Sat Oct 8 16:45:06 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 16:45:06 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 = 4459 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5450926 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): 15.97600 79.54100 ymin,ymax (A): 119.3750 184.6850 zmin,zma (A): -1.110000 59.87800 x,y,z range (A): 63.56500 65.31000 60.98800 scale (grids/A): 0.5450926 object centre (A): 47.75850 152.0300 29.38400 number of atom coordinates read : 4459 total number of charged atoms : 4289 net assigned charge : 3.500043 assigned positive charge : 682.0656 centred at (gu) : 92.10341 89.74294 87.54062 assigned negative charge : -678.5690 centred at (gu) : 92.11276 89.66946 87.56525 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8583 nv = 96 ne = 84 npr = 89277 no. pairs analyzed = 89277 no. exposed pairs = 5581 no. arc points = 38408 no. surface atoms = 1871 nbur = 2588 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 364 mr = 4565 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4019 ## 546 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 11432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2015522E-10 -1.5098303E-11 midg,1,midg; midg,igrid,midg -5.4743327E-10 8.5360435E-10 1,midg,midg; igrid,midg,midg 1.7824328E-10 1.8755006E-10 gauss-seidel spectral radius is 0.9827595 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 16:45:07 rms-change max change #iterations 8.9865103E-02 13.40015 at 10iterations 6.5091834E-03 0.9444885 at 20iterations 1.0433578E-03 0.1495876 at 30iterations 3.4254501E-04 4.3428421E-02 at 40iterations 1.2358496E-04 1.5438557E-02 at 50iterations finished qdiffx linear iterations at : 16:45:11 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.2358496E-04 1.5438557E-02 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 16:45:11 4.676u 0.376s 0:05.39 93.5% 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 Sat Oct 8 2011 at 16:45:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4459 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.635278 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): 15.97600 79.54100 ymin,ymax (A): 119.3750 184.6850 zmin,zma (A): -1.110000 59.87800 x,y,z range (A): 63.56500 65.31000 60.98800 scale (grids/A): 1.635278 object centre (A): 47.75850 152.0300 29.38400 number of atom coordinates read : 4459 total number of charged atoms : 4289 net assigned charge : 3.500043 assigned positive charge : 682.0656 centred at (gu) : 96.30960 89.22774 82.62054 assigned negative charge : -678.5690 centred at (gu) : 96.33791 89.00805 82.69541 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 96000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30583 mr = 66778 m= 3537 mr = 20943 m= 123 mr = 1866 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 1107 time to turn everything in is 0.7900000 number of dielectric boundary points 40634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 530 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 32858 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) : 0.5450926 object centre at (A) : 47.75850 152.0300 29.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0411714E-03 7.6547125E-03 midg,1,midg; midg,igrid,midg 1.1969378E-02 2.8708203E-02 1,midg,midg; igrid,midg,midg -1.1534501E-02 -1.9526703E-02 gauss-seidel spectral radius is 0.9983364 estimated iterations to convergence 195 setup time was (sec) 1.090000 now iterating at: 16:45:13 rms-change max change #iterations 4.255992 164.6752 at 10iterations 1.834521 56.62721 at 20iterations 0.7929076 26.28920 at 30iterations 0.3439102 10.80628 at 40iterations 0.1490619 4.597365 at 50iterations 6.4562470E-02 2.185333 at 60iterations 2.8097294E-02 0.8326435 at 70iterations 1.2306398E-02 0.3673315 at 80iterations 5.4112901E-03 0.1668568 at 90iterations 2.4531097E-03 7.4823380E-02 at 100iterations 1.1651044E-03 3.8383305E-02 at 110iterations 5.9422926E-04 1.8224716E-02 at 120iterations finished qdiffx linear iterations at : 16:45:23 total time elapsed so far: 11.51000 # loops : 120 mean,max change (kT/e) : 5.9422926E-04 1.8224716E-02 energy calculations done at 11.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 16:45:24 11.681u 0.460s 0:12.46 97.4% 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 16:45:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4459 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.452917 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): 15.97600 79.54100 ymin,ymax (A): 119.3750 184.6850 zmin,zma (A): -1.110000 59.87800 x,y,z range (A): 63.56500 65.31000 60.98800 scale (grids/A): 2.452917 object centre (A): 47.75850 152.0300 29.38400 number of atom coordinates read : 4459 total number of charged atoms : 4289 net assigned charge : 3.500043 assigned positive charge : 682.0656 centred at (gu) : 99.46401 88.84116 78.93056 assigned negative charge : -678.5690 centred at (gu) : 99.50681 88.51192 79.04305 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 223281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38408 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105550 mr = 163489 m= 31226 mr = 83510 m= 5736 mr = 23348 m= 502 mr = 3962 m= 12 mr = 273 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 3603 time to turn everything in is 1.950000 number of dielectric boundary points 91725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 34260 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) : 1.635278 object centre at (A) : 47.75850 152.0300 29.38400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2219141E-02 0.1706424 midg,1,midg; midg,igrid,midg 0.2076920 0.4846944 1,midg,midg; igrid,midg,midg -0.1625653 -0.3142072 gauss-seidel spectral radius is 0.9992178 estimated iterations to convergence 282 setup time was (sec) 2.300000 now iterating at: 16:45:26 rms-change max change #iterations 11.00308 325.8906 at 10iterations 6.410930 144.5072 at 20iterations 3.708357 71.63547 at 30iterations 2.136677 39.96856 at 40iterations 1.225960 23.50628 at 50iterations 0.7014130 12.87599 at 60iterations 0.3999040 7.217646 at 70iterations 0.2275817 3.932842 at 80iterations 0.1294440 2.475719 at 90iterations 7.3508143E-02 1.299062 at 100iterations 4.1792933E-02 0.8885550 at 110iterations 2.3764407E-02 0.4342051 at 120iterations 1.3506941E-02 0.2401447 at 130iterations 7.6525724E-03 0.1358452 at 140iterations 4.3634023E-03 7.3897123E-02 at 150iterations 2.4976651E-03 4.5082331E-02 at 160iterations 1.4443069E-03 2.4778366E-02 at 170iterations 8.4655971E-04 1.4734745E-02 at 180iterations finished qdiffx linear iterations at : 16:45:44 total time elapsed so far: 19.46000 # loops : 180 mean,max change (kT/e) : 8.4655971E-04 1.4734745E-02 energy calculations done at 19.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.62000 DelPhi exited at 16:45:44 19.629u 0.494s 0:20.48 98.1% 0+0k 0+0io 0pf+0w