Sat Oct 15 11:30:09 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+sph2.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 = amb2.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 15 2011 at 11:30:09 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 = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 466 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: 0.6229767 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): -31.92000 17.53200 ymin,ymax (A): -23.99900 22.77300 zmin,zma (A): -12.13100 45.01400 x,y,z range (A): 49.45200 46.77200 57.14500 scale (grids/A): 0.6229767 object centre (A): -7.194000 -0.6130009 16.44150 number of atom coordinates read : 2586 total number of charged atoms : 2453 net assigned charge : 3.906009 assigned positive charge : 392.8371 centred at (gu) : 88.50762 89.14304 89.59967 assigned negative charge : -388.9315 centred at (gu) : 88.41443 89.17409 89.49519 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6612 nv = 96 ne = 84 npr = 53529 no. pairs analyzed = 53529 no. exposed pairs = 3008 no. arc points = 21696 no. surface atoms = 1011 nbur = 1575 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3706 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3200000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8201 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4833155E-09 1.0107835E-08 midg,1,midg; midg,igrid,midg 6.9942629E-09 1.1120060E-09 1,midg,midg; igrid,midg,midg -4.6356941E-09 7.3985658E-09 gauss-seidel spectral radius is 0.9866515 estimated iterations to convergence 71 setup time was (sec) 0.6600000 now iterating at: 11:30:10 rms-change max change #iterations 0.1335011 19.73184 at 10iterations 1.2239143E-02 1.953411 at 20iterations 1.1344854E-03 0.1812363 at 30iterations 1.0569923E-04 1.6630173E-02 at 40iterations 1.0052164E-05 1.4142990E-03 at 50iterations finished qdiffx linear iterations at : 11:30:15 total time elapsed so far: 5.100000 # loops : 50 mean,max change (kT/e) : 1.0052164E-05 1.4142990E-03 energy calculations done at 5.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.270000 DelPhi exited at 11:30:15 5.273u 0.450s 0:06.01 95.1% 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 15 2011 at 11:30:15 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 466 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: 1.868930 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): -31.92000 17.53200 ymin,ymax (A): -23.99900 22.77300 zmin,zma (A): -12.13100 45.01400 x,y,z range (A): 49.45200 46.77200 57.14500 scale (grids/A): 1.868930 object centre (A): -7.194000 -0.6130009 16.44150 number of atom coordinates read : 2586 total number of charged atoms : 2453 net assigned charge : 3.906009 assigned positive charge : 392.8371 centred at (gu) : 85.52245 87.42872 88.79805 assigned negative charge : -388.9315 centred at (gu) : 85.24309 87.52211 88.48537 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71996 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21696 grid for indexing accessible points = 1.400000 m= 25899 mr = 50507 m= 3887 mr = 19409 m= 213 mr = 2470 m= 3 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 4321 time to turn everything in is 0.6200000 number of dielectric boundary points 29533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19246 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) : 0.6229767 object centre at (A) : -7.194000 -0.6130009 16.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8331319E-02 1.9160133E-02 midg,1,midg; midg,igrid,midg 1.1753435E-02 2.8220848E-03 1,midg,midg; igrid,midg,midg -5.0830706E-03 3.1151146E-02 gauss-seidel spectral radius is 0.9985797 estimated iterations to convergence 210 setup time was (sec) 0.9900000 now iterating at: 11:30:17 rms-change max change #iterations 4.071895 147.3375 at 10iterations 1.881786 61.85211 at 20iterations 0.8679930 26.07988 at 30iterations 0.3989557 13.88971 at 40iterations 0.1844173 5.744764 at 50iterations 8.5096441E-02 2.573252 at 60iterations 3.9392903E-02 1.330740 at 70iterations 1.8156165E-02 0.6502380 at 80iterations 8.3746649E-03 0.2700882 at 90iterations 3.8675314E-03 0.1190243 at 100iterations 1.7859529E-03 6.7949295E-02 at 110iterations 8.2491490E-04 2.5951624E-02 at 120iterations finished qdiffx linear iterations at : 11:30:28 total time elapsed so far: 12.53000 # loops : 120 mean,max change (kT/e) : 8.2491490E-04 2.5951624E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 11:30:29 12.704u 0.550s 0:13.65 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 15 2011 at 11:30:29 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 = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 466 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: 2.803395 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): -31.92000 17.53200 ymin,ymax (A): -23.99900 22.77300 zmin,zma (A): -12.13100 45.01400 x,y,z range (A): 49.45200 46.77200 57.14500 scale (grids/A): 2.803395 object centre (A): -7.194000 -0.6130009 16.44150 number of atom coordinates read : 2586 total number of charged atoms : 2453 net assigned charge : 3.906009 assigned positive charge : 392.8371 centred at (gu) : 83.28349 86.14301 88.19695 assigned negative charge : -388.9315 centred at (gu) : 82.86452 86.28309 87.72797 start vw surface at 0.1100000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21696 grid for indexing accessible points = 1.400000 m= 84847 mr = 122072 m= 29869 mr = 70449 m= 7084 mr = 24162 m= 928 mr = 5455 m= 34 mr = 610 m= 0 mr = 9 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 14828 time to turn everything in is 1.620000 number of dielectric boundary points 66486 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 19623 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) : 1.868930 object centre at (A) : -7.194000 -0.6130009 16.44150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1119179 0.1517416 midg,1,midg; midg,igrid,midg 0.1570377 4.0671166E-02 1,midg,midg; igrid,midg,midg -3.8726006E-02 0.3921728 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 2.010000 now iterating at: 11:30:31 rms-change max change #iterations 9.565055 332.5034 at 10iterations 5.485052 116.7420 at 20iterations 3.122907 59.63107 at 30iterations 1.782132 33.61198 at 40iterations 1.014874 19.89898 at 50iterations 0.5778941 10.28515 at 60iterations 0.3292226 6.084991 at 70iterations 0.1875173 3.635951 at 80iterations 0.1066697 2.154755 at 90iterations 6.0623147E-02 1.070742 at 100iterations 3.4564499E-02 0.7334595 at 110iterations 1.9630143E-02 0.3486307 at 120iterations 1.1175963E-02 0.1978936 at 130iterations 6.3812672E-03 0.1203327 at 140iterations 3.6230788E-03 6.7268372E-02 at 150iterations 2.0610429E-03 4.0784836E-02 at 160iterations 1.1760152E-03 2.2286415E-02 at 170iterations 6.6838635E-04 1.2949705E-02 at 180iterations finished qdiffx linear iterations at : 11:30:52 total time elapsed so far: 22.30000 # loops : 180 mean,max change (kT/e) : 6.6838635E-04 1.2949705E-02 energy calculations done at 22.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.47000 DelPhi exited at 11:30:53 22.474u 0.560s 0:23.56 97.7% 0+0k 0+0io 0pf+0w