Tue Oct 11 03:44:29 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 Tue Oct 11 2011 at 03:44:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2723 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6488063 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): -4.511000 46.62400 ymin,ymax (A): 16.37400 66.70600 zmin,zma (A): -18.16300 36.70700 x,y,z range (A): 51.13500 50.33200 54.87000 scale (grids/A): 0.6488063 object centre (A): 21.05650 41.54000 9.271998 number of atom coordinates read : 2723 total number of charged atoms : 2575 net assigned charge : 5.500025 assigned positive charge : 412.6828 centred at (gu) : 89.51361 91.25783 90.81841 assigned negative charge : -407.1833 centred at (gu) : 89.27989 91.04517 90.81730 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7627 nv = 96 ne = 84 npr = 55429 no. pairs analyzed = 55429 no. exposed pairs = 3310 no. arc points = 23015 no. surface atoms = 1119 nbur = 1604 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4283 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3600000 number of dielectric boundary points 3729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2347 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9205 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3871372E-09 1.2109624E-08 midg,1,midg; midg,igrid,midg -1.7909318E-08 5.5298340E-08 1,midg,midg; igrid,midg,midg -3.0096675E-08 4.0896694E-08 gauss-seidel spectral radius is 0.9876989 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 03:44:30 rms-change max change #iterations 0.1619763 22.72256 at 10iterations 1.6503174E-02 2.587706 at 20iterations 1.7099890E-03 0.2262993 at 30iterations 1.9397706E-04 2.7076721E-02 at 40iterations 2.8139073E-05 4.8866272E-03 at 50iterations finished qdiffx linear iterations at : 03:44:34 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 2.8139073E-05 4.8866272E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 03:44:34 4.099u 0.281s 0:05.07 86.1% 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 Tue Oct 11 2011 at 03:44:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2723 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.946419 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): -4.511000 46.62400 ymin,ymax (A): 16.37400 66.70600 zmin,zma (A): -18.16300 36.70700 x,y,z range (A): 51.13500 50.33200 54.87000 scale (grids/A): 1.946419 object centre (A): 21.05650 41.54000 9.271998 number of atom coordinates read : 2723 total number of charged atoms : 2575 net assigned charge : 5.500025 assigned positive charge : 412.6828 centred at (gu) : 88.54045 93.77299 92.45450 assigned negative charge : -407.1833 centred at (gu) : 87.83939 93.13522 92.45168 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 82190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23015 grid for indexing accessible points = 1.400000 m= 31147 mr = 57704 m= 5187 mr = 23431 m= 330 mr = 3339 m= 3 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.7400000 number of dielectric boundary points 34265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20311 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) : 0.6488063 object centre at (A) : 21.05650 41.54000 9.271998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8561807E-03 -3.6932241E-02 midg,1,midg; midg,igrid,midg -5.4868632E-03 0.1110231 1,midg,midg; igrid,midg,midg -5.2776791E-02 5.6885205E-02 gauss-seidel spectral radius is 0.9987035 estimated iterations to convergence 220 setup time was (sec) 1.020000 now iterating at: 03:44:36 rms-change max change #iterations 4.559421 203.4592 at 10iterations 2.175435 79.55361 at 20iterations 1.039964 31.50698 at 30iterations 0.4988243 16.01787 at 40iterations 0.2382086 7.842179 at 50iterations 0.1140893 3.574880 at 60iterations 5.4592699E-02 1.558438 at 70iterations 2.6074095E-02 0.7990990 at 80iterations 1.2547762E-02 0.3795962 at 90iterations 6.0056304E-03 0.1831303 at 100iterations 2.8860837E-03 9.8762512E-02 at 110iterations 1.3860604E-03 4.0538788E-02 at 120iterations finished qdiffx linear iterations at : 03:44:44 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 1.3860604E-03 4.0538788E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 03:44:45 9.577u 0.307s 0:10.17 97.0% 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 Tue Oct 11 2011 at 03:44:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2723 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.919628 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): -4.511000 46.62400 ymin,ymax (A): 16.37400 66.70600 zmin,zma (A): -18.16300 36.70700 x,y,z range (A): 51.13500 50.33200 54.87000 scale (grids/A): 2.919628 object centre (A): 21.05650 41.54000 9.271998 number of atom coordinates read : 2723 total number of charged atoms : 2575 net assigned charge : 5.500025 assigned positive charge : 412.6828 centred at (gu) : 87.81056 95.65935 93.68169 assigned negative charge : -407.1833 centred at (gu) : 86.75903 94.70267 93.67751 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 189794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23015 grid for indexing accessible points = 1.400000 m= 99174 mr = 139308 m= 37193 mr = 82058 m= 9374 mr = 30431 m= 1469 mr = 7144 m= 92 mr = 1008 m= 0 mr = 38 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 2167 time to turn everything in is 1.910000 number of dielectric boundary points 77109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 20600 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) : 1.946419 object centre at (A) : 21.05650 41.54000 9.271998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1636967 -0.9652911 midg,1,midg; midg,igrid,midg 5.4717056E-02 1.050219 1,midg,midg; igrid,midg,midg -0.7652009 0.7701867 gauss-seidel spectral radius is 0.9992760 estimated iterations to convergence 293 setup time was (sec) 2.240000 now iterating at: 03:44:47 rms-change max change #iterations 10.50003 392.0452 at 10iterations 6.153143 147.8121 at 20iterations 3.595643 80.27250 at 30iterations 2.099145 58.40718 at 40iterations 1.221163 25.75033 at 50iterations 0.7100250 13.66091 at 60iterations 0.4126954 7.581926 at 70iterations 0.2393221 3.987535 at 80iterations 0.1387485 2.327428 at 90iterations 8.0362082E-02 1.577089 at 100iterations 4.6618972E-02 0.8083590 at 110iterations 2.7039256E-02 0.4703188 at 120iterations 1.5666019E-02 0.2657776 at 130iterations 9.0705520E-03 0.1613108 at 140iterations 5.2499436E-03 0.1039524 at 150iterations 3.0373540E-03 5.6327820E-02 at 160iterations 1.7579700E-03 3.1772614E-02 at 170iterations 1.0202697E-03 1.6559601E-02 at 180iterations finished qdiffx linear iterations at : 03:45:01 total time elapsed so far: 16.05000 # loops : 180 mean,max change (kT/e) : 1.0202697E-03 1.6559601E-02 energy calculations done at 16.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.22000 DelPhi exited at 03:45:02 16.219u 0.310s 0:17.00 97.1% 0+0k 0+0io 0pf+0w