Mon Oct 10 14:39:59 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 14:39:59 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2845 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: 0.5659688 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): -42.93900 19.96200 ymin,ymax (A): -26.02200 33.75600 zmin,zma (A): -9.825000 45.85100 x,y,z range (A): 62.90100 59.77800 55.67600 scale (grids/A): 0.5659688 object centre (A): -11.48850 3.867001 18.01300 number of atom coordinates read : 2845 total number of charged atoms : 2692 net assigned charge : -11.49998 assigned positive charge : 429.7790 centred at (gu) : 91.13744 87.74782 89.21738 assigned negative charge : -441.2800 centred at (gu) : 91.03809 87.77419 89.18660 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6053 nv = 96 ne = 84 npr = 56279 no. pairs analyzed = 56279 no. exposed pairs = 3847 no. arc points = 27677 no. surface atoms = 1280 nbur = 1565 mkacc time = 0.1000000 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 = 1.540000 m= 243 mr = 2993 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2100000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2737 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7795 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3439115E-09 -9.3834329E-10 midg,1,midg; midg,igrid,midg -1.9872683E-09 -1.1224796E-09 1,midg,midg; igrid,midg,midg -2.2070641E-09 -2.5407515E-10 gauss-seidel spectral radius is 0.9838914 estimated iterations to convergence 65 setup time was (sec) 0.4000000 now iterating at: 14:40:00 rms-change max change #iterations 9.0017870E-02 17.38603 at 10iterations 6.6024610E-03 1.097984 at 20iterations 5.1098119E-04 0.1096268 at 30iterations 4.9790880E-05 8.7804794E-03 at 40iterations 7.2340954E-06 1.6632080E-03 at 50iterations finished qdiffx linear iterations at : 14:40:03 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 7.2340954E-06 1.6632080E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:40:03 3.396u 0.180s 0:03.89 91.7% 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 Mon Oct 10 2011 at 14:40:03 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2845 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: 1.697906 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): -42.93900 19.96200 ymin,ymax (A): -26.02200 33.75600 zmin,zma (A): -9.825000 45.85100 x,y,z range (A): 62.90100 59.77800 55.67600 scale (grids/A): 1.697906 object centre (A): -11.48850 3.867001 18.01300 number of atom coordinates read : 2845 total number of charged atoms : 2692 net assigned charge : -11.49998 assigned positive charge : 429.7790 centred at (gu) : 93.41158 83.24242 87.65145 assigned negative charge : -441.2800 centred at (gu) : 93.11386 83.32212 87.55914 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27677 grid for indexing accessible points = 1.400000 m= 20005 mr = 44183 m= 2188 mr = 13127 m= 71 mr = 1055 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 795 time to turn everything in is 0.3300000 number of dielectric boundary points 30844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 257 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20761 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) : 0.5659688 object centre at (A) : -11.48850 3.867001 18.01300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6276391E-02 -1.1059043E-03 midg,1,midg; midg,igrid,midg -2.1580264E-02 -1.1866443E-02 1,midg,midg; igrid,midg,midg -2.6888708E-03 -1.2251486E-02 gauss-seidel spectral radius is 0.9983188 estimated iterations to convergence 194 setup time was (sec) 0.5400000 now iterating at: 14:40:04 rms-change max change #iterations 3.620133 152.1591 at 10iterations 1.552470 62.82403 at 20iterations 0.6659737 25.53650 at 30iterations 0.2857612 10.52419 at 40iterations 0.1227968 4.862595 at 50iterations 5.2888624E-02 1.877018 at 60iterations 2.2677159E-02 0.7721949 at 70iterations 9.7651798E-03 0.3524990 at 80iterations 4.2107864E-03 0.1467419 at 90iterations 1.8217550E-03 6.5519333E-02 at 100iterations 7.8314863E-04 2.9369354E-02 at 110iterations 3.4025649E-04 1.2340531E-02 at 120iterations finished qdiffx linear iterations at : 14:40:11 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 3.4025649E-04 1.2340531E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:40:11 7.697u 0.211s 0:08.26 95.6% 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 14:40:12 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2845 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: 2.546859 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): -42.93900 19.96200 ymin,ymax (A): -26.02200 33.75600 zmin,zma (A): -9.825000 45.85100 x,y,z range (A): 62.90100 59.77800 55.67600 scale (grids/A): 2.546859 object centre (A): -11.48850 3.867001 18.01300 number of atom coordinates read : 2845 total number of charged atoms : 2692 net assigned charge : -11.49998 assigned positive charge : 429.7790 centred at (gu) : 95.11723 79.86346 86.47699 assigned negative charge : -441.2800 centred at (gu) : 94.67088 79.98304 86.33861 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27677 grid for indexing accessible points = 1.400000 m= 68845 mr = 108545 m= 19712 mr = 53376 m= 3570 mr = 14283 m= 304 mr = 2287 m= 2 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 2600 time to turn everything in is 0.8400000 number of dielectric boundary points 69552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 21528 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) : 1.697906 object centre at (A) : -11.48850 3.867001 18.01300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2303975 0.1583015 midg,1,midg; midg,igrid,midg -0.2567191 -0.1132997 1,midg,midg; igrid,midg,midg 0.1065508 -0.2798204 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.070000 now iterating at: 14:40:13 rms-change max change #iterations 9.258612 308.8351 at 10iterations 5.283525 120.7868 at 20iterations 2.994659 72.91664 at 30iterations 1.687174 35.78062 at 40iterations 0.9482343 20.08214 at 50iterations 0.5317903 10.95193 at 60iterations 0.2983530 6.789444 at 70iterations 0.1669846 3.855972 at 80iterations 9.3394436E-02 1.964973 at 90iterations 5.2076921E-02 1.068349 at 100iterations 2.9091578E-02 0.5756626 at 110iterations 1.6239787E-02 0.3460417 at 120iterations 9.0594124E-03 0.1845338 at 130iterations 5.0437599E-03 0.1002502 at 140iterations 2.8187116E-03 6.1184883E-02 at 150iterations 1.5739221E-03 3.2734632E-02 at 160iterations 8.7998417E-04 1.7143250E-02 at 170iterations 4.9171195E-04 9.7188950E-03 at 180iterations finished qdiffx linear iterations at : 14:40:24 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 4.9171195E-04 9.7188950E-03 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 14:40:25 12.370u 0.201s 0:13.13 95.7% 0+0k 0+0io 0pf+0w