Mon Oct 10 13:58:55 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 13:58:55 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7233126 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): -14.68900 33.21600 ymin,ymax (A): -21.32800 26.85300 zmin,zma (A): -4.841000 44.37700 x,y,z range (A): 47.90500 48.18100 49.21800 scale (grids/A): 0.7233126 object centre (A): 9.263500 2.762500 19.76800 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -6.999980 assigned positive charge : 318.4919 centred at (gu) : 89.18105 87.80943 88.01018 assigned negative charge : -325.4920 centred at (gu) : 89.20509 87.78693 88.23067 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 44077 no. pairs analyzed = 44077 no. exposed pairs = 2690 no. arc points = 19027 no. surface atoms = 907 nbur = 1218 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4195 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.1900000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1629 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0439157E-07 -1.7174423E-07 midg,1,midg; midg,igrid,midg -1.5706003E-07 -4.8165649E-08 1,midg,midg; igrid,midg,midg -8.1560458E-08 -9.0227012E-08 gauss-seidel spectral radius is 0.9900440 estimated iterations to convergence 82 setup time was (sec) 0.3800000 now iterating at: 13:58:55 rms-change max change #iterations 0.2247502 30.16977 at 10iterations 2.8635656E-02 3.633717 at 20iterations 3.7329604E-03 0.5040979 at 30iterations 4.7871249E-04 6.6194534E-02 at 40iterations 6.1748215E-05 8.3379745E-03 at 50iterations finished qdiffx linear iterations at : 13:58:58 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.1748215E-05 8.3379745E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:58:59 3.392u 0.180s 0:03.95 90.3% 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 13:58:59 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.169938 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): -14.68900 33.21600 ymin,ymax (A): -21.32800 26.85300 zmin,zma (A): -4.841000 44.37700 x,y,z range (A): 47.90500 48.18100 49.21800 scale (grids/A): 2.169938 object centre (A): 9.263500 2.762500 19.76800 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -6.999980 assigned positive charge : 318.4919 centred at (gu) : 87.54302 83.42802 84.03031 assigned negative charge : -325.4920 centred at (gu) : 87.61520 83.36083 84.69212 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19027 grid for indexing accessible points = 1.400000 m= 31139 mr = 54806 m= 5905 mr = 23482 m= 540 mr = 3991 m= 13 mr = 292 m= 0 mr = 1 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1945 time to turn everything in is 0.4200000 number of dielectric boundary points 35014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15780 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) : 0.7233126 object centre at (A) : 9.263500 2.762500 19.76800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8299594E-02 -9.4373263E-02 midg,1,midg; midg,igrid,midg -2.2520861E-02 -1.2617838E-02 1,midg,midg; igrid,midg,midg -7.0544872E-03 -4.5084137E-02 gauss-seidel spectral radius is 0.9988821 estimated iterations to convergence 237 setup time was (sec) 0.6300000 now iterating at: 13:59:00 rms-change max change #iterations 4.917595 192.3946 at 10iterations 2.446451 86.47942 at 20iterations 1.231749 40.16075 at 30iterations 0.6164194 18.74301 at 40iterations 0.3112132 9.437060 at 50iterations 0.1562187 4.846126 at 60iterations 7.8616180E-02 2.475579 at 70iterations 3.9476156E-02 1.218079 at 80iterations 1.9900465E-02 0.6510158 at 90iterations 9.9963509E-03 0.2866459 at 100iterations 5.0306292E-03 0.1595535 at 110iterations 2.5320526E-03 7.7433109E-02 at 120iterations finished qdiffx linear iterations at : 13:59:07 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.5320526E-03 7.7433109E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 13:59:07 7.954u 0.199s 0:08.52 95.5% 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 13:59:08 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.254907 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): -14.68900 33.21600 ymin,ymax (A): -21.32800 26.85300 zmin,zma (A): -4.841000 44.37700 x,y,z range (A): 47.90500 48.18100 49.21800 scale (grids/A): 3.254907 object centre (A): 9.263500 2.762500 19.76800 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -6.999980 assigned positive charge : 318.4919 centred at (gu) : 86.31457 80.14198 81.04542 assigned negative charge : -325.4920 centred at (gu) : 86.42278 80.04124 82.03824 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 184437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19027 grid for indexing accessible points = 1.400000 m= 96628 mr = 132319 m= 39467 mr = 79929 m= 11170 mr = 32384 m= 2352 mr = 8759 m= 234 mr = 1790 m= 8 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 6237 time to turn everything in is 1.260000 number of dielectric boundary points 78971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 15880 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) : 2.169938 object centre at (A) : 9.263500 2.762500 19.76800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7008981 -0.8227714 midg,1,midg; midg,igrid,midg -0.1556666 -1.6616436E-02 1,midg,midg; igrid,midg,midg -5.8652230E-02 -0.5523822 gauss-seidel spectral radius is 0.9993176 estimated iterations to convergence 302 setup time was (sec) 1.490000 now iterating at: 13:59:09 rms-change max change #iterations 10.77428 362.4802 at 10iterations 6.349791 125.1653 at 20iterations 3.734479 65.29459 at 30iterations 2.197366 38.16555 at 40iterations 1.292124 22.59640 at 50iterations 0.7600105 12.59717 at 60iterations 0.4457984 8.507888 at 70iterations 0.2620037 4.454494 at 80iterations 0.1532591 2.691529 at 90iterations 9.0113401E-02 1.464219 at 100iterations 5.2872863E-02 0.8891217 at 110iterations 3.1055752E-02 0.4917512 at 120iterations 1.8214753E-02 0.3136940 at 130iterations 1.0686531E-02 0.1849146 at 140iterations 6.2741130E-03 0.1168766 at 150iterations 3.6743165E-03 5.8773041E-02 at 160iterations 2.1606905E-03 3.7903786E-02 at 170iterations 1.2683992E-03 2.3739815E-02 at 180iterations finished qdiffx linear iterations at : 13:59:21 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 1.2683992E-03 2.3739815E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 13:59:22 13.052u 0.247s 0:14.91 89.1% 0+0k 0+0io 0pf+0w