Sun Oct 9 12:56:11 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 12:56:11 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 0.6963052 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): -5.829000 44.13600 ymin,ymax (A): -14.20700 36.92000 zmin,zma (A): 2.046000 44.56500 x,y,z range (A): 49.96500 51.12700 42.51900 scale (grids/A): 0.6963052 object centre (A): 19.15350 11.35650 23.30550 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500021 assigned positive charge : 370.3039 centred at (gu) : 89.53324 91.18278 90.87976 assigned negative charge : -367.8044 centred at (gu) : 89.55577 91.39057 90.98895 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 48507 no. pairs analyzed = 48507 no. exposed pairs = 3027 no. arc points = 20965 no. surface atoms = 1017 nbur = 1395 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4384 m= 0 mr = 92 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.1900000 number of dielectric boundary points 3890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1889 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6006819E-08 -3.8401097E-08 midg,1,midg; midg,igrid,midg 8.6774143E-08 -9.9511063E-08 1,midg,midg; igrid,midg,midg 3.0775340E-08 7.1183917E-09 gauss-seidel spectral radius is 0.9892853 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 12:56:12 rms-change max change #iterations 0.2064545 30.74487 at 10iterations 2.5113020E-02 3.176231 at 20iterations 3.1477527E-03 0.4013386 at 30iterations 4.8006061E-04 6.6671371E-02 at 40iterations 1.0414638E-04 1.3240814E-02 at 50iterations finished qdiffx linear iterations at : 12:56:14 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0414638E-04 1.3240814E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 12:56:15 3.409u 0.167s 0:03.84 92.7% 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 Sun Oct 9 2011 at 12:56:15 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 2.088916 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): -5.829000 44.13600 ymin,ymax (A): -14.20700 36.92000 zmin,zma (A): 2.046000 44.56500 x,y,z range (A): 49.96500 51.12700 42.51900 scale (grids/A): 2.088916 object centre (A): 19.15350 11.35650 23.30550 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500021 assigned positive charge : 370.3039 centred at (gu) : 88.59896 93.54787 92.63862 assigned negative charge : -367.8044 centred at (gu) : 88.66689 94.17150 92.96665 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 32796 mr = 57580 m= 6526 mr = 24674 m= 701 mr = 4415 m= 16 mr = 408 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 676 time to turn everything in is 0.4400000 number of dielectric boundary points 35826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 18005 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) : 0.6963052 object centre at (A) : 19.15350 11.35650 23.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4754607E-02 6.7408895E-03 midg,1,midg; midg,igrid,midg 1.7985618E-02 -7.6581709E-02 1,midg,midg; igrid,midg,midg 5.5004437E-02 -7.8249788E-03 gauss-seidel spectral radius is 0.9988363 estimated iterations to convergence 232 setup time was (sec) 0.6500000 now iterating at: 12:56:16 rms-change max change #iterations 4.990453 284.2104 at 10iterations 2.469522 78.41013 at 20iterations 1.224353 36.06127 at 30iterations 0.6066863 17.64991 at 40iterations 0.3012695 9.741840 at 50iterations 0.1498240 4.592587 at 60iterations 7.4611351E-02 2.155724 at 70iterations 3.7075266E-02 1.084294 at 80iterations 1.8425168E-02 0.5290489 at 90iterations 9.1884332E-03 0.2567111 at 100iterations 4.6015205E-03 0.1420898 at 110iterations 2.3255260E-03 6.9284201E-02 at 120iterations finished qdiffx linear iterations at : 12:56:23 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.3255260E-03 6.9284201E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 12:56:23 7.942u 0.205s 0:08.41 96.7% 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 Sun Oct 9 2011 at 12:56:23 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 3.133373 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): -5.829000 44.13600 ymin,ymax (A): -14.20700 36.92000 zmin,zma (A): 2.046000 44.56500 x,y,z range (A): 49.96500 51.12700 42.51900 scale (grids/A): 3.133373 object centre (A): 19.15350 11.35650 23.30550 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500021 assigned positive charge : 370.3039 centred at (gu) : 87.89829 95.32172 93.95766 assigned negative charge : -367.8044 centred at (gu) : 88.00035 96.25733 94.44987 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 190973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 101898 mr = 138999 m= 41635 mr = 84187 m= 12411 mr = 34034 m= 2768 mr = 9759 m= 356 mr = 2144 m= 7 mr = 220 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2192 time to turn everything in is 1.280000 number of dielectric boundary points 80705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 18160 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) : 2.088916 object centre at (A) : 19.15350 11.35650 23.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5203424 -2.7155681E-02 midg,1,midg; midg,igrid,midg 0.4465472 -0.7434357 1,midg,midg; igrid,midg,midg 0.8057923 -0.3320420 gauss-seidel spectral radius is 0.9993022 estimated iterations to convergence 299 setup time was (sec) 1.510000 now iterating at: 12:56:25 rms-change max change #iterations 11.15458 471.9425 at 10iterations 6.627756 134.7912 at 20iterations 3.913185 85.85397 at 30iterations 2.317856 41.82201 at 40iterations 1.365751 24.50957 at 50iterations 0.8045813 12.97423 at 60iterations 0.4737384 8.926901 at 70iterations 0.2791371 4.949287 at 80iterations 0.1636382 2.713100 at 90iterations 9.6152619E-02 1.551754 at 100iterations 5.6424513E-02 0.9364471 at 110iterations 3.3148933E-02 0.5596542 at 120iterations 1.9492280E-02 0.3306036 at 130iterations 1.1482034E-02 0.2132626 at 140iterations 6.8148607E-03 0.1322532 at 150iterations 4.0874481E-03 7.4306488E-02 at 160iterations 2.4944998E-03 4.9008369E-02 at 170iterations 1.5663307E-03 3.3653259E-02 at 180iterations finished qdiffx linear iterations at : 12:56:37 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 1.5663307E-03 3.3653259E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 12:56:37 13.189u 0.215s 0:13.67 97.9% 0+0k 0+0io 0pf+0w