Mon Oct 10 13:57:24 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 13:57:24 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5729092 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): 111.1330 173.2720 ymin,ymax (A): -44.77600 8.509000 zmin,zma (A): 46.06600 103.9290 x,y,z range (A): 62.13898 53.28500 57.86300 scale (grids/A): 0.5729092 object centre (A): 142.2025 -18.13350 74.99750 number of atom coordinates read : 2960 total number of charged atoms : 2808 net assigned charge : 5.014019 assigned positive charge : 434.4897 centred at (gu) : 89.70255 88.98833 88.91137 assigned negative charge : -429.4762 centred at (gu) : 89.71504 89.04989 88.75536 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6581 nv = 96 ne = 84 npr = 57504 no. pairs analyzed = 57504 no. exposed pairs = 4470 no. arc points = 31871 no. surface atoms = 1496 nbur = 1464 mkacc time = 0.2000000 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 = 1.484000 m= 345 mr = 2947 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3118 ## 298 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8277 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3405038E-09 2.6551883E-09 midg,1,midg; midg,igrid,midg 2.4098825E-09 -1.2024580E-10 1,midg,midg; igrid,midg,midg 1.1597737E-09 6.2144551E-10 gauss-seidel spectral radius is 0.9842960 estimated iterations to convergence 66 setup time was (sec) 0.7300000 now iterating at: 13:57:25 rms-change max change #iterations 9.2630349E-02 13.82503 at 10iterations 6.9058407E-03 1.174554 at 20iterations 5.1819312E-04 7.7931404E-02 at 30iterations 4.1014810E-05 7.0836842E-03 at 40iterations 4.0115515E-06 6.0844421E-04 at 50iterations finished qdiffx linear iterations at : 13:57:29 total time elapsed so far: 4.620000 # loops : 50 mean,max change (kT/e) : 4.0115515E-06 6.0844421E-04 energy calculations done at 4.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 13:57:30 4.845u 0.381s 0:06.01 86.8% 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 13:57:30 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.718728 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): 111.1330 173.2720 ymin,ymax (A): -44.77600 8.509000 zmin,zma (A): 46.06600 103.9290 x,y,z range (A): 62.13898 53.28500 57.86300 scale (grids/A): 1.718728 object centre (A): 142.2025 -18.13350 74.99750 number of atom coordinates read : 2960 total number of charged atoms : 2808 net assigned charge : 5.014019 assigned positive charge : 434.4897 centred at (gu) : 89.10715 86.96480 86.73359 assigned negative charge : -429.4762 centred at (gu) : 89.14462 87.14923 86.26575 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 70246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31871 grid for indexing accessible points = 1.400000 m= 22976 mr = 43277 m= 3309 mr = 14708 m= 122 mr = 1606 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.7500000 number of dielectric boundary points 37051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21741 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) : 0.5729092 object centre at (A) : 142.2025 -18.13350 74.99750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8893613E-02 2.1288306E-02 midg,1,midg; midg,igrid,midg 2.2468934E-02 1.1195174E-02 1,midg,midg; igrid,midg,midg 8.9575415E-03 1.0466336E-02 gauss-seidel spectral radius is 0.9983926 estimated iterations to convergence 198 setup time was (sec) 1.090000 now iterating at: 13:57:32 rms-change max change #iterations 3.688619 163.3715 at 10iterations 1.602552 59.25537 at 20iterations 0.6994768 24.91171 at 30iterations 0.3066009 10.33608 at 40iterations 0.1339056 4.849751 at 50iterations 5.8720112E-02 2.095249 at 60iterations 2.5758024E-02 0.8519506 at 70iterations 1.1320660E-02 0.4119263 at 80iterations 4.9550547E-03 0.2009525 at 90iterations 2.1718284E-03 7.2769165E-02 at 100iterations 9.5542311E-04 3.4178734E-02 at 110iterations 4.1890022E-04 1.6273499E-02 at 120iterations finished qdiffx linear iterations at : 13:57:42 total time elapsed so far: 11.07000 # loops : 120 mean,max change (kT/e) : 4.1890022E-04 1.6273499E-02 energy calculations done at 11.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 13:57:43 11.303u 0.425s 0:12.61 92.9% 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 13:57:43 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2960 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.578092 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): 111.1330 173.2720 ymin,ymax (A): -44.77600 8.509000 zmin,zma (A): 46.06600 103.9290 x,y,z range (A): 62.13898 53.28500 57.86300 scale (grids/A): 2.578092 object centre (A): 142.2025 -18.13350 74.99750 number of atom coordinates read : 2960 total number of charged atoms : 2808 net assigned charge : 5.014019 assigned positive charge : 434.4897 centred at (gu) : 88.66074 85.44724 85.10001 assigned negative charge : -429.4762 centred at (gu) : 88.71689 85.72374 84.39851 start vw surface at 0.1500000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 162146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31871 grid for indexing accessible points = 1.400000 m= 74111 mr = 106707 m= 25567 mr = 55285 m= 5404 mr = 18502 m= 509 mr = 3457 m= 10 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 1.870000 number of dielectric boundary points 83569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 22441 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) : 1.718728 object centre at (A) : 142.2025 -18.13350 74.99750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2339613 0.2843282 midg,1,midg; midg,igrid,midg 0.2935688 0.1970572 1,midg,midg; igrid,midg,midg 0.1849072 0.1240932 gauss-seidel spectral radius is 0.9992191 estimated iterations to convergence 283 setup time was (sec) 2.260000 now iterating at: 13:57:46 rms-change max change #iterations 9.483505 390.2721 at 10iterations 5.579014 152.0675 at 20iterations 3.237356 71.04132 at 30iterations 1.867625 43.18676 at 40iterations 1.070640 26.47764 at 50iterations 0.6125689 12.84241 at 60iterations 0.3499379 8.270712 at 70iterations 0.1994457 4.471133 at 80iterations 0.1135942 2.403488 at 90iterations 6.4660907E-02 1.593138 at 100iterations 3.6557186E-02 0.8128967 at 110iterations 2.0761998E-02 0.4557915 at 120iterations 1.1783444E-02 0.2603474 at 130iterations 6.6605029E-03 0.1352425 at 140iterations 3.7755382E-03 7.8313828E-02 at 150iterations 2.1376305E-03 4.2053223E-02 at 160iterations 1.2092827E-03 2.2666931E-02 at 170iterations 6.8515737E-04 1.3514519E-02 at 180iterations finished qdiffx linear iterations at : 13:58:02 total time elapsed so far: 18.65000 # loops : 180 mean,max change (kT/e) : 6.8515737E-04 1.3514519E-02 energy calculations done at 18.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.87000 DelPhi exited at 13:58:03 18.873u 0.464s 0:19.79 97.6% 0+0k 0+0io 0pf+0w