Sat Oct 15 12:57:41 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 Sat Oct 15 2011 at 12:57:41 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 0.6784312 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): -7.506000 44.68800 ymin,ymax (A): -14.05400 38.42000 zmin,zma (A): 2.077000 45.13500 x,y,z range (A): 52.19400 52.47400 43.05800 scale (grids/A): 0.6784312 object centre (A): 18.59100 12.18300 23.60600 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.89827 90.81517 90.77280 assigned negative charge : -356.4896 centred at (gu) : 89.92967 90.95790 90.81034 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7412 nv = 96 ne = 84 npr = 47285 no. pairs analyzed = 47285 no. exposed pairs = 2944 no. arc points = 20840 no. surface atoms = 994 nbur = 1373 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4134 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1992 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8444 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2011246E-08 4.6679540E-09 midg,1,midg; midg,igrid,midg 4.6912291E-08 -3.1811933E-08 1,midg,midg; igrid,midg,midg 2.4425633E-08 5.7772800E-09 gauss-seidel spectral radius is 0.9887154 estimated iterations to convergence 77 setup time was (sec) 0.4300000 now iterating at: 12:57:41 rms-change max change #iterations 0.1797813 24.87882 at 10iterations 2.0678252E-02 2.923874 at 20iterations 2.7350693E-03 0.4039040 at 30iterations 5.4999057E-04 8.5708618E-02 at 40iterations 1.6041081E-04 2.5253296E-02 at 50iterations finished qdiffx linear iterations at : 12:57:45 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.6041081E-04 2.5253296E-02 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 12:57:45 3.901u 0.246s 0:04.49 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 Sat Oct 15 2011 at 12:57:45 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 2.035294 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): -7.506000 44.68800 ymin,ymax (A): -14.05400 38.42000 zmin,zma (A): 2.077000 45.13500 x,y,z range (A): 52.19400 52.47400 43.05800 scale (grids/A): 2.035294 object centre (A): 18.59100 12.18300 23.60600 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.69429 92.44470 92.31776 assigned negative charge : -356.4896 centred at (gu) : 89.78892 92.87333 92.43087 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 30791 mr = 54754 m= 5606 mr = 23196 m= 451 mr = 3649 m= 7 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 0.4100000 number of dielectric boundary points 33767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17605 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) : 0.6784312 object centre at (A) : 18.59100 12.18300 23.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6552720E-02 1.1804841E-02 midg,1,midg; midg,igrid,midg 1.3210207E-02 -3.8758084E-02 1,midg,midg; igrid,midg,midg 4.7606453E-02 -5.7764342E-03 gauss-seidel spectral radius is 0.9987790 estimated iterations to convergence 227 setup time was (sec) 0.6600000 now iterating at: 12:57:46 rms-change max change #iterations 4.590927 195.0838 at 10iterations 2.234203 83.19610 at 20iterations 1.088356 35.54633 at 30iterations 0.5334870 17.16250 at 40iterations 0.2592760 8.165988 at 50iterations 0.1267572 3.977177 at 60iterations 6.1951552E-02 1.826696 at 70iterations 3.0358452E-02 0.8803234 at 80iterations 1.5003591E-02 0.4435806 at 90iterations 7.4738185E-03 0.2358856 at 100iterations 3.7792136E-03 0.1144075 at 110iterations 1.9755231E-03 6.1524391E-02 at 120iterations finished qdiffx linear iterations at : 12:57:54 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 1.9755231E-03 6.1524391E-02 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 12:57:55 8.936u 0.274s 0:09.59 95.9% 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 Sat Oct 15 2011 at 12:57:55 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 3.052941 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): -7.506000 44.68800 ymin,ymax (A): -14.05400 38.42000 zmin,zma (A): 2.077000 45.13500 x,y,z range (A): 52.19400 52.47400 43.05800 scale (grids/A): 3.052941 object centre (A): 18.59100 12.18300 23.60600 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.54131 93.66692 93.47659 assigned negative charge : -356.4896 centred at (gu) : 89.68327 94.30991 93.64626 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 181499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20840 grid for indexing accessible points = 1.400000 m= 96538 mr = 131850 m= 37978 mr = 79815 m= 10277 mr = 31105 m= 1953 mr = 7972 m= 186 mr = 1424 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 789 time to turn everything in is 1.120000 number of dielectric boundary points 76157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 17794 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) : 2.035294 object centre at (A) : 18.59100 12.18300 23.60600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3658796 9.0307780E-03 midg,1,midg; midg,igrid,midg 0.2505765 -0.4272186 1,midg,midg; igrid,midg,midg 0.5048360 -0.1727708 gauss-seidel spectral radius is 0.9992856 estimated iterations to convergence 295 setup time was (sec) 1.410000 now iterating at: 12:57:57 rms-change max change #iterations 10.55739 397.6945 at 10iterations 6.249238 145.2306 at 20iterations 3.684470 73.58333 at 30iterations 2.171381 45.85096 at 40iterations 1.276350 24.82262 at 50iterations 0.7474721 13.01674 at 60iterations 0.4370306 7.829071 at 70iterations 0.2560346 4.650814 at 80iterations 0.1492521 2.585657 at 90iterations 8.7377228E-02 1.511108 at 100iterations 5.1225960E-02 0.9370136 at 110iterations 3.0098537E-02 0.5387764 at 120iterations 1.7798699E-02 0.3431168 at 130iterations 1.0691247E-02 0.2118950 at 140iterations 6.6334507E-03 0.1376438 at 150iterations 4.2845118E-03 0.1001968 at 160iterations 2.9352040E-03 6.1798096E-02 at 170iterations 2.1455949E-03 4.5272827E-02 at 180iterations finished qdiffx linear iterations at : 12:58:10 total time elapsed so far: 14.70000 # loops : 180 mean,max change (kT/e) : 2.1455949E-03 4.5272827E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.84000 DelPhi exited at 12:58:10 14.840u 0.280s 0:15.43 97.9% 0+0k 0+0io 0pf+0w