Mon Oct 10 19:32:25 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 19:32:25 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4718 !!! WARNING: HEM 808 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: 0.4837417 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): -24.78900 36.81500 ymin,ymax (A): -19.23300 44.46100 zmin,zma (A): 8.480000 82.07300 x,y,z range (A): 61.60400 63.69400 73.59299 scale (grids/A): 0.4837417 object centre (A): 6.013001 12.61400 45.27650 number of atom coordinates read : 4718 total number of charged atoms : 4478 net assigned charge : 15.30006 assigned positive charge : 715.6660 centred at (gu) : 90.82370 89.45997 89.07406 assigned negative charge : -700.3700 centred at (gu) : 90.84113 89.60117 89.05537 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6867 nv = 96 ne = 84 npr = 94392 no. pairs analyzed = 94392 no. exposed pairs = 6140 no. arc points = 42002 no. surface atoms = 2075 nbur = 2643 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 = 1.764000 m= 228 mr = 3420 m= 0 mr = 3 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3937 ## 662 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9248 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9944674E-11 5.8439226E-11 midg,1,midg; midg,igrid,midg 1.9242360E-10 -4.0863313E-11 1,midg,midg; igrid,midg,midg 5.9316337E-11 5.9526495E-11 gauss-seidel spectral radius is 0.9781563 estimated iterations to convergence 56 setup time was (sec) 0.5000000 now iterating at: 19:32:26 rms-change max change #iterations 5.0989110E-02 8.041561 at 10iterations 3.6560530E-03 0.6132355 at 20iterations 9.7879500E-04 0.1904488 at 30iterations 3.4737168E-04 6.2892914E-02 at 40iterations 1.2575580E-04 2.1152496E-02 at 50iterations finished qdiffx linear iterations at : 19:32:29 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.2575580E-04 2.1152496E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 19:32:29 3.539u 0.171s 0:04.10 90.2% 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 19:32:29 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4718 !!! WARNING: HEM 808 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.451225 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): -24.78900 36.81500 ymin,ymax (A): -19.23300 44.46100 zmin,zma (A): 8.480000 82.07300 x,y,z range (A): 61.60400 63.69400 73.59299 scale (grids/A): 1.451225 object centre (A): 6.013001 12.61400 45.27650 number of atom coordinates read : 4718 total number of charged atoms : 4478 net assigned charge : 15.30006 assigned positive charge : 715.6660 centred at (gu) : 92.46951 88.37864 87.22056 assigned negative charge : -700.3700 centred at (gu) : 92.52306 88.80301 87.16588 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 78853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 20840 mr = 53186 m= 1432 mr = 13181 m= 17 mr = 470 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.4000000 number of dielectric boundary points 34305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 681 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 33005 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) : 0.4837417 object centre at (A) : 6.013001 12.61400 45.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4295367E-02 2.3059154E-02 midg,1,midg; midg,igrid,midg 1.3116539E-02 -6.0266536E-03 1,midg,midg; igrid,midg,midg 1.8336718E-03 4.4512013E-03 gauss-seidel spectral radius is 0.9978643 estimated iterations to convergence 172 setup time was (sec) 0.6200000 now iterating at: 19:32:30 rms-change max change #iterations 3.299927 152.6098 at 10iterations 1.274417 53.22470 at 20iterations 0.4939660 17.84315 at 30iterations 0.1917724 7.921547 at 40iterations 7.4535675E-02 2.518952 at 50iterations 2.9135603E-02 0.9569113 at 60iterations 1.1555141E-02 0.4247665 at 70iterations 4.7594197E-03 0.1856041 at 80iterations 2.1631636E-03 8.6116791E-02 at 90iterations 1.1362183E-03 4.8641205E-02 at 100iterations 6.8746042E-04 2.9525757E-02 at 110iterations 4.5227140E-04 1.8451691E-02 at 120iterations finished qdiffx linear iterations at : 19:32:37 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 4.5227140E-04 1.8451691E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 19:32:38 7.805u 0.193s 0:08.48 94.2% 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 19:32:38 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: 344 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4718 !!! WARNING: HEM 808 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.176838 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): -24.78900 36.81500 ymin,ymax (A): -19.23300 44.46100 zmin,zma (A): 8.480000 82.07300 x,y,z range (A): 61.60400 63.69400 73.59299 scale (grids/A): 2.176838 object centre (A): 6.013001 12.61400 45.27650 number of atom coordinates read : 4718 total number of charged atoms : 4478 net assigned charge : 15.30006 assigned positive charge : 715.6660 centred at (gu) : 93.70395 87.56764 85.83054 assigned negative charge : -700.3700 centred at (gu) : 93.78442 88.20428 85.74878 start vw surface at 0.1300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42002 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 77339 mr = 131649 m= 16727 mr = 58746 m= 1761 mr = 11322 m= 65 mr = 951 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 906 time to turn everything in is 0.9400000 number of dielectric boundary points 77556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 35647 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) : 1.451225 object centre at (A) : 6.013001 12.61400 45.27650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.182529 0.5296736 midg,1,midg; midg,igrid,midg 0.2336316 -0.1394299 1,midg,midg; igrid,midg,midg 2.8257249E-02 9.8385610E-02 gauss-seidel spectral radius is 0.9990876 estimated iterations to convergence 262 setup time was (sec) 1.180000 now iterating at: 19:32:39 rms-change max change #iterations 9.424109 292.2880 at 10iterations 5.285513 124.9516 at 20iterations 2.942698 68.84079 at 30iterations 1.627955 34.75998 at 40iterations 0.8945486 18.36635 at 50iterations 0.4902070 11.20182 at 60iterations 0.2684065 6.326289 at 70iterations 0.1464477 3.096375 at 80iterations 7.9666592E-02 1.607006 at 90iterations 4.3353382E-02 0.8664284 at 100iterations 2.3657598E-02 0.5008755 at 110iterations 1.2854797E-02 0.2540741 at 120iterations 7.0103607E-03 0.1448059 at 130iterations 3.8513432E-03 8.8287354E-02 at 140iterations 2.1347948E-03 4.5852661E-02 at 150iterations 1.2063179E-03 2.6168823E-02 at 160iterations 7.0545328E-04 1.5560150E-02 at 170iterations 4.3328819E-04 1.1199951E-02 at 180iterations finished qdiffx linear iterations at : 19:32:51 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 4.3328819E-04 1.1199951E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 19:32:52 12.736u 0.221s 0:14.14 91.5% 0+0k 0+0io 0pf+0w