Sun Oct 9 11:17:19 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 Sun Oct 9 2011 at 11:17:19 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 = 2848 !!! WARNING: HIR 208 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6234349 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): -22.57100 34.53200 ymin,ymax (A): -25.31600 26.09500 zmin,zma (A): -30.87400 25.93500 x,y,z range (A): 57.10300 51.41100 56.80900 scale (grids/A): 0.6234349 object centre (A): 5.980498 0.3894997 -2.469501 number of atom coordinates read : 2848 total number of charged atoms : 2760 net assigned charge : 5.014010 assigned positive charge : 422.5591 centred at (gu) : 90.68672 90.38208 92.12358 assigned negative charge : -417.5468 centred at (gu) : 90.68591 90.34099 92.06870 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7794 nv = 96 ne = 84 npr = 54904 no. pairs analyzed = 54904 no. exposed pairs = 3973 no. arc points = 28058 no. surface atoms = 1324 nbur = 1524 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 3984 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2697 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9303 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0476527E-11 1.3766405E-08 midg,1,midg; midg,igrid,midg 1.0255501E-09 8.2052294E-09 1,midg,midg; igrid,midg,midg 3.7009260E-09 5.0941176E-09 gauss-seidel spectral radius is 0.9867147 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 11:17:20 rms-change max change #iterations 0.1375994 20.25751 at 10iterations 1.3143653E-02 1.876761 at 20iterations 1.3748175E-03 0.1977654 at 30iterations 2.2398707E-04 3.5776138E-02 at 40iterations 5.3929187E-05 9.2992783E-03 at 50iterations finished qdiffx linear iterations at : 11:17:23 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.3929187E-05 9.2992783E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:17:23 3.413u 0.182s 0:03.89 92.2% 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 Sun Oct 9 2011 at 11:17:23 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 = 2848 !!! WARNING: HIR 208 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.870305 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): -22.57100 34.53200 ymin,ymax (A): -25.31600 26.09500 zmin,zma (A): -30.87400 25.93500 x,y,z range (A): 57.10300 51.41100 56.80900 scale (grids/A): 1.870305 object centre (A): 5.980498 0.3894997 -2.469501 number of atom coordinates read : 2848 total number of charged atoms : 2760 net assigned charge : 5.014010 assigned positive charge : 422.5591 centred at (gu) : 92.05900 91.14538 96.36965 assigned negative charge : -417.5468 centred at (gu) : 92.05766 91.02289 96.20608 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28058 grid for indexing accessible points = 1.400000 m= 30064 mr = 55373 m= 5212 mr = 21379 m= 301 mr = 3194 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.4000000 number of dielectric boundary points 38988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 21661 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) : 0.6234349 object centre at (A) : 5.980498 0.3894997 -2.469501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3913104E-03 2.2591675E-02 midg,1,midg; midg,igrid,midg 2.5698068E-02 3.2860283E-02 1,midg,midg; igrid,midg,midg 1.0147227E-02 -2.5558338E-02 gauss-seidel spectral radius is 0.9986370 estimated iterations to convergence 215 setup time was (sec) 0.6200000 now iterating at: 11:17:24 rms-change max change #iterations 4.299510 181.9126 at 10iterations 2.006796 75.70901 at 20iterations 0.9377782 32.17980 at 30iterations 0.4382787 13.58794 at 40iterations 0.2049874 6.655637 at 50iterations 9.6061572E-02 2.890653 at 60iterations 4.5081265E-02 1.414934 at 70iterations 2.1066990E-02 0.6648650 at 80iterations 9.8840026E-03 0.3048000 at 90iterations 4.6707797E-03 0.1552277 at 100iterations 2.2022978E-03 7.9740524E-02 at 110iterations 1.0428845E-03 3.2727718E-02 at 120iterations finished qdiffx linear iterations at : 11:17:31 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 1.0428845E-03 3.2727718E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 11:17:32 7.920u 0.204s 0:08.43 96.3% 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 Sun Oct 9 2011 at 11:17:32 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 = 2848 !!! WARNING: HIR 208 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.805457 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): -22.57100 34.53200 ymin,ymax (A): -25.31600 26.09500 zmin,zma (A): -30.87400 25.93500 x,y,z range (A): 57.10300 51.41100 56.80900 scale (grids/A): 2.805457 object centre (A): 5.980498 0.3894997 -2.469501 number of atom coordinates read : 2848 total number of charged atoms : 2760 net assigned charge : 5.014010 assigned positive charge : 422.5591 centred at (gu) : 93.08818 91.71792 99.55429 assigned negative charge : -417.5468 centred at (gu) : 93.08640 91.53420 99.30894 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 192653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28058 grid for indexing accessible points = 1.400000 m= 95344 mr = 135240 m= 36317 mr = 75578 m= 9397 mr = 28572 m= 1321 mr = 6846 m= 57 mr = 801 m= 0 mr = 13 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 1865 time to turn everything in is 1.060000 number of dielectric boundary points 88039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 22072 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) : 1.870305 object centre at (A) : 5.980498 0.3894997 -2.469501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9178123E-02 0.1830364 midg,1,midg; midg,igrid,midg 0.3822251 0.3706557 1,midg,midg; igrid,midg,midg 0.1492938 -0.4240593 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 1.290000 now iterating at: 11:17:33 rms-change max change #iterations 10.32837 293.4018 at 10iterations 6.183342 125.8972 at 20iterations 3.649170 79.21809 at 30iterations 2.150152 47.52284 at 40iterations 1.264526 25.77697 at 50iterations 0.7394596 14.04705 at 60iterations 0.4311697 8.114143 at 70iterations 0.2512468 4.280991 at 80iterations 0.1461648 2.448767 at 90iterations 8.4852584E-02 1.537094 at 100iterations 4.9410809E-02 0.9498386 at 110iterations 2.8693607E-02 0.5801058 at 120iterations 1.6672952E-02 0.3073813 at 130iterations 9.6929446E-03 0.1787186 at 140iterations 5.6434679E-03 9.4614506E-02 at 150iterations 3.2916428E-03 5.8489799E-02 at 160iterations 1.9257769E-03 3.6033154E-02 at 170iterations 1.1350866E-03 2.0034790E-02 at 180iterations finished qdiffx linear iterations at : 11:17:45 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.1350866E-03 2.0034790E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 11:17:46 13.007u 0.220s 0:13.65 96.8% 0+0k 0+0io 0pf+0w