Sat Oct 8 14:44:49 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 8 2011 at 14:44:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 0.6386796 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): -12.18400 43.55600 ymin,ymax (A): -23.01000 22.40600 zmin,zma (A): -6.631000 47.83100 x,y,z range (A): 55.74000 45.41600 54.46200 scale (grids/A): 0.6386796 object centre (A): 15.68600 -0.3020000 20.60000 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.999993 assigned positive charge : 453.5475 centred at (gu) : 88.83480 89.86954 91.25093 assigned negative charge : -455.5482 centred at (gu) : 88.79357 89.77188 91.21918 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8212 nv = 96 ne = 84 npr = 63548 no. pairs analyzed = 63548 no. exposed pairs = 3450 no. arc points = 24304 no. surface atoms = 1176 nbur = 1858 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 4770 m= 0 mr = 38 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2365 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3292872E-09 1.9132618E-09 midg,1,midg; midg,igrid,midg -1.6206341E-08 9.6841442E-09 1,midg,midg; igrid,midg,midg -1.0562418E-08 2.0275901E-09 gauss-seidel spectral radius is 0.9873321 estimated iterations to convergence 73 setup time was (sec) 0.7000000 now iterating at: 14:44:51 rms-change max change #iterations 0.1537547 21.14877 at 10iterations 1.5269277E-02 2.099964 at 20iterations 1.5827811E-03 0.2128911 at 30iterations 1.6032760E-04 1.9466400E-02 at 40iterations 1.8201121E-05 2.2754669E-03 at 50iterations finished qdiffx linear iterations at : 14:44:55 total time elapsed so far: 5.140000 # loops : 50 mean,max change (kT/e) : 1.8201121E-05 2.2754669E-03 energy calculations done at 5.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 14:44:56 5.307u 0.493s 0:06.07 95.3% 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 Sat Oct 8 2011 at 14:44:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 1.916039 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): -12.18400 43.55600 ymin,ymax (A): -23.01000 22.40600 zmin,zma (A): -6.631000 47.83100 x,y,z range (A): 55.74000 45.41600 54.46200 scale (grids/A): 1.916039 object centre (A): 15.68600 -0.3020000 20.60000 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.999993 assigned positive charge : 453.5475 centred at (gu) : 86.50375 89.60813 93.75197 assigned negative charge : -455.5482 centred at (gu) : 86.38058 89.31538 93.65701 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24304 grid for indexing accessible points = 1.400000 m= 32289 mr = 64823 m= 4594 mr = 24165 m= 271 mr = 2745 m= 7 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.7700000 number of dielectric boundary points 35091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22749 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) : 0.6386796 object centre at (A) : 15.68600 -0.3020000 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1658908E-02 3.4234149E-03 midg,1,midg; midg,igrid,midg -7.9120593E-03 1.6878154E-02 1,midg,midg; igrid,midg,midg -3.9364509E-02 1.2142133E-02 gauss-seidel spectral radius is 0.9986863 estimated iterations to convergence 219 setup time was (sec) 1.140000 now iterating at: 14:44:57 rms-change max change #iterations 4.664879 212.2110 at 10iterations 2.223228 72.78796 at 20iterations 1.055227 33.12793 at 30iterations 0.5028245 14.30196 at 40iterations 0.2396802 6.937037 at 50iterations 0.1139994 3.296875 at 60iterations 5.4195188E-02 1.593128 at 70iterations 2.5765691E-02 0.6918182 at 80iterations 1.2284980E-02 0.3378885 at 90iterations 5.8331639E-03 0.1727734 at 100iterations 2.7811576E-03 7.5015068E-02 at 110iterations 1.3264801E-03 3.9939880E-02 at 120iterations finished qdiffx linear iterations at : 14:45:09 total time elapsed so far: 12.70000 # loops : 120 mean,max change (kT/e) : 1.3264801E-03 3.9939880E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 14:45:09 12.865u 0.553s 0:13.72 97.7% 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 Sat Oct 8 2011 at 14:45:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NDP 318 has a net charge of -3.0000 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: 2.874058 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): -12.18400 43.55600 ymin,ymax (A): -23.01000 22.40600 zmin,zma (A): -6.631000 47.83100 x,y,z range (A): 55.74000 45.41600 54.46200 scale (grids/A): 2.874058 object centre (A): 15.68600 -0.3020000 20.60000 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.999993 assigned positive charge : 453.5475 centred at (gu) : 84.75546 89.41196 95.62775 assigned negative charge : -455.5482 centred at (gu) : 84.57086 88.97298 95.48547 start vw surface at 0.1400000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 207702 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24304 grid for indexing accessible points = 1.400000 m= 106052 mr = 156329 m= 36821 mr = 88323 m= 8223 mr = 29533 m= 1139 mr = 5938 m= 70 mr = 756 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 549 time to turn everything in is 1.970000 number of dielectric boundary points 79103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 23096 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) : 1.916039 object centre at (A) : 15.68600 -0.3020000 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8479976E-02 0.1636528 midg,1,midg; midg,igrid,midg -6.1474483E-02 0.1965687 1,midg,midg; igrid,midg,midg -0.5700482 0.1794664 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 2.370000 now iterating at: 14:45:12 rms-change max change #iterations 10.98362 406.9615 at 10iterations 6.456647 125.5996 at 20iterations 3.766433 85.35603 at 30iterations 2.199493 42.02336 at 40iterations 1.277970 22.62558 at 50iterations 0.7435794 13.43974 at 60iterations 0.4318354 7.447536 at 70iterations 0.2504371 4.580292 at 80iterations 0.1452565 2.625523 at 90iterations 8.4294811E-02 1.406732 at 100iterations 4.8728433E-02 0.8135834 at 110iterations 2.8191511E-02 0.4570999 at 120iterations 1.6333068E-02 0.2582130 at 130iterations 9.4608944E-03 0.1559696 at 140iterations 5.4698293E-03 8.6997986E-02 at 150iterations 3.1642879E-03 5.1706910E-02 at 160iterations 1.8317369E-03 3.4905434E-02 at 170iterations 1.0624789E-03 1.9870758E-02 at 180iterations finished qdiffx linear iterations at : 14:45:32 total time elapsed so far: 21.89000 # loops : 180 mean,max change (kT/e) : 1.0624789E-03 1.9870758E-02 energy calculations done at 21.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.06000 DelPhi exited at 14:45:32 22.065u 0.554s 0:22.89 98.7% 0+0k 0+0io 0pf+0w