Mon Oct 10 19:34:24 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 Mon Oct 10 2011 at 19:34:24 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 !!! WARNING: HIR 257 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6838526 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): -16.68000 35.37800 ymin,ymax (A): -7.218000 37.77600 zmin,zma (A): -2.227000 49.28500 x,y,z range (A): 52.05800 44.99400 51.51200 scale (grids/A): 0.6838526 object centre (A): 9.349001 15.27900 23.52900 number of atom coordinates read : 2405 total number of charged atoms : 2269 net assigned charge : 2.014004 assigned positive charge : 360.8979 centred at (gu) : 92.28772 90.52060 90.89826 assigned negative charge : -358.8846 centred at (gu) : 92.20164 90.68588 90.96539 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7686 nv = 96 ne = 84 npr = 48816 no. pairs analyzed = 48816 no. exposed pairs = 3164 no. arc points = 21623 no. surface atoms = 1063 nbur = 1342 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4204 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2000000 number of dielectric boundary points 3903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1963 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6068102E-08 -1.5526101E-08 midg,1,midg; midg,igrid,midg 5.6363270E-08 -5.1015927E-08 1,midg,midg; igrid,midg,midg -1.1845920E-08 5.9781343E-08 gauss-seidel spectral radius is 0.9888987 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 19:34:25 rms-change max change #iterations 0.1851162 28.15545 at 10iterations 2.1273995E-02 2.564102 at 20iterations 2.5537424E-03 0.4094048 at 30iterations 3.6787050E-04 5.2967072E-02 at 40iterations 8.8211593E-05 1.3967037E-02 at 50iterations finished qdiffx linear iterations at : 19:34:28 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 8.8211593E-05 1.3967037E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 19:34:28 3.397u 0.186s 0:04.03 88.5% 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 Mon Oct 10 2011 at 19:34:28 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 !!! WARNING: HIR 257 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.051558 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): -16.68000 35.37800 ymin,ymax (A): -7.218000 37.77600 zmin,zma (A): -2.227000 49.28500 x,y,z range (A): 52.05800 44.99400 51.51200 scale (grids/A): 2.051558 object centre (A): 9.349001 15.27900 23.52900 number of atom coordinates read : 2405 total number of charged atoms : 2269 net assigned charge : 2.014004 assigned positive charge : 360.8979 centred at (gu) : 96.86250 91.56130 92.69434 assigned negative charge : -358.8846 centred at (gu) : 96.60491 92.05732 92.89593 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 32139 mr = 56442 m= 6548 mr = 23856 m= 671 mr = 4317 m= 17 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 868 time to turn everything in is 0.4200000 number of dielectric boundary points 35959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17991 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) : 0.6838526 object centre at (A) : 9.349001 15.27900 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4890605E-02 1.2514601E-02 midg,1,midg; midg,igrid,midg 2.7548013E-02 -1.4406145E-03 1,midg,midg; igrid,midg,midg -6.1329952E-03 2.1911858E-02 gauss-seidel spectral radius is 0.9987976 estimated iterations to convergence 228 setup time was (sec) 0.6300000 now iterating at: 19:34:29 rms-change max change #iterations 4.717596 295.6635 at 10iterations 2.303483 73.80358 at 20iterations 1.135085 35.66978 at 30iterations 0.5551074 16.63230 at 40iterations 0.2724996 7.966070 at 50iterations 0.1338973 4.162459 at 60iterations 6.5781191E-02 2.079258 at 70iterations 3.2312889E-02 0.9543114 at 80iterations 1.5832338E-02 0.4468060 at 90iterations 7.8006838E-03 0.2163839 at 100iterations 3.8591609E-03 0.1204386 at 110iterations 1.9168197E-03 5.3737640E-02 at 120iterations finished qdiffx linear iterations at : 19:34:36 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.9168197E-03 5.3737640E-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) 7.930000 DelPhi exited at 19:34:37 7.935u 0.212s 0:08.60 94.6% 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 Mon Oct 10 2011 at 19:34:37 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2405 !!! WARNING: HIR 257 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.077337 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): -16.68000 35.37800 ymin,ymax (A): -7.218000 37.77600 zmin,zma (A): -2.227000 49.28500 x,y,z range (A): 52.05800 44.99400 51.51200 scale (grids/A): 3.077337 object centre (A): 9.349001 15.27900 23.52900 number of atom coordinates read : 2405 total number of charged atoms : 2269 net assigned charge : 2.014004 assigned positive charge : 360.8979 centred at (gu) : 100.2937 92.34180 94.04144 assigned negative charge : -358.8846 centred at (gu) : 99.90725 93.08609 94.34379 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 188129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 99294 mr = 136546 m= 41210 mr = 81311 m= 12515 mr = 33540 m= 2715 mr = 9624 m= 305 mr = 2019 m= 9 mr = 200 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2703 time to turn everything in is 1.270000 number of dielectric boundary points 80937 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 18151 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) : 2.051558 object centre at (A) : 9.349001 15.27900 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4039319 0.6345765 midg,1,midg; midg,igrid,midg 0.2046257 0.1780377 1,midg,midg; igrid,midg,midg 3.2798160E-02 5.3592227E-02 gauss-seidel spectral radius is 0.9993007 estimated iterations to convergence 298 setup time was (sec) 1.510000 now iterating at: 19:34:38 rms-change max change #iterations 10.82063 542.5280 at 10iterations 6.438193 155.7785 at 20iterations 3.815443 89.60904 at 30iterations 2.262825 39.91390 at 40iterations 1.334483 26.36141 at 50iterations 0.7849473 14.01694 at 60iterations 0.4619608 8.209384 at 70iterations 0.2704110 4.551886 at 80iterations 0.1586976 2.831110 at 90iterations 9.2989326E-02 1.664444 at 100iterations 5.4636665E-02 0.9562931 at 110iterations 3.1871129E-02 0.6186562 at 120iterations 1.8673308E-02 0.3023453 at 130iterations 1.0940221E-02 0.1934261 at 140iterations 6.4042313E-03 0.1048012 at 150iterations 3.7687342E-03 6.1851501E-02 at 160iterations 2.2310081E-03 3.5585403E-02 at 170iterations 1.3350574E-03 2.7404785E-02 at 180iterations finished qdiffx linear iterations at : 19:34:50 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 1.3350574E-03 2.7404785E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 19:34:51 13.164u 0.227s 0:13.80 96.9% 0+0k 0+0io 0pf+0w