Sat Oct 8 12:13:46 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 12:13:46 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3626 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: HIZ 449 has a net charge of 0.2000 !!! WARNING: HIZ 453 has a net charge of 0.2000 !!! WARNING: HIZ 459 has a net charge of 0.2000 !!! WARNING: ZN5 520 has a net charge of 1.4000 !!! WARNING: ZN5 521 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5558245 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): -17.39900 46.65000 ymin,ymax (A): -20.66400 42.06500 zmin,zma (A): -33.20100 25.02000 x,y,z range (A): 64.04900 62.72900 58.22100 scale (grids/A): 0.5558245 object centre (A): 14.62550 10.70050 -4.090500 number of atom coordinates read : 3626 total number of charged atoms : 3479 net assigned charge : 2.000010 assigned positive charge : 563.0674 centred at (gu) : 92.85966 90.18125 90.38511 assigned negative charge : -561.0698 centred at (gu) : 92.88999 90.30783 90.36588 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7272 nv = 96 ne = 84 npr = 70196 no. pairs analyzed = 70196 no. exposed pairs = 4822 no. arc points = 34797 no. surface atoms = 1610 nbur = 2016 mkacc time = 0.1200000 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= 302 mr = 3533 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3582 ## 500 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9476 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0989263E-11 4.6464910E-10 midg,1,midg; midg,igrid,midg 1.6057657E-09 -1.3988813E-09 1,midg,midg; igrid,midg,midg 2.7942809E-10 -3.5838371E-10 gauss-seidel spectral radius is 0.9833633 estimated iterations to convergence 64 setup time was (sec) 0.4700000 now iterating at: 12:13:47 rms-change max change #iterations 8.7553099E-02 14.47894 at 10iterations 6.1060796E-03 0.9036255 at 20iterations 4.2617656E-04 5.9930801E-02 at 30iterations 3.1817090E-05 4.8437119E-03 at 40iterations 2.8092420E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 12:13:50 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 2.8092420E-06 3.9672852E-04 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 12:13:50 3.763u 0.209s 0:04.27 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 Sat Oct 8 2011 at 12:13:50 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3626 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: HIZ 449 has a net charge of 0.2000 !!! WARNING: HIZ 453 has a net charge of 0.2000 !!! WARNING: HIZ 459 has a net charge of 0.2000 !!! WARNING: ZN5 520 has a net charge of 1.4000 !!! WARNING: ZN5 521 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.667473 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): -17.39900 46.65000 ymin,ymax (A): -20.66400 42.06500 zmin,zma (A): -33.20100 25.02000 x,y,z range (A): 64.04900 62.72900 58.22100 scale (grids/A): 1.667473 object centre (A): 14.62550 10.70050 -4.090500 number of atom coordinates read : 3626 total number of charged atoms : 3479 net assigned charge : 2.000010 assigned positive charge : 563.0674 centred at (gu) : 98.57752 90.54269 91.15398 assigned negative charge : -561.0698 centred at (gu) : 98.66970 90.92290 91.09737 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23344 mr = 52898 m= 2520 mr = 15199 m= 94 mr = 1217 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 481 time to turn everything in is 0.4000000 number of dielectric boundary points 37537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 400 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 26747 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) : 0.5558245 object centre at (A) : 14.62550 10.70050 -4.090500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8483465E-03 1.1359310E-02 midg,1,midg; midg,igrid,midg 1.7480075E-02 -1.7655665E-02 1,midg,midg; igrid,midg,midg -4.4660730E-04 -2.5176836E-02 gauss-seidel spectral radius is 0.9983289 estimated