Tue Oct 11 06:22:20 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 06:22:21 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 = 2052 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: 0.7194681 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): 3.368000 47.18200 ymin,ymax (A): 0.6660000 42.34400 zmin,zma (A): -2.570000 46.91100 x,y,z range (A): 43.81400 41.67800 49.48100 scale (grids/A): 0.7194681 object centre (A): 25.27500 21.50500 22.17050 number of atom coordinates read : 2052 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.87486 89.91412 90.31474 assigned negative charge : -304.2972 centred at (gu) : 90.06055 89.89767 90.34995 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7266 nv = 96 ne = 84 npr = 41194 no. pairs analyzed = 41194 no. exposed pairs = 2463 no. arc points = 16886 no. surface atoms = 840 nbur = 1212 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 4236 m= 8 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1570 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7951 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9755361E-08 6.5188381E-08 midg,1,midg; midg,igrid,midg 7.4585245E-08 9.2591982E-08 1,midg,midg; igrid,midg,midg 2.0313053E-07 -3.4059312E-08 gauss-seidel spectral radius is 0.9899245 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 06:22:21 rms-change max change #iterations 0.2193423 28.87993 at 10iterations 2.7904835E-02 3.810747 at 20iterations 3.7488022E-03 0.5233793 at 30iterations 5.8508286E-04 7.9366684E-02 at 40iterations 1.2960305E-04 1.8424988E-02 at 50iterations finished qdiffx linear iterations at : 06:22:24 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.2960305E-04 1.8424988E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:22:25 3.355u 0.184s 0:04.04 87.3% 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 Tue Oct 11 2011 at 06:22:25 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 = 2052 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: 2.158404 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): 3.368000 47.18200 ymin,ymax (A): 0.6660000 42.34400 zmin,zma (A): -2.570000 46.91100 x,y,z range (A): 43.81400 41.67800 49.48100 scale (grids/A): 2.158404 object centre (A): 25.27500 21.50500 22.17050 number of atom coordinates read : 2052 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.62447 89.74214 90.94429 assigned negative charge : -304.2972 centred at (gu) : 90.18172 89.69308 91.04980 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 77171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 31143 mr = 55221 m= 6174 mr = 23819 m= 590 mr = 4105 m= 16 mr = 291 m= 0 mr = 3 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 31655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15339 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) : 0.7194681 object centre at (A) : 25.27500 21.50500 22.17050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2157821E-02 6.7884147E-02 midg,1,midg; midg,igrid,midg 5.4809907E-03 2.8386720E-02 1,midg,midg; igrid,midg,midg 5.1935274E-02 1.1592007E-02 gauss-seidel spectral radius is 0.9988629 estimated iterations to convergence 235 setup time was (sec) 0.6000000 now iterating at: 06:22:25 rms-change max change #iterations 4.676398 200.2556 at 10iterations 2.330027 79.35967 at 20iterations 1.173016 36.62176 at 30iterations 0.5876393 17.69687 at 40iterations 0.2946421 9.368238 at 50iterations 0.1477348 4.440320 at 60iterations 7.4170694E-02 2.133873 at 70iterations 3.7053525E-02 1.148121 at 80iterations 1.8593639E-02 0.5588875 at 90iterations 9.4182892E-03 0.2737255 at 100iterations 4.7893492E-03 0.1552429 at 110iterations 2.4485553E-03 6.6778183E-02 at 120iterations finished qdiffx linear iterations at : 06:22:33 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 2.4485553E-03 6.6778183E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 06:22:33 7.891u 0.237s 0:08.55 94.9% 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 Tue Oct 11 2011 at 06:22:33 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 = 2052 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.237606 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): 3.368000 47.18200 ymin,ymax (A): 0.6660000 42.34400 zmin,zma (A): -2.570000 46.91100 x,y,z range (A): 43.81400 41.67800 49.48100 scale (grids/A): 3.237606 object centre (A): 25.27500 21.50500 22.17050 number of atom coordinates read : 2052 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.43677 89.61319 91.41646 assigned negative charge : -304.2972 centred at (gu) : 90.27264 89.53976 91.57489 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 177914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 97050 mr = 132765 m= 39684 mr = 81144 m= 11690 mr = 32924 m= 2353 mr = 8983 m= 278 mr = 1665 m= 10 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 71315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15432 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) : 2.158404 object centre at (A) : 25.27500 21.50500 22.17050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5143391 0.6222706 midg,1,midg; midg,igrid,midg -1.3747653E-02 0.2127975 1,midg,midg; igrid,midg,midg 0.3587345 0.2031588 gauss-seidel spectral radius is 0.9992997 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 06:22:35 rms-change max change #iterations 10.31716 401.5997 at 10iterations 6.128063 131.9498 at 20iterations 3.627736 89.28394 at 30iterations 2.140225 43.56753 at 40iterations 1.262662 24.58929 at 50iterations 0.7443687 15.28152 at 60iterations 0.4383028 7.720727 at 70iterations 0.2575797 4.386551 at 80iterations 0.1510914 2.704491 at 90iterations 8.9010172E-02 1.616367 at 100iterations 5.2419599E-02 0.9730949 at 110iterations 3.1009307E-02 0.6113319 at 120iterations 1.8485768E-02 0.3239098 at 130iterations 1.1208745E-02 0.2103424 at 140iterations 6.9898153E-03 0.1208572 at 150iterations 4.5363270E-03 8.1642151E-02 at 160iterations 3.1146137E-03 5.6396484E-02 at 170iterations 2.2704909E-03 4.2922974E-02 at 180iterations finished qdiffx linear iterations at : 06:22:46 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 2.2704909E-03 4.2922974E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 06:22:47 12.739u 0.207s 0:13.24 97.6% 0+0k 0+0io 0pf+0w