Sun Oct 9 03:15:29 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 Sun Oct 9 2011 at 03:15:29 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4611 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4426044 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): -3.074000 77.35900 ymin,ymax (A): 0.5080000 65.49200 zmin,zma (A): 173.9150 235.3160 x,y,z range (A): 80.43300 64.98399 61.40100 scale (grids/A): 0.4426044 object centre (A): 37.14250 33.00000 204.6155 number of atom coordinates read : 4611 total number of charged atoms : 4375 net assigned charge : 18.00001 assigned positive charge : 676.7337 centred at (gu) : 86.26910 91.37516 88.67460 assigned negative charge : -658.7387 centred at (gu) : 86.24061 91.34108 88.69536 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5318 nv = 96 ne = 84 npr = 94511 no. pairs analyzed = 94511 no. exposed pairs = 5865 no. arc points = 40071 no. surface atoms = 1999 nbur = 2612 mkacc time = 0.2100000 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 = 1.904000 m= 159 mr = 2549 m= 0 mr = 1 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 2927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3310 ## 631 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3789752E-11 4.0393327E-12 midg,1,midg; midg,igrid,midg 3.2615098E-12 1.5637618E-11 1,midg,midg; igrid,midg,midg 1.5843183E-11 3.3647685E-12 gauss-seidel spectral radius is 0.9739487 estimated iterations to convergence 52 setup time was (sec) 0.6800000 now iterating at: 03:15:30 rms-change max change #iterations 3.2726847E-02 6.482143 at 10iterations 3.3949853E-03 0.5457134 at 20iterations 8.7448192E-04 0.1578846 at 30iterations 2.3798981E-04 4.4870377E-02 at 40iterations 6.5044616E-05 1.2628555E-02 at 50iterations finished qdiffx linear iterations at : 03:15:33 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 6.5044616E-05 1.2628555E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 03:15:33 3.614u 0.239s 0:04.18 91.8% 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 Sun Oct 9 2011 at 03:15:34 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4611 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.327813 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): -3.074000 77.35900 ymin,ymax (A): 0.5080000 65.49200 zmin,zma (A): 173.9150 235.3160 x,y,z range (A): 80.43300 64.98399 61.40100 scale (grids/A): 1.327813 object centre (A): 37.14250 33.00000 204.6155 number of atom coordinates read : 4611 total number of charged atoms : 4375 net assigned charge : 18.00001 assigned positive charge : 676.7337 centred at (gu) : 78.80523 94.12399 86.02230 assigned negative charge : -658.7387 centred at (gu) : 78.72153 94.02274 86.08564 start vw surface at 0.2000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 61781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40071 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 14994 mr = 40475 m= 864 mr = 9187 m= 4 mr = 208 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 891 time to turn everything in is 0.5100000 number of dielectric boundary points 27773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 638 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 30797 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) : 0.4426044 object centre at (A) : 37.14250 33.00000 204.6155 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1634263E-03 7.3093188E-04 midg,1,midg; midg,igrid,midg 2.0767306E-03 2.5874511E-03 1,midg,midg; igrid,midg,midg 2.1225024E-02 2.7595307E-03 gauss-seidel spectral radius is 0.9973512 estimated iterations to convergence 155 setup time was (sec) 0.8100000 now iterating at: 03:15:35 rms-change max change #iterations 2.529940 121.5176 at 10iterations 0.8772234 43.11810 at 20iterations 0.3060295 13.03893 at 30iterations 0.1067144 4.150217 at 40iterations 3.7651233E-02 1.660675 at 50iterations 1.3647119E-02 0.5536652 at 60iterations 5.3336695E-03 0.2425308 at 70iterations 2.4341764E-03 9.6897125E-02 at 80iterations 1.3113022E-03 5.3997040E-02 at 90iterations 7.9174933E-04 3.2352448E-02 at 100iterations 5.0059712E-04 2.0477295E-02 at 110iterations 3.2159218E-04 1.3311386E-02 at 120iterations finished qdiffx linear iterations at : 03:15:41 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 3.2159218E-04 1.3311386E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 03:15:42 7.780u 0.250s 0:08.40 95.5% 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 Sun Oct 9 2011 at 03:15:42 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4611 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 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: 1.991720 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): -3.074000 77.35900 ymin,ymax (A): 0.5080000 65.49200 zmin,zma (A): 173.9150 235.3160 x,y,z range (A): 80.43300 64.98399 61.40100 scale (grids/A): 1.991720 object centre (A): 37.14250 33.00000 204.6155 number of atom coordinates read : 4611 total number of charged atoms : 4375 net assigned charge : 18.00001 assigned positive charge : 676.7337 centred at (gu) : 73.20747 96.18559 84.03300 assigned negative charge : -658.7387 centred at (gu) : 73.08229 96.03402 84.12854 start vw surface at 0.1900000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 144766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40071 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 56783 mr = 100957 m= 11227 mr = 42190 m= 886 mr = 7407 m= 22 mr = 374 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 3096 time to turn everything in is 1.080000 number of dielectric boundary points 62756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 34611 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) : 1.327813 object centre at (A) : 37.14250 33.00000 204.6155 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7959292E-02 9.9841384E-03 midg,1,midg; midg,igrid,midg 4.7836956E-02 2.6035313E-02 1,midg,midg; igrid,midg,midg 0.5183867 3.4907781E-02 gauss-seidel spectral radius is 0.9988897 estimated iterations to convergence 237 setup time was (sec) 1.410000 now iterating at: 03:15:44 rms-change max change #iterations 7.576131 232.1323 at 10iterations 3.967459 101.4047 at 20iterations 2.066988 56.91888 at 30iterations 1.070810 26.61632 at 40iterations 0.5503897 14.31574 at 50iterations 0.2821156 7.290423 at 60iterations 0.1447464 3.527985 at 70iterations 7.3951356E-02 1.714001 at 80iterations 3.7724011E-02 0.9582915 at 90iterations 1.9302735E-02 0.4439926 at 100iterations 9.9100443E-03 0.2377090 at 110iterations 5.1488485E-03 0.1460447 at 120iterations 2.7235968E-03 6.2593460E-02 at 130iterations 1.4928860E-03 3.6010742E-02 at 140iterations 8.6590374E-04 2.2645950E-02 at 150iterations 5.3762679E-04 1.3441086E-02 at 160iterations 3.5551170E-04 8.8844299E-03 at 170iterations 2.4746722E-04 5.9432983E-03 at 180iterations finished qdiffx linear iterations at : 03:15:54 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 2.4746722E-04 5.9432983E-03 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 03:15:55 12.464u 0.262s 0:13.01 97.7% 0+0k 0+0io 0pf+0w