Sat Oct 8 14:33:18 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 14:33:18 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6395975 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): -11.82400 43.83600 ymin,ymax (A): -22.64200 22.72900 zmin,zma (A): -7.099000 47.11300 x,y,z range (A): 55.66000 45.37100 54.21200 scale (grids/A): 0.6395975 object centre (A): 16.00600 4.3499947E-02 20.00700 number of atom coordinates read : 3041 total number of charged atoms : 2894 net assigned charge : 7.1674585E-06 assigned positive charge : 456.7425 centred at (gu) : 88.79603 89.56101 91.71053 assigned negative charge : -456.7433 centred at (gu) : 88.77383 89.48871 91.62395 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8214 nv = 96 ne = 84 npr = 64239 no. pairs analyzed = 64239 no. exposed pairs = 3402 no. arc points = 23907 no. surface atoms = 1153 nbur = 1888 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 4833 m= 0 mr = 53 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3300000 number of dielectric boundary points 3737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2299 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10045 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2480103E-09 1.6720977E-08 midg,1,midg; midg,igrid,midg -1.0984065E-08 8.6961300E-09 1,midg,midg; igrid,midg,midg -4.0848724E-09 2.2069804E-09 gauss-seidel spectral radius is 0.9873652 estimated iterations to convergence 73 setup time was (sec) 0.6100000 now iterating at: 14:33:18 rms-change max change #iterations 0.1570920 22.46847 at 10iterations 1.6052185E-02 2.158195 at 20iterations 1.6293061E-03 0.2271881 at 30iterations 1.9590746E-04 2.4536133E-02 at 40iterations 3.0589850E-05 4.2238235E-03 at 50iterations finished qdiffx linear iterations at : 14:33:22 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 3.0589850E-05 4.2238235E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 14:33:22 4.236u 0.212s 0:04.74 93.6% 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 8 2011 at 14:33:22 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.918792 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): -11.82400 43.83600 ymin,ymax (A): -22.64200 22.72900 zmin,zma (A): -7.099000 47.11300 x,y,z range (A): 55.66000 45.37100 54.21200 scale (grids/A): 1.918792 object centre (A): 16.00600 4.3499947E-02 20.00700 number of atom coordinates read : 3041 total number of charged atoms : 2894 net assigned charge : 7.1674585E-06 assigned positive charge : 456.7425 centred at (gu) : 86.38733 88.68238 95.13105 assigned negative charge : -456.7433 centred at (gu) : 86.32130 88.46576 94.87171 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 89479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23907 grid for indexing accessible points = 1.400000 m= 32963 mr = 64975 m= 5322 mr = 24947 m= 302 mr = 3421 m= 3 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 804 time to turn everything in is 0.6500000 number of dielectric boundary points 34638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22783 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) : 0.6395975 object centre at (A) : 16.00600 4.3499947E-02 20.00700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9125508E-02 2.1595491E-02 midg,1,midg; midg,igrid,midg 8.2776195E-04 1.4877340E-02 1,midg,midg; igrid,midg,midg -3.2664869E-02 5.2710753E-03 gauss-seidel spectral radius is 0.9986869 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 14:33:24 rms-change max change #iterations 4.759672 185.7909 at 10iterations 2.275476 70.15047 at 20iterations 1.081092 31.28061 at 30iterations 0.5141872 14.54655 at 40iterations 0.2447119 7.210711 at 50iterations 0.1166402 3.304965 at 60iterations 5.5512868E-02 1.633221 at 70iterations 2.6487343E-02 0.7295837 at 80iterations 1.2583321E-02 0.3462887 at 90iterations 6.0075736E-03 0.1828499 at 100iterations 2.8645622E-03 8.8395655E-02 at 110iterations 1.3669006E-03 4.4609070E-02 at 120iterations finished qdiffx linear iterations at : 14:33:32 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 1.3669006E-03 4.4609070E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 14:33:33 9.674u 0.279s 0:10.24 97.0% 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 14:33:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3041 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.878189 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): -11.82400 43.83600 ymin,ymax (A): -22.64200 22.72900 zmin,zma (A): -7.099000 47.11300 x,y,z range (A): 55.66000 45.37100 54.21200 scale (grids/A): 2.878189 object centre (A): 16.00600 4.3499947E-02 20.00700 number of atom coordinates read : 3041 total number of charged atoms : 2894 net assigned charge : 7.1674585E-06 assigned positive charge : 456.7425 centred at (gu) : 84.58092 88.02356 97.69660 assigned negative charge : -456.7433 centred at (gu) : 84.48187 87.69854 97.30744 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 207039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23907 grid for indexing accessible points = 1.400000 m= 107146 mr = 156442 m= 39145 mr = 89631 m= 9450 mr = 31967 m= 1430 mr = 7212 m= 71 mr = 958 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2775 time to turn everything in is 1.700000 number of dielectric boundary points 78064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 23147 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) : 1.918792 object centre at (A) : 16.00600 4.3499947E-02 20.00700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2256151 0.3267190 midg,1,midg; midg,igrid,midg 1.0991110E-02 0.1875954 1,midg,midg; igrid,midg,midg -0.4948460 0.1101391 gauss-seidel spectral radius is 0.9992753 estimated iterations to convergence 293 setup time was (sec) 2.050000 now iterating at: 14:33:35 rms-change max change #iterations 10.98492 337.2218 at 10iterations 6.443382 126.8624 at 20iterations 3.750489 74.50089 at 30iterations 2.181294 39.70301 at 40iterations 1.264185 20.98914 at 50iterations 0.7354193 12.75140 at 60iterations 0.4264849 7.899992 at 70iterations 0.2468929 4.493195 at 80iterations 0.1430501 2.438854 at 90iterations 8.2784884E-02 1.415628 at 100iterations 4.7883194E-02 0.7928486 at 110iterations 2.7650163E-02 0.5022755 at 120iterations 1.6021173E-02 0.2595749 at 130iterations 9.2796087E-03 0.1541557 at 140iterations 5.3625060E-03 0.1036983 at 150iterations 3.1028572E-03 4.9229860E-02 at 160iterations 1.7935658E-03 3.1135321E-02 at 170iterations 1.0408206E-03 1.7497778E-02 at 180iterations finished qdiffx linear iterations at : 14:33:49 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 1.0408206E-03 1.7497778E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 14:33:49 15.738u 0.284s 0:16.33 98.0% 0+0k 0+0io 0pf+0w