Thu Jan 19 13:33:29 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:30 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6958 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 0.4321437 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): -5.021000 77.35900 ymin,ymax (A): -0.7980000 73.96400 zmin,zma (A): 165.4150 235.2390 x,y,z range (A): 82.38000 74.76200 69.82401 scale (grids/A): 0.4321437 object centre (A): 36.16900 36.58300 200.3270 number of atom coordinates read : 6958 total number of charged atoms : 6789 net assigned charge : 5.200047 assigned positive charge : 1056.429 centred at (gu) : 89.22246 90.29610 89.70109 assigned negative charge : -1051.237 centred at (gu) : 89.18937 90.32089 89.66721 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7598 nv = 96 ne = 84 npr = 141213 no. pairs analyzed = 141213 no. exposed pairs = 9147 no. arc points = 61625 no. surface atoms = 3093 nbur = 3865 mkacc time = 0.2400000 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 = 1.932000 m= 206 mr = 3563 m= 0 mr = 1 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5107 ## 1072 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3699331E-12 3.3565197E-12 midg,1,midg; midg,igrid,midg 2.7628587E-12 -6.3776160E-13 1,midg,midg; igrid,midg,midg -1.5267567E-12 2.8541069E-12 gauss-seidel spectral radius is 0.9728342 estimated iterations to convergence 51 setup time was (sec) 0.6400000 now iterating at: 13:33:32 rms-change max change #iterations 3.2083575E-02 5.476639 at 10iterations 1.9351223E-03 0.3292789 at 20iterations 5.8586447E-04 9.0211868E-02 at 30iterations 2.1520973E-04 3.1845093E-02 at 40iterations 7.9912286E-05 1.1287689E-02 at 50iterations finished qdiffx linear iterations at : 13:33:37 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 7.9912286E-05 1.1287689E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 13:33:38 3.837u 0.190s 0:07.72 52.0% 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 Thu Jan 19 2012 at 13:33:38 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6958 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 1.296431 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): -5.021000 77.35900 ymin,ymax (A): -0.7980000 73.96400 zmin,zma (A): 165.4150 235.2390 x,y,z range (A): 82.38000 74.76200 69.82401 scale (grids/A): 1.296431 object centre (A): 36.16900 36.58300 200.3270 number of atom coordinates read : 6958 total number of charged atoms : 6789 net assigned charge : 5.200047 assigned positive charge : 1056.429 centred at (gu) : 87.66573 90.88664 89.10143 assigned negative charge : -1051.237 centred at (gu) : 87.56786 90.96233 89.00110 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 88472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61625 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 20768 mr = 57716 m= 1065 mr = 12187 m= 6 mr = 220 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 621 time to turn everything in is 0.4800000 number of dielectric boundary points 40188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1185 ## 43 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 47200 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) : 0.4321437 object centre at (A) : 36.16900 36.58300 200.3270 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4225991E-04 1.2647513E-04 midg,1,midg; midg,igrid,midg 6.2710431E-04 2.0324574E-03 1,midg,midg; igrid,midg,midg 2.4008185E-03 6.8757394E-03 gauss-seidel spectral radius is 0.9974490 estimated iterations to convergence 158 setup time was (sec) 0.7200000 now iterating at: 13:33:41 rms-change max change #iterations 3.135396 135.1899 at 10iterations 1.114770 40.35032 at 20iterations 0.3931087 14.66440 at 30iterations 0.1400023 4.903841 at 40iterations 4.9933881E-02 2.023853 at 50iterations 1.7789703E-02 0.6500015 at 60iterations 6.4947903E-03 0.2210155 at 70iterations 2.5064824E-03 0.1022797 at 80iterations 1.1219293E-03 4.8131943E-02 at 90iterations 6.2594778E-04 2.4984360E-02 at 100iterations 4.0927276E-04 1.5474319E-02 at 110iterations 2.8367649E-04 1.0859489E-02 at 120iterations finished qdiffx linear iterations at : 13:33:58 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 2.8367649E-04 1.0859489E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 13:33:59 8.237u 0.222s 0:20.79 40.6% 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 Thu Jan 19 2012 at 13:33:59 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6958 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 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: 1.944647 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): -5.021000 77.35900 ymin,ymax (A): -0.7980000 73.96400 zmin,zma (A): 165.4150 235.2390 x,y,z range (A): 82.38000 74.76200 69.82401 scale (grids/A): 1.944647 object centre (A): 36.16900 36.58300 200.3270 number of atom coordinates read : 6958 total number of charged atoms : 6789 net assigned charge : 5.200047 assigned positive charge : 1056.429 centred at (gu) : 86.49806 91.32941 88.65184 assigned negative charge : -1051.237 centred at (gu) : 86.35155 91.44344 88.50157 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 207322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 61625 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 79931 mr = 144169 m= 14732 mr = 58522 m= 1075 mr = 9251 m= 25 mr = 398 m= 0 mr = 1 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1995 time to turn everything in is 1.090000 number of dielectric boundary points 90744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 53621 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) : 1.296431 object centre at (A) : 36.16900 36.58300 200.3270 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9750623E-02 -4.9525807E-03 midg,1,midg; midg,igrid,midg 2.0022327E-02 8.8720366E-02 1,midg,midg; igrid,midg,midg 0.2058287 0.2423735 gauss-seidel spectral radius is 0.9989981 estimated iterations to convergence 250 setup time was (sec) 1.360000 now iterating at: 13:34:06 rms-change max change #iterations 9.677265 276.8186 at 10iterations 5.309309 161.8013 at 20iterations 2.871020 81.60276 at 30iterations 1.545297 37.84799 at 40iterations 0.8247125 19.81244 at 50iterations 0.4410249 11.25128 at 60iterations 0.2342075 5.187521 at 70iterations 0.1239302 2.815339 at 80iterations 6.5598130E-02 1.422749 at 90iterations 3.4619354E-02 0.7340407 at 100iterations 1.8296845E-02 0.3959274 at 110iterations 9.6576568E-03 0.1851559 at 120iterations 5.0952062E-03 0.1147079 at 130iterations 2.6944717E-03 5.2515030E-02 at 140iterations 1.4363524E-03 3.1715393E-02 at 150iterations 7.7481876E-04 1.6597748E-02 at 160iterations 4.3042560E-04 1.0784149E-02 at 170iterations 2.4995263E-04 6.0634613E-03 at 180iterations finished qdiffx linear iterations at : 13:34:42 total time elapsed so far: 13.72000 # loops : 180 mean,max change (kT/e) : 2.4995263E-04 6.0634613E-03 energy calculations done at 13.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.86000 DelPhi exited at 13:34:44 13.864u 0.234s 0:44.84 31.4% 0+0k 0+0io 0pf+0w