Mon Oct 10 14:03:43 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 14:03:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 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: 0.7032515 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): -7.529000 38.56000 ymin,ymax (A): -18.60600 30.50000 zmin,zma (A): 22.54300 73.16500 x,y,z range (A): 46.08900 49.10600 50.62200 scale (grids/A): 0.7032515 object centre (A): 15.51550 5.947001 47.85400 number of atom coordinates read : 2199 total number of charged atoms : 2056 net assigned charge : -9.999976 assigned positive charge : 331.2758 centred at (gu) : 88.45899 88.40314 90.07678 assigned negative charge : -341.2759 centred at (gu) : 88.37684 88.18377 89.79958 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 45182 no. pairs analyzed = 45182 no. exposed pairs = 2815 no. arc points = 20278 no. surface atoms = 941 nbur = 1258 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 459 mr = 4001 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.1900000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1811 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0944290E-07 5.9788469E-08 midg,1,midg; midg,igrid,midg -2.5088843E-07 2.2206148E-08 1,midg,midg; igrid,midg,midg -1.5344615E-07 -2.5495559E-08 gauss-seidel spectral radius is 0.9894814 estimated iterations to convergence 79 setup time was (sec) 0.4000000 now iterating at: 14:03:44 rms-change max change #iterations 0.2049285 31.58577 at 10iterations 2.4753394E-02 3.353926 at 20iterations 2.9620128E-03 0.3939123 at 30iterations 3.6238023E-04 4.7052383E-02 at 40iterations 4.3784443E-05 5.4016113E-03 at 50iterations finished qdiffx linear iterations at : 14:03:47 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 4.3784443E-05 5.4016113E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 14:03:48 3.719u 0.202s 0:04.69 83.3% 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 14:03:48 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 = 2199 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: 2.109755 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): -7.529000 38.56000 ymin,ymax (A): -18.60600 30.50000 zmin,zma (A): 22.54300 73.16500 x,y,z range (A): 46.08900 49.10600 50.62200 scale (grids/A): 2.109755 object centre (A): 15.51550 5.947001 47.85400 number of atom coordinates read : 2199 total number of charged atoms : 2056 net assigned charge : -9.999976 assigned positive charge : 331.2758 centred at (gu) : 85.37682 85.20917 90.23002 assigned negative charge : -341.2759 centred at (gu) : 85.13032 84.55137 89.39868 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 78239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 29502 mr = 53006 m= 5381 mr = 22080 m= 432 mr = 3590 m= 12 mr = 220 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3167 time to turn everything in is 0.4100000 number of dielectric boundary points 34668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 16332 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) : 0.7032515 object centre at (A) : 15.51550 5.947001 47.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1168578 -1.1152087E-02 midg,1,midg; midg,igrid,midg -0.1116925 1.0870172E-02 1,midg,midg; igrid,midg,midg -1.8440595E-02 2.0373384E-03 gauss-seidel spectral radius is 0.9988384 estimated iterations to convergence 232 setup time was (sec) 0.6400000 now iterating at: 14:03:49 rms-change max change #iterations 4.793222 187.9920 at 10iterations 2.366680 79.59140 at 20iterations 1.170713 37.66519 at 30iterations 0.5801734 18.00914 at 40iterations 0.2881390 9.378578 at 50iterations 0.1427747 4.299755 at 60iterations 7.0700191E-02 2.099506 at 70iterations 3.5084713E-02 1.039734 at 80iterations 1.7427059E-02 0.5209932 at 90iterations 8.6286189E-03 0.2628937 at 100iterations 4.2999992E-03 0.1313782 at 110iterations 2.1345066E-03 6.7711115E-02 at 120iterations finished qdiffx linear iterations at : 14:03:56 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 2.1345066E-03 6.7711115E-02 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 14:03:57 8.398u 0.241s 0:09.44 91.4% 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 14:03:57 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2199 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.164632 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): -7.529000 38.56000 ymin,ymax (A): -18.60600 30.50000 zmin,zma (A): 22.54300 73.16500 x,y,z range (A): 46.08900 49.10600 50.62200 scale (grids/A): 3.164632 object centre (A): 15.51550 5.947001 47.85400 number of atom coordinates read : 2199 total number of charged atoms : 2056 net assigned charge : -9.999976 assigned positive charge : 331.2758 centred at (gu) : 83.06523 82.81380 90.34498 assigned negative charge : -341.2759 centred at (gu) : 82.69550 81.82698 89.09801 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 180442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20278 grid for indexing accessible points = 1.400000 m= 92231 mr = 128222 m= 36329 mr = 75596 m= 10092 mr = 29830 m= 1887 mr = 7917 m= 184 mr = 1387 m= 5 mr = 91 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 10358 time to turn everything in is 1.240000 number of dielectric boundary points 78125 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 16448 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) : 2.109755 object centre at (A) : 15.51550 5.947001 47.85400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.121630 -3.6912534E-02 midg,1,midg; midg,igrid,midg -0.9095259 6.5849207E-02 1,midg,midg; igrid,midg,midg -6.8018340E-02 2.3398817E-02 gauss-seidel spectral radius is 0.9993040 estimated iterations to convergence 299 setup time was (sec) 1.510000 now iterating at: 14:03:59 rms-change max change #iterations 10.78167 385.1674 at 10iterations 6.344163 126.6713 at 20iterations 3.719749 69.83771 at 30iterations 2.182473 39.33068 at 40iterations 1.275900 22.90855 at 50iterations 0.7468137 12.18706 at 60iterations 0.4363002 8.658276 at 70iterations 0.2547062 4.588364 at 80iterations 0.1490636 2.415461 at 90iterations 8.7004222E-02 1.615709 at 100iterations 5.0713979E-02 0.9212494 at 110iterations 2.9682122E-02 0.5136375 at 120iterations 1.7290857E-02 0.2981730 at 130iterations 1.0107579E-02 0.1620936 at 140iterations 5.9083742E-03 0.1020885 at 150iterations 3.4444770E-03 6.0968637E-02 at 160iterations 2.0128444E-03 3.5018921E-02 at 170iterations 1.1763711E-03 2.0142555E-02 at 180iterations finished qdiffx linear iterations at : 14:04:12 total time elapsed so far: 14.14000 # loops : 180 mean,max change (kT/e) : 1.1763711E-03 2.0142555E-02 energy calculations done at 14.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.29000 DelPhi exited at 14:04:12 14.292u 0.242s 0:15.30 94.9% 0+0k 0+0io 0pf+0w