Mon Oct 10 22:02:36 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 Mon Oct 10 2011 at 22:02:36 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 = 2809 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: 0.5585189 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 0.5585189 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2809 total number of charged atoms : 2728 net assigned charge : 2.500007 assigned positive charge : 414.4883 centred at (gu) : 88.80892 89.11561 90.63747 assigned negative charge : -411.9895 centred at (gu) : 88.68767 89.19777 90.53872 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5986 nv = 96 ne = 84 npr = 54592 no. pairs analyzed = 54592 no. exposed pairs = 3803 no. arc points = 27194 no. surface atoms = 1272 nbur = 1537 mkacc time = 0.1200000 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 = 1.540000 m= 225 mr = 2955 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2843 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1197281E-10 1.4044345E-09 midg,1,midg; midg,igrid,midg 1.2962795E-09 -4.4286849E-10 1,midg,midg; igrid,midg,midg -1.2720968E-09 1.0589961E-09 gauss-seidel spectral radius is 0.9834637 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 22:02:37 rms-change max change #iterations 7.6029196E-02 12.92968 at 10iterations 5.5433908E-03 0.9561462 at 20iterations 4.4945756E-04 6.5818787E-02 at 30iterations 5.2022788E-05 7.7590942E-03 at 40iterations 8.9481146E-06 1.2207031E-03 at 50iterations finished qdiffx linear iterations at : 22:02:39 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 8.9481146E-06 1.2207031E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 22:02:40 3.127u 0.144s 0:03.93 82.9% 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 22:02:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 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: 1.675557 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 1.675557 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2809 total number of charged atoms : 2728 net assigned charge : 2.500007 assigned positive charge : 414.4883 centred at (gu) : 86.42570 87.34616 91.91167 assigned negative charge : -411.9895 centred at (gu) : 86.06280 87.59309 91.61577 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19740 mr = 42960 m= 2181 mr = 13158 m= 73 mr = 1081 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 585 time to turn everything in is 0.4600000 number of dielectric boundary points 30139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 312 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21023 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) : 0.5585189 object centre at (A) : 5.560500 -5.153999 25.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7115416E-02 1.0359514E-02 midg,1,midg; midg,igrid,midg 2.5280630E-03 -8.6206868E-03 1,midg,midg; igrid,midg,midg -4.5425617E-03 1.7499657E-02 gauss-seidel spectral radius is 0.9982765 estimated iterations to convergence 191 setup time was (sec) 0.7200000 now iterating at: 22:02:41 rms-change max change #iterations 3.349710 154.3723 at 10iterations 1.425828 64.26788 at 20iterations 0.6083643 23.13025 at 30iterations 0.2590935 9.110575 at 40iterations 0.1104622 3.910518 at 50iterations 4.7068410E-02 1.687346 at 60iterations 2.0030990E-02 0.7469468 at 70iterations 8.5484777E-03 0.2974482 at 80iterations 3.6444750E-03 0.1306629 at 90iterations 1.5605777E-03 5.4976463E-02 at 100iterations 6.6357659E-04 2.3895264E-02 at 110iterations 2.8440676E-04 9.6969604E-03 at 120iterations finished qdiffx linear iterations at : 22:02:47 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 2.8440676E-04 9.6969604E-03 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 22:02:47 6.872u 0.195s 0:07.40 95.4% 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 Mon Oct 10 2011 at 22:02:47 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 = 2809 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: 2.513335 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): -20.77800 31.89900 ymin,ymax (A): -33.66100 23.35300 zmin,zma (A): -6.438000 57.30200 x,y,z range (A): 52.67700 57.01400 63.74000 scale (grids/A): 2.513335 object centre (A): 5.560500 -5.153999 25.43200 number of atom coordinates read : 2809 total number of charged atoms : 2728 net assigned charge : 2.500007 assigned positive charge : 414.4883 centred at (gu) : 84.63831 86.01900 92.86743 assigned negative charge : -411.9895 centred at (gu) : 84.09416 86.38970 92.42370 start vw surface at 0.1500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 151948 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 grid for indexing accessible points = 1.400000 m= 67525 mr = 105841 m= 19812 mr = 52227 m= 3431 mr = 14557 m= 268 mr = 2262 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1959 time to turn everything in is 1.070000 number of dielectric boundary points 67983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 21805 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) : 1.675557 object centre at (A) : 5.560500 -5.153999 25.43200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4425306 0.2317499 midg,1,midg; midg,igrid,midg 3.1644598E-02 -0.1032611 1,midg,midg; igrid,midg,midg -7.8441277E-02 0.2708247 gauss-seidel spectral radius is 0.9991703 estimated iterations to convergence 274 setup time was (sec) 1.340000 now iterating at: 22:02:49 rms-change max change #iterations 8.654946 387.8250 at 10iterations 4.935068 123.8135 at 20iterations 2.798077 63.18615 at 30iterations 1.577271 35.36065 at 40iterations 0.8847151 22.51628 at 50iterations 0.4964853 10.51352 at 60iterations 0.2771522 5.970901 at 70iterations 0.1548570 3.293879 at 80iterations 8.6347409E-02 1.925713 at 90iterations 4.8061457E-02 1.030999 at 100iterations 2.6797036E-02 0.5681036 at 110iterations 1.4864624E-02 0.3150688 at 120iterations 8.2822349E-03 0.1613998 at 130iterations 4.6047610E-03 9.4902039E-02 at 140iterations 2.5627736E-03 5.2108765E-02 at 150iterations 1.4225240E-03 3.0393600E-02 at 160iterations 7.9059403E-04 1.6506195E-02 at 170iterations 4.4098156E-04 8.8577271E-03 at 180iterations finished qdiffx linear iterations at : 22:02:58 total time elapsed so far: 10.80000 # loops : 180 mean,max change (kT/e) : 4.4098156E-04 8.8577271E-03 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 22:02:59 10.981u 0.191s 0:11.47 97.3% 0+0k 0+0io 0pf+0w