Sat Oct 8 14:27:57 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 14:27:57 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 = 3029 !!! 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: 0.6419388 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): -11.98600 43.47100 ymin,ymax (A): -23.77600 22.41900 zmin,zma (A): -7.933000 47.42800 x,y,z range (A): 55.45700 46.19500 55.36100 scale (grids/A): 0.6419388 object centre (A): 15.74250 -0.6785002 19.74750 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : 7.1674585E-06 assigned positive charge : 453.2306 centred at (gu) : 88.70203 90.02327 91.77184 assigned negative charge : -453.2313 centred at (gu) : 88.69073 89.93577 91.68631 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8156 nv = 96 ne = 84 npr = 64578 no. pairs analyzed = 64578 no. exposed pairs = 3444 no. arc points = 23327 no. surface atoms = 1169 nbur = 1860 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4824 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2218 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9964 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5667624E-09 1.7569871E-08 midg,1,midg; midg,igrid,midg -1.2770924E-08 1.2235505E-08 1,midg,midg; igrid,midg,midg -2.4315319E-09 1.0582494E-09 gauss-seidel spectral radius is 0.9874547 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 14:27:58 rms-change max change #iterations 0.1673442 23.42338 at 10iterations 1.6657865E-02 1.950539 at 20iterations 1.6957194E-03 0.2266960 at 30iterations 1.9038965E-04 2.4524689E-02 at 40iterations 3.0028772E-05 4.0264130E-03 at 50iterations finished qdiffx linear iterations at : 14:28:00 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 3.0028772E-05 4.0264130E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:28:01 3.117u 0.135s 0:03.54 91.5% 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 Sat Oct 8 2011 at 14:28:01 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 = 3029 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.925816 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): -11.98600 43.47100 ymin,ymax (A): -23.77600 22.41900 zmin,zma (A): -7.933000 47.42800 x,y,z range (A): 55.45700 46.19500 55.36100 scale (grids/A): 1.925816 object centre (A): 15.74250 -0.6785002 19.74750 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : 7.1674585E-06 assigned positive charge : 453.2306 centred at (gu) : 86.10522 90.06915 95.31466 assigned negative charge : -453.2313 centred at (gu) : 86.07166 89.80702 95.05872 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23327 grid for indexing accessible points = 1.400000 m= 32916 mr = 65090 m= 4980 mr = 24904 m= 282 mr = 3127 m= 7 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 547 time to turn everything in is 0.5900000 number of dielectric boundary points 34239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22693 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) : 0.6419388 object centre at (A) : 15.74250 -0.6785002 19.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7982270E-02 2.1616768E-02 midg,1,midg; midg,igrid,midg 2.9715286E-03 2.4012860E-02 1,midg,midg; igrid,midg,midg -3.7842400E-02 6.2569063E-03 gauss-seidel spectral radius is 0.9986918 estimated iterations to convergence 219 setup time was (sec) 0.8500000 now iterating at: 14:28:02 rms-change max change #iterations 4.735939 193.9115 at 10iterations 2.270145 68.90360 at 20iterations 1.079202 33.91571 at 30iterations 0.5159796 13.77129 at 40iterations 0.2451633 7.429478 at 50iterations 0.1170712 3.226902 at 60iterations 5.5892978E-02 1.519028 at 70iterations 2.6653761E-02 0.8671722 at 80iterations 1.2704802E-02 0.4085159 at 90iterations 6.0843090E-03 0.1819839 at 100iterations 2.8955524E-03 9.0631485E-02 at 110iterations 1.3815449E-03 3.9608002E-02 at 120iterations finished qdiffx linear iterations at : 14:28:08 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.3815449E-03 3.9608002E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 14:28:08 6.965u 0.173s 0:07.39 96.4% 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 14:28:08 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 = 3029 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.888725 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): -11.98600 43.47100 ymin,ymax (A): -23.77600 22.41900 zmin,zma (A): -7.933000 47.42800 x,y,z range (A): 55.45700 46.19500 55.36100 scale (grids/A): 2.888725 object centre (A): 15.74250 -0.6785002 19.74750 number of atom coordinates read : 3029 total number of charged atoms : 2882 net assigned charge : 7.1674585E-06 assigned positive charge : 453.2306 centred at (gu) : 84.15775 90.10368 97.97182 assigned negative charge : -453.2313 centred at (gu) : 84.10744 89.71052 97.58815 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 206923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23327 grid for indexing accessible points = 1.400000 m= 107229 mr = 157072 m= 38553 mr = 89812 m= 8931 mr = 31317 m= 1212 mr = 6601 m= 74 mr = 794 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1965 time to turn everything in is 1.520000 number of dielectric boundary points 77306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 23055 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) : 1.925816 object centre at (A) : 15.74250 -0.6785002 19.74750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1800479 0.2904688 midg,1,midg; midg,igrid,midg 4.7488306E-02 0.2929425 1,midg,midg; igrid,midg,midg -0.4533749 0.1596648 gauss-seidel spectral radius is 0.9992746 estimated iterations to convergence 293 setup time was (sec) 1.800000 now iterating at: 14:28:10 rms-change max change #iterations 10.95772 395.7828 at 10iterations 6.423432 142.3949 at 20iterations 3.744983 68.72083 at 30iterations 2.182744 39.24683 at 40iterations 1.269711 26.04918 at 50iterations 0.7383811 13.40805 at 60iterations 0.4286935 8.446487 at 70iterations 0.2487559 4.127883 at 80iterations 0.1440559 2.404441 at 90iterations 8.3579838E-02 1.428114 at 100iterations 4.8295375E-02 0.8503482 at 110iterations 2.8108131E-02 0.4923019 at 120iterations 1.6359584E-02 0.2720833 at 130iterations 9.5150108E-03 0.1806989 at 140iterations 5.5840644E-03 9.1355681E-02 at 150iterations 3.3053418E-03 5.6909561E-02 at 160iterations 1.9939565E-03 3.4599066E-02 at 170iterations 1.2379731E-03 2.2693634E-02 at 180iterations finished qdiffx linear iterations at : 14:28:20 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 1.2379731E-03 2.2693634E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 14:28:20 11.503u 0.176s 0:11.94 97.7% 0+0k 0+0io 0pf+0w