05.42 93.5% 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 Mon Oct 10 2011 at 14:05:27 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: HIZ 44 has a net charge of 0.2000 !!! WARNING: GLM 424 has a net charge of -0.6000 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.494940 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): 25.80700 97.24800 ymin,ymax (A): -0.7270000 63.88400 zmin,zma (A): 15.54700 72.05900 x,y,z range (A): 71.44100 64.61100 56.51200 scale (grids/A): 1.494940 object centre (A): 61.52750 31.57850 43.80300 number of atom coordinates read : 4556 total number of charged atoms : 4395 net assigned charge : 11.30004 assigned positive charge : 693.7935 centred at (gu) : 89.63232 87.52026 88.78801 assigned negative charge : -682.4985 centred at (gu) : 89.39718 87.05489 88.51569 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 81102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42264 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 21593 mr = 53619 m= 1676 mr = 13791 m= 40 mr = 658 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 354 time to turn everything in is 0.6800000 number of dielectric boundary points 36344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 688 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 32723 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) : 0.4983133 object centre at (A) : 61.52750 31.57850 43.80300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8886224E-03 1.7804800E-03 midg,1,midg; midg,igrid,midg 2.0058289E-02 1.9387852E-02 1,midg,midg; igrid,midg,midg 3.6546951E-03 1.1317684E-02 gauss-seidel spectral radius is 0.9979956 estimated iterations to convergence 178 setup time was (sec) 1.030000 now iterating at: 14:05:29 rms-change max change #iterations 3.446957 162.1567 at 10iterations 1.369583 50.61034 at 20iterations 0.5423591 19.65999 at 30iterations 0.2161739 7.203779 at 40iterations 8.6324744E-02 3.289227 at 50iterations 3.4438327E-02 1.165321 at 60iterations 1.3711798E-02 0.4584923 at 70iterations 5.5053891E-03 0.1937561 at 80iterations 2.2102986E-03 7.7341080E-02 at 90iterations 8.9638762E-04 3.3527374E-02 at 100iterations 3.7488397E-04 1.4023781E-02 at 110iterations 1.6844153E-04 7.2125196E-03 at 120iterations finished qdiffx linear iterations at : 14:05:39 total time elapsed so far: 11.28000 # loops : 120 mean,max change (kT/e) : 1.6844153E-04 7.2125196E-03 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 14:05:40 11.448u 0.452s 0:12.27 96.9% 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 14:05:40 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4556 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: HIZ 44 has a net charge of 0.2000 !!! WARNING: GLM 424 has a net charge of -0.6000 !!! WARNING: ZN7 778 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.242410 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): 25.80700 97.24800 ymin,ymax (A): -0.7270000 63.88400 zmin,zma (A): 15.54700 72.05900 x,y,z range (A): 71.44100 64.61100 56.51200 scale (grids/A): 2.242410 object centre (A): 61.52750 31.57850 43.80300 number of atom coordinates read : 4556 total number of charged atoms : 4395 net assigned charge : 11.30004 assigned positive charge : 693.7935 centred at (gu) : 89.44811 86.27995 88.18166 assigned negative charge : -682.4985 centred at (gu) : 89.09572 85.58218 87.77328 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 189329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42264 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 78662 mr = 132756 m= 18144 mr = 59890 m= 2200 mr = 12465 m= 97 mr = 1270 m= 0 mr = 20 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 1180 time to turn everything in is 1.620000 number of dielectric boundary points 82031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 35035 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) : 1.494940 object centre at (A) : 61.52750 31.57850 43.80300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1104690 1.2107106E-02 midg,1,midg; midg,igrid,midg 0.5190919 0.3310439 1,midg,midg; igrid,midg,midg 0.2399465 0.3126790 gauss-seidel spectral radius is 0.9991258 estimated iterations to convergence 267 setup time was (sec) 1.970000 now iterating at: 14:05:42 rms-change max change #iterations 9.714215 283.1766 at 10iterations 5.572374 181.8219 at 20iterations 3.158810 79.16683 at 30iterations 1.773420 49.16785 at 40iterations 0.9899069 22.15400 at 50iterations 0.5510914 12.45894 at 60iterations 0.3060331 6.300675 at 70iterations 0.1692653 3.143886 at 80iterations 9.3402676E-02 1.967769 at 90iterations 5.1547892E-02 1.044716 at 100iterations 2.8375333E-02 0.5634136 at 110iterations 1.5597275E-02 0.3372183 at 120iterations 8.6186044E-03 0.1822662 at 130iterations 4.7447993E-03 9.5214844E-02 at 140iterations 2.6117193E-03 5.3077698E-02 at 150iterations 1.4490953E-03 2.8381288E-02 at 160iterations 8.0998446E-04 1.5167236E-02 at 170iterations 4.6002193E-04 1.1384964E-02 at 180iterations finished qdiffx linear iterations at : 14:05:59 total time elapsed so far: 19.01000 # loops : 180 mean,max change (kT/e) : 4.6002193E-04 1.1384964E-02 energy calculations done at 19.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.17000 DelPhi exited at 14:06:00 19.179u 0.471s 0:19.97 98.3% 0+0k 0+0io 0pf+0w