Mon Oct 10 17:01:35 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 Mon Oct 10 2011 at 17:01:35 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4482 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: ZN8 822 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5100871 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): -16.68600 37.47000 ymin,ymax (A): -33.25100 32.75300 zmin,zma (A): -4.230000 65.56200 x,y,z range (A): 54.15600 66.00400 69.79200 scale (grids/A): 0.5100871 object centre (A): 10.39200 -0.2489986 30.66600 number of atom coordinates read : 4482 total number of charged atoms : 4234 net assigned charge : 4.606027 assigned positive charge : 667.5560 centred at (gu) : 90.17401 91.10952 87.53091 assigned negative charge : -662.9540 centred at (gu) : 90.03991 91.13061 87.55467 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7457 nv = 96 ne = 84 npr = 90510 no. pairs analyzed = 90510 no. exposed pairs = 5813 no. arc points = 40590 no. surface atoms = 1929 nbur = 2553 mkacc time = 0.2200000 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= 258 mr = 3764 m= 0 mr = 11 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3877 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2573125E-10 4.2434238E-12 midg,1,midg; midg,igrid,midg 8.3232969E-11 1.5880942E-11 1,midg,midg; igrid,midg,midg -2.4480498E-10 3.8673253E-10 gauss-seidel spectral radius is 0.9803274 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:01:36 rms-change max change #iterations 6.5987833E-02 9.165110 at 10iterations 3.9558071E-03 0.5834498 at 20iterations 5.7958649E-04 7.6334953E-02 at 30iterations 1.9864913E-04 2.5045753E-02 at 40iterations 7.3184114E-05 1.0350987E-02 at 50iterations finished qdiffx linear iterations at : 17:01:38 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 7.3184114E-05 1.0350987E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:01:40 3.559u 0.141s 0:04.68 78.8% 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 Mon Oct 10 2011 at 17:01:40 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4482 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: ZN8 822 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.530261 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): -16.68600 37.47000 ymin,ymax (A): -33.25100 32.75300 zmin,zma (A): -4.230000 65.56200 x,y,z range (A): 54.15600 66.00400 69.79200 scale (grids/A): 1.530261 object centre (A): 10.39200 -0.2489986 30.66600 number of atom coordinates read : 4482 total number of charged atoms : 4234 net assigned charge : 4.606027 assigned positive charge : 667.5560 centred at (gu) : 90.52074 93.32711 82.59126 assigned negative charge : -662.9540 centred at (gu) : 90.11954 93.39149 82.66376 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 84583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40590 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23830 mr = 57734 m= 1956 mr = 15267 m= 46 mr = 805 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.6200000 number of dielectric boundary points 36609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 472 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 31788 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) : 0.5100871 object centre at (A) : 10.39200 -0.2489986 30.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7433819E-03 9.5306253E-03 midg,1,midg; midg,igrid,midg 1.6846906E-03 -4.9537215E-03 1,midg,midg; igrid,midg,midg -3.8265020E-03 9.1366759E-03 gauss-seidel spectral radius is 0.9980817 estimated iterations to convergence 181 setup time was (sec) 0.9100000 now iterating at: 17:01:41 rms-change max change #iterations 3.633697 151.3618 at 10iterations 1.472640 52.02620 at 20iterations 0.5988471 20.69038 at 30iterations 0.2434338 8.019494 at 40iterations 9.9396974E-02 3.375999 at 50iterations 4.0484779E-02 1.292299 at 60iterations 1.6554296E-02 0.6380444 at 70iterations 6.8360418E-03 0.2240562 at 80iterations 2.8527440E-03 0.1015434 at 90iterations 1.2313039E-03 4.0008545E-02 at 100iterations 5.7611312E-04 2.1965981E-02 at 110iterations 3.0418587E-04 1.0189056E-02 at 120iterations finished qdiffx linear iterations at : 17:01:48 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 3.0418587E-04 1.0189056E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 17:01:50 7.921u 0.233s 0:10.28 79.2% 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 Mon Oct 10 2011 at 17:01:50 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4482 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: ZN8 822 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.295392 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): -16.68600 37.47000 ymin,ymax (A): -33.25100 32.75300 zmin,zma (A): -4.230000 65.56200 x,y,z range (A): 54.15600 66.00400 69.79200 scale (grids/A): 2.295392 object centre (A): 10.39200 -0.2489986 30.66600 number of atom coordinates read : 4482 total number of charged atoms : 4234 net assigned charge : 4.606027 assigned positive charge : 667.5560 centred at (gu) : 90.78074 94.99041 78.88647 assigned negative charge : -662.9540 centred at (gu) : 90.17915 95.08702 78.99575 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 197439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40590 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 86204 mr = 142157 m= 20801 mr = 66473 m= 2795 mr = 14402 m= 146 mr = 1635 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 833 time to turn everything in is 1.570000 number of dielectric boundary points 82671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 33785 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) : 1.530261 object centre at (A) : 10.39200 -0.2489986 30.66600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1449345 0.2687219 midg,1,midg; midg,igrid,midg 1.7993035E-02 -0.2299038 1,midg,midg; igrid,midg,midg -3.8616881E-02 0.1214803 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.880000 now iterating at: 17:01:52 rms-change max change #iterations 9.850327 267.6885 at 10iterations 5.609012 137.5230 at 20iterations 3.166143 74.94606 at 30iterations 1.781433 39.24101 at 40iterations 1.000981 27.39136 at 50iterations 0.5588802 12.55809 at 60iterations 0.3113406 6.784052 at 70iterations 0.1730368 3.397493 at 80iterations 9.6392490E-02 1.982209 at 90iterations 5.3510290E-02 1.298794 at 100iterations 2.9695028E-02 0.6274719 at 110iterations 1.6449822E-02 0.3307781 at 120iterations 9.1188094E-03 0.1917038 at 130iterations 5.0565023E-03 0.1052437 at 140iterations 2.8083862E-03 5.5435181E-02 at 150iterations 1.5676963E-03 3.4431458E-02 at 160iterations 8.7570667E-04 1.7342329E-02 at 170iterations 4.9594668E-04 1.0235637E-02 at 180iterations finished qdiffx linear iterations at : 17:02:03 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 4.9594668E-04 1.0235637E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 17:02:04 13.291u 0.290s 0:14.22 95.4% 0+0k 0+0io 0pf+0w