Sat Oct 8 17:56:52 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 17:56:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4657 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: 0.5111418 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): -1.006000 62.47000 ymin,ymax (A): -30.02300 31.61800 zmin,zma (A): -22.41200 47.23600 x,y,z range (A): 63.47600 61.64100 69.64799 scale (grids/A): 0.5111418 object centre (A): 30.73200 0.7974997 12.41200 number of atom coordinates read : 4657 total number of charged atoms : 4503 net assigned charge : -10.99997 assigned positive charge : 708.8169 centred at (gu) : 90.67963 91.04401 90.14815 assigned negative charge : -719.8220 centred at (gu) : 90.70457 91.00116 90.12667 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7881 nv = 96 ne = 84 npr = 91295 no. pairs analyzed = 91295 no. exposed pairs = 6259 no. arc points = 43556 no. surface atoms = 2092 nbur = 2565 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 = 1.652000 m= 291 mr = 3869 m= 3 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4297 ## 632 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10536 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1005253E-10 -1.0734319E-10 midg,1,midg; midg,igrid,midg -2.1049676E-10 -5.9409179E-11 1,midg,midg; igrid,midg,midg -7.9702023E-11 -2.7161109E-10 gauss-seidel spectral radius is 0.9804295 estimated iterations to convergence 59 setup time was (sec) 0.6700000 now iterating at: 17:56:53 rms-change max change #iterations 6.5454662E-02 10.32233 at 10iterations 3.8688637E-03 0.5888367 at 20iterations 3.9288370E-04 6.0436249E-02 at 30iterations 8.7004191E-05 1.5530586E-02 at 40iterations 2.2740556E-05 4.0588379E-03 at 50iterations finished qdiffx linear iterations at : 17:56:55 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.2740556E-05 4.0588379E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:56:56 3.432u 0.196s 0:03.90 92.8% 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 Sat Oct 8 2011 at 17:56:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4657 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: 1.533425 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): -1.006000 62.47000 ymin,ymax (A): -30.02300 31.61800 zmin,zma (A): -22.41200 47.23600 x,y,z range (A): 63.47600 61.64100 69.64799 scale (grids/A): 1.533425 object centre (A): 30.73200 0.7974997 12.41200 number of atom coordinates read : 4657 total number of charged atoms : 4503 net assigned charge : -10.99997 assigned positive charge : 708.8169 centred at (gu) : 92.03749 93.13076 90.44308 assigned negative charge : -719.8220 centred at (gu) : 92.11372 93.00363 90.37971 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43556 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25296 mr = 58852 m= 2202 mr = 16240 m= 33 mr = 864 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 153 time to turn everything in is 0.6300000 number of dielectric boundary points 40333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 634 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 33841 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) : 0.5111418 object centre at (A) : 30.73200 0.7974997 12.41200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4187552E-03 -2.1483993E-02 midg,1,midg; midg,igrid,midg -1.4928097E-02 -8.1976047E-03 1,midg,midg; igrid,midg,midg 5.7213516E-03 -3.6170827E-03 gauss-seidel spectral radius is 0.9981164 estimated iterations to convergence 183 setup time was (sec) 0.9200000 now iterating at: 17:56:57 rms-change max change #iterations 3.780589 155.2328 at 10iterations 1.540111 51.29336 at 20iterations 0.6345684 22.88680 at 30iterations 0.2591354 9.653485 at 40iterations 0.1064735 3.424988 at 50iterations 4.3687288E-02 1.437151 at 60iterations 1.7989619E-02 0.6094906 at 70iterations 7.3812399E-03 0.2224426 at 80iterations 3.0621900E-03 0.1026583 at 90iterations 1.2896840E-03 4.3151855E-02 at 100iterations 5.5586227E-04 1.7819285E-02 at 110iterations 2.5356570E-04 9.1891289E-03 at 120iterations finished qdiffx linear iterations at : 17:57:03 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.5356570E-04 9.1891289E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 17:57:04 7.659u 0.230s 0:08.23 95.7% 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 17:57:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4657 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: 2.300138 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): -1.006000 62.47000 ymin,ymax (A): -30.02300 31.61800 zmin,zma (A): -22.41200 47.23600 x,y,z range (A): 63.47600 61.64100 69.64799 scale (grids/A): 2.300138 object centre (A): 30.73200 0.7974997 12.41200 number of atom coordinates read : 4657 total number of charged atoms : 4503 net assigned charge : -10.99997 assigned positive charge : 708.8169 centred at (gu) : 93.05590 94.69598 90.66429 assigned negative charge : -719.8220 centred at (gu) : 93.17055 94.50534 90.56956 start vw surface at 0.1800000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 206588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43556 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90967 mr = 145144 m= 22824 mr = 69550 m= 2989 mr = 15966 m= 142 mr = 1723 m= 0 mr = 34 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 510 time to turn everything in is 1.490000 number of dielectric boundary points 91093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 35917 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) : 1.533425 object centre at (A) : 30.73200 0.7974997 12.41200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5957142E-02 -0.2954111 midg,1,midg; midg,igrid,midg -0.3866419 -0.1356928 1,midg,midg; igrid,midg,midg 6.3400306E-02 -9.9310413E-02 gauss-seidel spectral radius is 0.9991626 estimated iterations to convergence 273 setup time was (sec) 1.800000 now iterating at: 17:57:06 rms-change max change #iterations 10.42854 337.1175 at 10iterations 6.067100 158.6755 at 20iterations 3.483729 95.29301 at 30iterations 1.990166 46.22837 at 40iterations 1.128110 25.69059 at 50iterations 0.6373952 14.09183 at 60iterations 0.3576417 6.957750 at 70iterations 0.2004453 4.144115 at 80iterations 0.1123261 2.217219 at 90iterations 6.2778063E-02 1.169394 at 100iterations 3.5098094E-02 0.6778278 at 110iterations 1.9573973E-02 0.3505964 at 120iterations 1.0892562E-02 0.2238159 at 130iterations 6.0651987E-03 0.1140251 at 140iterations 3.3862919E-03 6.2527657E-02 at 150iterations 1.8908246E-03 3.5602570E-02 at 160iterations 1.0564568E-03 1.9498825E-02 at 170iterations 5.9403083E-04 1.0743856E-02 at 180iterations finished qdiffx linear iterations at : 17:57:18 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 5.9403083E-04 1.0743856E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 17:57:18 13.942u 0.243s 0:14.46 98.0% 0+0k 0+0io 0pf+0w