Sun Oct 9 19:02:53 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 Sun Oct 9 2011 at 19:02:53 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5368 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5491539 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): 3.253000 68.08000 ymin,ymax (A): -8.956000 53.32500 zmin,zma (A): -1.005000 63.63200 x,y,z range (A): 64.82700 62.28100 64.63700 scale (grids/A): 0.5491539 object centre (A): 35.66650 22.18450 31.31350 number of atom coordinates read : 5368 total number of charged atoms : 5215 net assigned charge : 1.621048 assigned positive charge : 822.9297 centred at (gu) : 88.21436 89.12991 89.21967 assigned negative charge : -821.3152 centred at (gu) : 88.12258 89.13937 89.17806 start vw surface at 0.2300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 10557 nv = 96 ne = 84 npr = 109647 no. pairs analyzed = 109647 no. exposed pairs = 6127 no. arc points = 41903 no. surface atoms = 2094 nbur = 3274 mkacc time = 0.2500000 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 = 1.568000 m= 446 mr = 6112 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4285 ## 482 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 13874 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2646687E-10 5.8658045E-10 midg,1,midg; midg,igrid,midg 3.3798070E-10 1.1411637E-11 1,midg,midg; igrid,midg,midg -1.7839550E-09 8.9415592E-10 gauss-seidel spectral radius is 0.9830720 estimated iterations to convergence 63 setup time was (sec) 0.7700000 now iterating at: 19:02:54 rms-change max change #iterations 0.1061304 12.95932 at 10iterations 9.8614302E-03 1.278870 at 20iterations 2.8722503E-03 0.3210220 at 30iterations 1.2908785E-03 0.1545348 at 40iterations 6.0195808E-04 7.6889455E-02 at 50iterations finished qdiffx linear iterations at : 19:02:56 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 6.0195808E-04 7.6889455E-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) 3.590000 DelPhi exited at 19:02:57 3.592u 0.146s 0:04.02 92.7% 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 Sun Oct 9 2011 at 19:02:57 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5368 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.647462 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): 3.253000 68.08000 ymin,ymax (A): -8.956000 53.32500 zmin,zma (A): -1.005000 63.63200 x,y,z range (A): 64.82700 62.28100 64.63700 scale (grids/A): 1.647462 object centre (A): 35.66650 22.18450 31.31350 number of atom coordinates read : 5368 total number of charged atoms : 5215 net assigned charge : 1.621048 assigned positive charge : 822.9297 centred at (gu) : 84.64162 87.38823 87.65730 assigned negative charge : -821.3152 centred at (gu) : 84.36745 87.41794 87.53403 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 117711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 40363 mr = 85987 m= 4675 mr = 29258 m= 136 mr = 2546 m= 0 mr = 17 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 205 time to turn everything in is 0.8400000 number of dielectric boundary points 45077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 40006 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) : 0.5491539 object centre at (A) : 35.66650 22.18450 31.31350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5003418E-02 1.7678104E-02 midg,1,midg; midg,igrid,midg 1.7759852E-02 7.7248216E-03 1,midg,midg; igrid,midg,midg -1.7321372E-02 6.0221832E-03 gauss-seidel spectral radius is 0.9984282 estimated iterations to convergence 200 setup time was (sec) 1.140000 now iterating at: 19:02:58 rms-change max change #iterations 4.898151 171.3747 at 10iterations 2.166086 75.50698 at 20iterations 0.9640620 25.61049 at 30iterations 0.4277541 11.43742 at 40iterations 0.1901247 6.261249 at 50iterations 8.5123010E-02 2.314987 at 60iterations 3.8429715E-02 1.045395 at 70iterations 1.7738331E-02 0.5030861 at 80iterations 8.7179309E-03 0.2530391 at 90iterations 4.7855298E-03 0.1406555 at 100iterations 2.9875797E-03 8.3175659E-02 at 110iterations 2.0812352E-03 5.2780151E-02 at 120iterations finished qdiffx linear iterations at : 19:03:04 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.0812352E-03 5.2780151E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 19:03:05 7.830u 0.158s 0:08.27 96.4% 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 Sun Oct 9 2011 at 19:03:05 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5368 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.471192 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): 3.253000 68.08000 ymin,ymax (A): -8.956000 53.32500 zmin,zma (A): -1.005000 63.63200 x,y,z range (A): 64.82700 62.28100 64.63700 scale (grids/A): 2.471192 object centre (A): 35.66650 22.18450 31.31350 number of atom coordinates read : 5368 total number of charged atoms : 5215 net assigned charge : 1.621048 assigned positive charge : 822.9297 centred at (gu) : 81.96203 86.08195 86.48550 assigned negative charge : -821.3152 centred at (gu) : 81.55119 86.12691 86.30094 start vw surface at 0.2300000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 273500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 137422 mr = 208748 m= 42634 mr = 112590 m= 7588 mr = 33075 m= 610 mr = 5239 m= 19 mr = 325 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 684 time to turn everything in is 2.120000 number of dielectric boundary points 101796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 41682 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) : 1.647462 object centre at (A) : 35.66650 22.18450 31.31350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4509572 0.4079365 midg,1,midg; midg,igrid,midg 0.1854812 -2.8338905E-03 1,midg,midg; igrid,midg,midg -0.4611038 6.2438011E-02 gauss-seidel spectral radius is 0.9992558 estimated iterations to convergence 289 setup time was (sec) 2.430000 now iterating at: 19:03:08 rms-change max change #iterations 12.40374 414.8124 at 10iterations 7.297840 156.2056 at 20iterations 4.269872 82.65973 at 30iterations 2.490026 42.05910 at 40iterations 1.447220 23.19814 at 50iterations 0.8390190 13.45643 at 60iterations 0.4860595 8.213299 at 70iterations 0.2808312 4.424694 at 80iterations 0.1620524 2.522320 at 90iterations 9.3611233E-02 1.613225 at 100iterations 5.4112863E-02 0.9691315 at 110iterations 3.1348817E-02 0.5482330 at 120iterations 1.8330852E-02 0.2917252 at 130iterations 1.0901098E-02 0.2058907 at 140iterations 6.6758548E-03 0.1051636 at 150iterations 4.2861039E-03 7.5813293E-02 at 160iterations 2.9380200E-03 5.1095009E-02 at 170iterations 2.1646998E-03 3.4951210E-02 at 180iterations finished qdiffx linear iterations at : 19:03:18 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 2.1646998E-03 3.4951210E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 19:03:19 13.176u 0.179s 0:13.63 97.8% 0+0k 0+0io 0pf+0w