Mon Oct 10 14:02:16 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 14:02:16 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2850 !!! WARNING: HIR 207 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5886340 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): -8.882999 46.66300 ymin,ymax (A): -51.93300 8.546000 zmin,zma (A): -32.58800 21.68600 x,y,z range (A): 55.54600 60.47900 54.27400 scale (grids/A): 0.5886340 object centre (A): 18.89000 -21.69350 -5.451001 number of atom coordinates read : 2850 total number of charged atoms : 2778 net assigned charge : 5.514015 assigned positive charge : 426.9799 centred at (gu) : 90.81138 88.75607 90.08760 assigned negative charge : -421.4677 centred at (gu) : 90.75201 88.73049 90.08319 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 53822 no. pairs analyzed = 53822 no. exposed pairs = 4140 no. arc points = 28940 no. surface atoms = 1377 nbur = 1473 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 = 1.456000 m= 351 mr = 3285 m= 0 mr = 22 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 306 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4610425E-09 1.7678043E-09 midg,1,midg; midg,igrid,midg 1.1805740E-09 1.7498539E-09 1,midg,midg; igrid,midg,midg -1.9926290E-11 3.9064134E-09 gauss-seidel spectral radius is 0.9851095 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 14:02:17 rms-change max change #iterations 0.1026182 19.66982 at 10iterations 8.2546324E-03 1.324888 at 20iterations 7.5901789E-04 0.1117096 at 30iterations 1.3814907E-04 2.3185015E-02 at 40iterations 4.2503649E-05 7.7667236E-03 at 50iterations finished qdiffx linear iterations at : 14:02:20 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 4.2503649E-05 7.7667236E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:02:21 3.377u 0.172s 0:04.34 81.5% 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 14:02:21 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2850 !!! WARNING: HIR 207 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: 1.765902 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): -8.882999 46.66300 ymin,ymax (A): -51.93300 8.546000 zmin,zma (A): -32.58800 21.68600 x,y,z range (A): 55.54600 60.47900 54.27400 scale (grids/A): 1.765902 object centre (A): 18.89000 -21.69350 -5.451001 number of atom coordinates read : 2850 total number of charged atoms : 2778 net assigned charge : 5.514015 assigned positive charge : 426.9799 centred at (gu) : 92.43308 86.26733 90.26160 assigned negative charge : -421.4677 centred at (gu) : 92.25610 86.19136 90.24934 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28940 grid for indexing accessible points = 1.400000 m= 25077 mr = 48105 m= 3659 mr = 16844 m= 160 mr = 1970 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 36205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21687 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) : 0.5886340 object centre at (A) : 18.89000 -21.69350 -5.451001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9922217E-03 -7.0376480E-03 midg,1,midg; midg,igrid,midg 2.7738190E-03 -1.8669266E-02 1,midg,midg; igrid,midg,midg 5.1355907E-03 3.1924874E-02 gauss-seidel spectral radius is 0.9984784 estimated iterations to convergence 203 setup time was (sec) 0.8500000 now iterating at: 14:02:22 rms-change max change #iterations 3.843541 176.2080 at 10iterations 1.718387 60.27271 at 20iterations 0.7676900 26.51982 at 30iterations 0.3452677 10.65246 at 40iterations 0.1549206 5.076423 at 50iterations 6.9418974E-02 2.345443 at 60iterations 3.1062853E-02 1.187225 at 70iterations 1.3908303E-02 0.4571260 at 80iterations 6.2413430E-03 0.2010989 at 90iterations 2.8221479E-03 8.9271545E-02 at 100iterations 1.2707390E-03 4.3304443E-02 at 110iterations 5.7737954E-04 2.3767471E-02 at 120iterations finished qdiffx linear iterations at : 14:02:28 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 5.7737954E-04 2.3767471E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 14:02:30 7.702u 0.249s 0:09.08 87.4% 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 14:02:30 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2850 !!! WARNING: HIR 207 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.648853 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): -8.882999 46.66300 ymin,ymax (A): -51.93300 8.546000 zmin,zma (A): -32.58800 21.68600 x,y,z range (A): 55.54600 60.47900 54.27400 scale (grids/A): 2.648853 object centre (A): 18.89000 -21.69350 -5.451001 number of atom coordinates read : 2850 total number of charged atoms : 2778 net assigned charge : 5.514015 assigned positive charge : 426.9799 centred at (gu) : 93.64938 84.40072 90.39221 assigned negative charge : -421.4677 centred at (gu) : 93.38419 84.28692 90.37398 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 171772 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28940 grid for indexing accessible points = 1.400000 m= 81080 mr = 118487 m= 28397 mr = 62265 m= 6415 mr = 21236 m= 708 mr = 4401 m= 23 mr = 381 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 81625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 22220 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) : 1.765902 object centre at (A) : 18.89000 -21.69350 -5.451001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2952775E-02 -0.1694474 midg,1,midg; midg,igrid,midg -5.7547368E-02 -0.6531049 1,midg,midg; igrid,midg,midg 5.5791952E-02 0.3462963 gauss-seidel spectral radius is 0.9992384 estimated iterations to convergence 286 setup time was (sec) 1.720000 now iterating at: 14:02:32 rms-change max change #iterations 9.667072 324.6175 at 10iterations 5.727131 152.9946 at 20iterations 3.354134 72.21400 at 30iterations 1.953995 43.30228 at 40iterations 1.133338 24.97583 at 50iterations 0.6552442 13.90996 at 60iterations 0.3769553 8.039562 at 70iterations 0.2165096 4.564770 at 80iterations 0.1243583 2.560379 at 90iterations 7.1269162E-02 1.389530 at 100iterations 4.0840309E-02 0.7978516 at 110iterations 2.3304317E-02 0.4577799 at 120iterations 1.3321969E-02 0.2458162 at 130iterations 7.6282457E-03 0.1458633 at 140iterations 4.3565012E-03 7.9635620E-02 at 150iterations 2.4968225E-03 4.6119571E-02 at 160iterations 1.4291427E-03 2.8684288E-02 at 170iterations 8.2436379E-04 1.6132355E-02 at 180iterations finished qdiffx linear iterations at : 14:02:42 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 8.2436379E-04 1.6132355E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 14:02:43 12.654u 0.228s 0:13.47 95.5% 0+0k 0+0io 0pf+0w