Sat Oct 15 13:58:50 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 15 2011 at 13:58:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4449 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5116486 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): -17.21500 37.42800 ymin,ymax (A): -33.09100 32.45000 zmin,zma (A): -4.023000 65.55600 x,y,z range (A): 54.64300 65.54100 69.57900 scale (grids/A): 0.5116486 object centre (A): 10.10650 -0.3204994 30.76650 number of atom coordinates read : 4449 total number of charged atoms : 4205 net assigned charge : 3.700025 assigned positive charge : 661.7540 centred at (gu) : 90.34528 90.95531 87.55139 assigned negative charge : -658.0582 centred at (gu) : 90.20471 90.98973 87.56956 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7443 nv = 96 ne = 84 npr = 90149 no. pairs analyzed = 90149 no. exposed pairs = 5701 no. arc points = 39498 no. surface atoms = 1894 nbur = 2555 mkacc time = 0.1600000 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 = 1.680000 m= 269 mr = 3822 m= 0 mr = 11 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3799 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9861 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8726182E-10 4.9929735E-12 midg,1,midg; midg,igrid,midg 1.0750412E-10 -4.2872414E-11 1,midg,midg; igrid,midg,midg -2.7494779E-10 4.3274331E-10 gauss-seidel spectral radius is 0.9804435 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 13:58:51 rms-change max change #iterations 6.6381104E-02 9.750490 at 10iterations 3.9541926E-03 0.6077061 at 20iterations 4.6686953E-04 6.9000244E-02 at 30iterations 1.5875119E-04 2.4896860E-02 at 40iterations 6.1470149E-05 9.6120834E-03 at 50iterations finished qdiffx linear iterations at : 13:58:57 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 6.1470149E-05 9.6120834E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 13:58:58 3.675u 0.192s 0:07.27 53.0% 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 13:59:00 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4449 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.534946 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): -17.21500 37.42800 ymin,ymax (A): -33.09100 32.45000 zmin,zma (A): -4.023000 65.55600 x,y,z range (A): 54.64300 65.54100 69.57900 scale (grids/A): 1.534946 object centre (A): 10.10650 -0.3204994 30.76650 number of atom coordinates read : 4449 total number of charged atoms : 4205 net assigned charge : 3.700025 assigned positive charge : 661.7540 centred at (gu) : 91.03477 92.86440 82.65310 assigned negative charge : -658.0582 centred at (gu) : 90.61389 92.96899 82.70841 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23989 mr = 57795 m= 2127 mr = 15800 m= 49 mr = 881 m= 0 mr = 4 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.4100000 number of dielectric boundary points 35993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 502 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 31659 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) : 0.5116486 object centre at (A) : 10.10650 -0.3204994 30.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4734154E-03 8.0284197E-03 midg,1,midg; midg,igrid,midg -1.7577526E-03 -1.1546432E-02 1,midg,midg; igrid,midg,midg -4.2710924E-03 1.0069778E-02 gauss-seidel spectral radius is 0.9980898 estimated iterations to convergence 182 setup time was (sec) 0.6400000 now iterating at: 13:59:01 rms-change max change #iterations 3.631224 155.7284 at 10iterations 1.474193 54.65608 at 20iterations 0.6007745 21.19897 at 30iterations 0.2448975 8.096008 at 40iterations 9.9732198E-02 3.651890 at 50iterations 4.0871590E-02 1.291248 at 60iterations 1.6654463E-02 0.4968109 at 70iterations 6.8620266E-03 0.2253036 at 80iterations 2.8415979E-03 9.1299057E-02 at 90iterations 1.2161488E-03 4.3483734E-02 at 100iterations 5.5255124E-04 1.9145966E-02 at 110iterations 2.8260885E-04 9.3231201E-03 at 120iterations finished qdiffx linear iterations at : 13:59:17 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 2.8260885E-04 9.3231201E-03 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.480000 DelPhi exited at 13:59:18 8.480u 0.258s 0:18.38 47.4% 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 15 2011 at 13:59:18 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4449 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.302419 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): -17.21500 37.42800 ymin,ymax (A): -33.09100 32.45000 zmin,zma (A): -4.023000 65.55600 x,y,z range (A): 54.64300 65.54100 69.57900 scale (grids/A): 2.302419 object centre (A): 10.10650 -0.3204994 30.76650 number of atom coordinates read : 4449 total number of charged atoms : 4205 net assigned charge : 3.700025 assigned positive charge : 661.7540 centred at (gu) : 91.55165 94.29642 78.97920 assigned negative charge : -658.0582 centred at (gu) : 90.92077 94.45341 79.06261 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 196703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87149 mr = 142362 m= 21527 mr = 67710 m= 3088 mr = 15320 m= 178 mr = 1842 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 1.030000 number of dielectric boundary points 81358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 33562 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) : 1.534946 object centre at (A) : 10.10650 -0.3204994 30.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1605341 0.2627980 midg,1,midg; midg,igrid,midg -0.1069232 -0.3372788 1,midg,midg; igrid,midg,midg -5.5052247E-02 0.1330311 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.310000 now iterating at: 13:59:20 rms-change max change #iterations 9.828554 289.9507 at 10iterations 5.600766 120.3329 at 20iterations 3.165579 68.77464 at 30iterations 1.780982 37.03597 at 40iterations 0.9984104 21.62531 at 50iterations 0.5593805 12.52963 at 60iterations 0.3107537 6.391294 at 70iterations 0.1730717 4.052260 at 80iterations 9.6234687E-02 2.055353 at 90iterations 5.3305451E-02 1.084084 at 100iterations 2.9596860E-02 0.6399155 at 110iterations 1.6384987E-02 0.3378717 at 120iterations 9.1029173E-03 0.1942635 at 130iterations 5.0286362E-03 0.1031780 at 140iterations 2.7932182E-03 5.8321476E-02 at 150iterations 1.5493272E-03 3.1171799E-02 at 160iterations 8.6518307E-04 1.7542839E-02 at 170iterations 4.8731835E-04 1.0484695E-02 at 180iterations finished qdiffx linear iterations at : 13:59:46 total time elapsed so far: 14.17000 # loops : 180 mean,max change (kT/e) : 4.8731835E-04 1.0484695E-02 energy calculations done at 14.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.30000 DelPhi exited at 13:59:47 14.301u 0.238s 0:28.80 50.4% 0+0k 0+0io 0pf+0w