iterations to convergence 194 setup time was (sec) 0.6600000 now iterating at: 12:13:51 rms-change max change #iterations 3.956264 172.8474 at 10iterations 1.702360 72.32811 at 20iterations 0.7338968 24.80141 at 30iterations 0.3162221 10.22624 at 40iterations 0.1369010 5.370698 at 50iterations 5.9093267E-02 1.997101 at 60iterations 2.5427938E-02 0.8270035 at 70iterations 1.0966636E-02 0.3612175 at 80iterations 4.7488166E-03 0.1704998 at 90iterations 2.0505220E-03 6.4713955E-02 at 100iterations 8.8370382E-04 2.8485775E-02 at 110iterations 3.8212378E-04 1.1986732E-02 at 120iterations finished qdiffx linear iterations at : 12:13:59 total time elapsed so far: 8.490000 # loops : 120 mean,max change (kT/e) : 3.8212378E-04 1.1986732E-02 energy calculations done at 8.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 12:13:59 8.621u 0.246s 0:09.16 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 Sat Oct 8 2011 at 12:13:59 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3626 !!! WARNING: HIZ 189 has a net charge of 0.2000 !!! WARNING: HIZ 193 has a net charge of 0.2000 !!! WARNING: HIZ 199 has a net charge of 0.2000 !!! WARNING: HIZ 449 has a net charge of 0.2000 !!! WARNING: HIZ 453 has a net charge of 0.2000 !!! WARNING: HIZ 459 has a net charge of 0.2000 !!! WARNING: ZN5 520 has a net charge of 1.4000 !!! WARNING: ZN5 521 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.501210 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): -17.39900 46.65000 ymin,ymax (A): -20.66400 42.06500 zmin,zma (A): -33.20100 25.02000 x,y,z range (A): 64.04900 62.72900 58.22100 scale (grids/A): 2.501210 object centre (A): 14.62550 10.70050 -4.090500 number of atom coordinates read : 3626 total number of charged atoms : 3479 net assigned charge : 2.000010 assigned positive charge : 563.0674 centred at (gu) : 102.8661 90.81368 91.73069 assigned negative charge : -561.0698 centred at (gu) : 103.0045 91.38432 91.64607 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 188132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34797 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81606 mr = 130497 m= 22479 mr = 62529 m= 3912 mr = 16157 m= 369 mr = 2504 m= 12 mr = 187 m= 0 mr = 5 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1670 time to turn everything in is 1.020000 number of dielectric boundary points 84631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 27797 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) : 1.667473 object centre at (A) : 14.62550 10.70050 -4.090500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3589832 0.2356694 midg,1,midg; midg,igrid,midg 0.2278136 -0.1960926 1,midg,midg; igrid,midg,midg -0.1551953 -0.9102078 gauss-seidel spectral radius is 0.9992050 estimated iterations to convergence 280 setup time was (sec) 1.320000 now iterating at: 12:14:01 rms-change max change #iterations 10.32677 323.6638 at 10iterations 5.981366 144.3564 at 20iterations 3.426166 74.58792 at 30iterations 1.957168 51.99644 at 40iterations 1.114302 25.47110 at 50iterations 0.6328555 15.51060 at 60iterations 0.3586571 7.898062 at 70iterations 0.2032595 4.022689 at 80iterations 0.1145759 2.486387 at 90iterations 6.4611718E-02 1.338072 at 100iterations 3.6485627E-02 0.6681175 at 110iterations 2.0553986E-02 0.4111862 at 120iterations 1.1562794E-02 0.2182655 at 130iterations 6.5201069E-03 0.1177557 at 140iterations 3.6640647E-03 8.0215454E-02 at 150iterations 2.0629680E-03 3.7208557E-02 at 160iterations 1.1604656E-03 2.1476746E-02 at 170iterations 6.5251923E-04 1.2432098E-02 at 180iterations finished qdiffx linear iterations at : 12:14:15 total time elapsed so far: 15.47000 # loops : 180 mean,max change (kT/e) : 6.5251923E-04 1.2432098E-02 energy calculations done at 15.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.60000 DelPhi exited at 12:14:16 15.606u 0.292s 0:16.19 98.1% 0+0k 0+0io 0pf+0w