Sat Oct 15 15:25:41 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 15 2011 at 15:25:41 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6461566 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): -11.34900 36.66800 ymin,ymax (A): -25.77400 22.69700 zmin,zma (A): -9.860001 45.23500 x,y,z range (A): 48.01700 48.47100 55.09500 scale (grids/A): 0.6461566 object centre (A): 12.65950 -1.538500 17.68750 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.140012 assigned positive charge : 411.0537 centred at (gu) : 90.18944 90.32683 91.79652 assigned negative charge : -407.9143 centred at (gu) : 89.92276 90.15479 91.74362 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7513 nv = 96 ne = 84 npr = 56560 no. pairs analyzed = 56560 no. exposed pairs = 3308 no. arc points = 22947 no. surface atoms = 1118 nbur = 1615 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 4260 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2000000 number of dielectric boundary points 3617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2304 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6192916E-09 1.8755310E-08 midg,1,midg; midg,igrid,midg -1.8721595E-08 3.1703614E-08 1,midg,midg; igrid,midg,midg -3.3042735E-08 4.4353783E-08 gauss-seidel spectral radius is 0.9875951 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 15:25:42 rms-change max change #iterations 0.1569716 20.98520 at 10iterations 1.6137637E-02 2.091553 at 20iterations 1.7371183E-03 0.2089958 at 30iterations 2.2352283E-04 3.6863327E-02 at 40iterations 4.5835783E-05 6.4620972E-03 at 50iterations finished qdiffx linear iterations at : 15:25:47 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 4.5835783E-05 6.4620972E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 15:25:47 3.497u 0.193s 0:06.04 60.9% 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 Sat Oct 15 2011 at 15:25:47 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.938470 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): -11.34900 36.66800 ymin,ymax (A): -25.77400 22.69700 zmin,zma (A): -9.860001 45.23500 x,y,z range (A): 48.01700 48.47100 55.09500 scale (grids/A): 1.938470 object centre (A): 12.65950 -1.538500 17.68750 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.140012 assigned positive charge : 411.0537 centred at (gu) : 90.56750 90.97983 95.38901 assigned negative charge : -407.9143 centred at (gu) : 89.76788 90.46404 95.23055 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22947 grid for indexing accessible points = 1.400000 m= 29690 mr = 57438 m= 4352 mr = 22030 m= 237 mr = 2711 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 863 time to turn everything in is 0.4100000 number of dielectric boundary points 33315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20356 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) : 0.6461566 object centre at (A) : 12.65950 -1.538500 17.68750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8466118E-02 5.9976536E-03 midg,1,midg; midg,igrid,midg -1.3291526E-02 2.8900299E-02 1,midg,midg; igrid,midg,midg -1.6130924E-02 5.8760758E-02 gauss-seidel spectral radius is 0.9986904 estimated iterations to convergence 219 setup time was (sec) 0.6500000 now iterating at: 15:25:48 rms-change max change #iterations 4.515007 200.9890 at 10iterations 2.152762 74.02221 at 20iterations 1.025172 31.21023 at 30iterations 0.4891897 17.96750 at 40iterations 0.2327118 7.319553 at 50iterations 0.1111423 3.353443 at 60iterations 5.2867189E-02 1.952988 at 70iterations 2.5261763E-02 0.7943096 at 80iterations 1.2050621E-02 0.4146481 at 90iterations 5.7367063E-03 0.1712608 at 100iterations 2.7376851E-03 8.5876465E-02 at 110iterations 1.3128552E-03 4.3243408E-02 at 120iterations finished qdiffx linear iterations at : 15:25:56 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 1.3128552E-03 4.3243408E-02 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 15:25:57 8.417u 0.235s 0:09.03 95.6% 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 Sat Oct 15 2011 at 15:25:57 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.907705 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): -11.34900 36.66800 ymin,ymax (A): -25.77400 22.69700 zmin,zma (A): -9.860001 45.23500 x,y,z range (A): 48.01700 48.47100 55.09500 scale (grids/A): 2.907705 object centre (A): 12.65950 -1.538500 17.68750 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.140012 assigned positive charge : 411.0537 centred at (gu) : 90.85114 91.46969 98.08329 assigned negative charge : -407.9143 centred at (gu) : 89.65175 90.69595 97.84575 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 187793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22947 grid for indexing accessible points = 1.400000 m= 96303 mr = 138513 m= 34388 mr = 79443 m= 7827 mr = 27758 m= 1009 mr = 5792 m= 58 mr = 659 m= 0 mr = 19 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 3067 time to turn everything in is 1.080000 number of dielectric boundary points 75194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 20644 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) : 1.938470 object centre at (A) : 12.65950 -1.538500 17.68750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4038815 0.2855400 midg,1,midg; midg,igrid,midg -0.1646419 0.3236782 1,midg,midg; igrid,midg,midg -0.1280215 0.4902914 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.350000 now iterating at: 15:25:58 rms-change max change #iterations 10.48658 441.8905 at 10iterations 6.137676 177.9808 at 20iterations 3.589692 80.50121 at 30iterations 2.095081 39.27109 at 40iterations 1.216811 22.97953 at 50iterations 0.7072340 13.54654 at 60iterations 0.4103921 8.078431 at 70iterations 0.2377066 4.069935 at 80iterations 0.1377171 2.457756 at 90iterations 7.9758167E-02 1.388617 at 100iterations 4.6175856E-02 0.7659736 at 110iterations 2.6734853E-02 0.4765053 at 120iterations 1.5505684E-02 0.2628078 at 130iterations 8.9750169E-03 0.1675720 at 140iterations 5.2199829E-03 9.3696594E-02 at 150iterations 3.0465873E-03 5.4634094E-02 at 160iterations 1.7997710E-03 3.1835556E-02 at 170iterations 1.0748639E-03 2.0900726E-02 at 180iterations finished qdiffx linear iterations at : 15:26:11 total time elapsed so far: 13.73000 # loops : 180 mean,max change (kT/e) : 1.0748639E-03 2.0900726E-02 energy calculations done at 13.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 15:26:11 13.872u 0.232s 0:14.41 97.8% 0+0k 0+0io 0pf+0w