Sat Oct 15 12:24:16 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 Sat Oct 15 2011 at 12:24:16 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4673 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: SEP 498 has a net charge of -0.4750 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4322381 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): -5.024000 77.33801 ymin,ymax (A): 0.5030001 67.25800 zmin,zma (A): 173.9150 235.3110 x,y,z range (A): 82.36201 66.75500 61.39600 scale (grids/A): 0.4322381 object centre (A): 36.15700 33.88050 204.6130 number of atom coordinates read : 4673 total number of charged atoms : 4434 net assigned charge : 18.52501 assigned positive charge : 687.4988 centred at (gu) : 86.79279 91.10677 88.67054 assigned negative charge : -668.9786 centred at (gu) : 86.72694 91.09209 88.69478 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 5078 nv = 96 ne = 84 npr = 95518 no. pairs analyzed = 95518 no. exposed pairs = 6050 no. arc points = 41390 no. surface atoms = 2048 nbur = 2625 mkacc time = 0.2800000 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 = 1.932000 m= 134 mr = 2323 m= 0 mr = 1 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 2888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3377 ## 709 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 7010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0701964E-12 2.1476306E-12 midg,1,midg; midg,igrid,midg 2.6027167E-12 6.9247945E-12 1,midg,midg; igrid,midg,midg 3.0370595E-12 2.7743201E-12 gauss-seidel spectral radius is 0.9727088 estimated iterations to convergence 51 setup time was (sec) 0.8600000 now iterating at: 12:24:17 rms-change max change #iterations 2.7870012E-02 5.593047 at 10iterations 2.7679065E-03 0.4767857 at 20iterations 7.8716659E-04 0.1272888 at 30iterations 2.3524638E-04 3.6629677E-02 at 40iterations 7.0644695E-05 1.1336327E-02 at 50iterations finished qdiffx linear iterations at : 12:24:20 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 7.0644695E-05 1.1336327E-02 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 12:24:21 4.545u 0.229s 0:05.18 91.8% 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 15 2011 at 12:24:21 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4673 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: SEP 498 has a net charge of -0.4750 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.296714 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): -5.024000 77.33801 ymin,ymax (A): 0.5030001 67.25800 zmin,zma (A): 173.9150 235.3110 x,y,z range (A): 82.36201 66.75500 61.39600 scale (grids/A): 1.296714 object centre (A): 36.15700 33.88050 204.6130 number of atom coordinates read : 4673 total number of charged atoms : 4434 net assigned charge : 18.52501 assigned positive charge : 687.4988 centred at (gu) : 80.37688 93.31847 86.01024 assigned negative charge : -668.9786 centred at (gu) : 80.18068 93.27569 86.08383 start vw surface at 0.2600000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 59393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 14143 mr = 38516 m= 712 mr = 8331 m= 8 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 160 time to turn everything in is 0.6400000 number of dielectric boundary points 27281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 740 ## 33 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 30926 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) : 0.4322381 object centre at (A) : 36.15700 33.88050 204.6130 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6753789E-03 5.3436036E-04 midg,1,midg; midg,igrid,midg 3.0071160E-03 2.5885173E-03 1,midg,midg; igrid,midg,midg 7.8414595E-03 3.0788577E-03 gauss-seidel spectral radius is 0.9972215 estimated iterations to convergence 151 setup time was (sec) 0.9900000 now iterating at: 12:24:22 rms-change max change #iterations 2.431642 136.8051 at 10iterations 0.8257585 34.70671 at 20iterations 0.2798563 13.11309 at 30iterations 9.5529571E-02 3.927109 at 40iterations 3.2812763E-02 1.395386 at 50iterations 1.1548296E-02 0.4771261 at 60iterations 4.4110557E-03 0.1902828 at 70iterations 1.9718737E-03 8.2695007E-02 at 80iterations 1.0951920E-03 4.1492462E-02 at 90iterations 7.0180529E-04 2.4770737E-02 at 100iterations 4.7131008E-04 1.5853882E-02 at 110iterations 3.2231948E-04 1.1072159E-02 at 120iterations finished qdiffx linear iterations at : 12:24:30 total time elapsed so far: 8.720000 # loops : 120 mean,max change (kT/e) : 3.2231948E-04 1.1072159E-02 energy calculations done at 8.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.950000 DelPhi exited at 12:24:31 8.950u 0.239s 0:09.58 95.8% 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 15 2011 at 12:24:31 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4673 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: SEP 498 has a net charge of -0.4750 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.945072 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): -5.024000 77.33801 ymin,ymax (A): 0.5030001 67.25800 zmin,zma (A): 173.9150 235.3110 x,y,z range (A): 82.36201 66.75500 61.39600 scale (grids/A): 1.945072 object centre (A): 36.15700 33.88050 204.6130 number of atom coordinates read : 4673 total number of charged atoms : 4434 net assigned charge : 18.52501 assigned positive charge : 687.4988 centred at (gu) : 75.56479 94.97729 84.01496 assigned negative charge : -668.9786 centred at (gu) : 75.27074 94.91348 84.12564 start vw surface at 0.2600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 139544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41390 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 53891 mr = 96512 m= 10204 mr = 39531 m= 708 mr = 6390 m= 12 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 1.390000 number of dielectric boundary points 61670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 34990 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) : 1.296714 object centre at (A) : 36.15700 33.88050 204.6130 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5998493E-02 7.4495804E-03 midg,1,midg; midg,igrid,midg 8.2831584E-02 5.5575591E-02 1,midg,midg; igrid,midg,midg 0.1966455 3.8713597E-02 gauss-seidel spectral radius is 0.9988505 estimated iterations to convergence 233 setup time was (sec) 1.770000 now iterating at: 12:24:33 rms-change max change #iterations 7.347272 253.9503 at 10iterations 3.793944 109.2882 at 20iterations 1.944056 52.26791 at 30iterations 0.9939924 26.79417 at 40iterations 0.5051629 14.22953 at 50iterations 0.2559644 7.287338 at 60iterations 0.1293379 3.298031 at 70iterations 6.5385543E-02 1.532463 at 80iterations 3.2905865E-02 0.7903843 at 90iterations 1.6649973E-02 0.3892832 at 100iterations 8.4191216E-03 0.1951866 at 110iterations 4.3065907E-03 0.1083570 at 120iterations 2.2331341E-03 5.8006287E-02 at 130iterations 1.2006360E-03 3.2463074E-02 at 140iterations 6.8603194E-04 1.6873837E-02 at 150iterations 4.2698940E-04 1.0404587E-02 at 160iterations 2.8783764E-04 6.4239502E-03 at 170iterations 2.0635083E-04 4.5032501E-03 at 180iterations finished qdiffx linear iterations at : 12:24:45 total time elapsed so far: 13.85000 # loops : 180 mean,max change (kT/e) : 2.0635083E-04 4.5032501E-03 energy calculations done at 13.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.08000 DelPhi exited at 12:24:46 14.085u 0.219s 0:15.42 92.6% 0+0k 0+0io 0pf+0w