Sun Oct 9 20:45:40 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 Sun Oct 9 2011 at 20:45:40 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4971 !!! WARNING: LLP 1 has a net charge of 1.5300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5393286 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): -2.466000 55.94400 ymin,ymax (A): -8.667000 57.34100 zmin,zma (A): -8.834000 52.00700 x,y,z range (A): 58.41000 66.00800 60.84100 scale (grids/A): 0.5393286 object centre (A): 26.73900 24.33700 21.58650 number of atom coordinates read : 4971 total number of charged atoms : 4830 net assigned charge : -2.469940 assigned positive charge : 760.2422 centred at (gu) : 89.81905 89.29629 89.62138 assigned negative charge : -762.7175 centred at (gu) : 89.86661 89.33839 89.67907 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9200 nv = 96 ne = 84 npr = 101864 no. pairs analyzed = 101864 no. exposed pairs = 5615 no. arc points = 38734 no. surface atoms = 1923 nbur = 3048 mkacc time = 0.2100000 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= 423 mr = 5282 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3934 ## 466 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 12371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2325157E-10 -5.8114114E-10 midg,1,midg; midg,igrid,midg 2.9720826E-10 -4.1852694E-10 1,midg,midg; igrid,midg,midg 3.0929340E-10 -5.2383731E-10 gauss-seidel spectral radius is 0.9824194 estimated iterations to convergence 62 setup time was (sec) 0.6800000 now iterating at: 20:45:41 rms-change max change #iterations 9.8638974E-02 13.85938 at 10iterations 1.1647880E-02 1.792862 at 20iterations 4.0492667E-03 0.6855927 at 30iterations 1.7300664E-03 0.2917786 at 40iterations 7.4945076E-04 0.1242676 at 50iterations finished qdiffx linear iterations at : 20:45:43 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 7.4945076E-04 0.1242676 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 20:45:44 3.320u 0.161s 0:03.75 92.8% 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 Sun Oct 9 2011 at 20:45:44 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4971 !!! WARNING: LLP 1 has a net charge of 1.5300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.617986 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): -2.466000 55.94400 ymin,ymax (A): -8.667000 57.34100 zmin,zma (A): -8.834000 52.00700 x,y,z range (A): 58.41000 66.00800 60.84100 scale (grids/A): 1.617986 object centre (A): 26.73900 24.33700 21.58650 number of atom coordinates read : 4971 total number of charged atoms : 4830 net assigned charge : -2.469940 assigned positive charge : 760.2422 centred at (gu) : 89.45561 87.88760 88.86267 assigned negative charge : -762.7175 centred at (gu) : 89.60007 88.01499 89.03735 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 103967 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38734 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 34338 mr = 75320 m= 3755 mr = 24559 m= 98 mr = 1883 m= 0 mr = 6 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.6700000 number of dielectric boundary points 40390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 36859 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) : 0.5393286 object centre at (A) : 26.73900 24.33700 21.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1953602E-02 -1.9041013E-02 midg,1,midg; midg,igrid,midg -1.5480869E-02 -2.2937765E-02 1,midg,midg; igrid,midg,midg 2.3545944E-03 -1.2571781E-02 gauss-seidel spectral radius is 0.9983370 estimated iterations to convergence 195 setup time was (sec) 0.9500000 now iterating at: 20:45:45 rms-change max change #iterations 4.479147 187.3384 at 10iterations 1.941567 67.94389 at 20iterations 0.8452629 27.59654 at 30iterations 0.3680119 11.15174 at 40iterations 0.1610499 4.934076 at 50iterations 7.1171775E-02 2.275398 at 60iterations 3.2101788E-02 1.088360 at 70iterations 1.5567612E-02 0.5298233 at 80iterations 8.4654782E-03 0.2968445 at 90iterations 5.2042920E-03 0.1828804 at 100iterations 3.5218871E-03 0.1172562 at 110iterations 2.5146524E-03 8.3251953E-02 at 120iterations finished qdiffx linear iterations at : 20:45:51 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 2.5146524E-03 8.3251953E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 20:45:52 7.336u 0.205s 0:07.85 95.9% 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 Sun Oct 9 2011 at 20:45:52 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4971 !!! WARNING: LLP 1 has a net charge of 1.5300 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.426979 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): -2.466000 55.94400 ymin,ymax (A): -8.667000 57.34100 zmin,zma (A): -8.834000 52.00700 x,y,z range (A): 58.41000 66.00800 60.84100 scale (grids/A): 2.426979 object centre (A): 26.73900 24.33700 21.58650 number of atom coordinates read : 4971 total number of charged atoms : 4830 net assigned charge : -2.469940 assigned positive charge : 760.2422 centred at (gu) : 89.18311 86.83085 88.29378 assigned negative charge : -762.7175 centred at (gu) : 89.40003 87.02245 88.55598 start vw surface at 0.2000000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 241987 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38734 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 117489 mr = 183601 m= 35480 mr = 95535 m= 5999 mr = 27195 m= 426 mr = 4010 m= 4 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1690 time to turn everything in is 1.700000 number of dielectric boundary points 90872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 38570 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) : 1.617986 object centre at (A) : 26.73900 24.33700 21.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1753267 -0.4660329 midg,1,midg; midg,igrid,midg -0.3940834 -0.3867761 1,midg,midg; igrid,midg,midg 9.1416106E-02 -0.1713068 gauss-seidel spectral radius is 0.9992220 estimated iterations to convergence 283 setup time was (sec) 2.010000 now iterating at: 20:45:54 rms-change max change #iterations 11.58510 290.1657 at 10iterations 6.739002 145.4294 at 20iterations 3.901375 78.22083 at 30iterations 2.243097 38.87628 at 40iterations 1.289819 26.40561 at 50iterations 0.7390125 12.54681 at 60iterations 0.4210135 7.867767 at 70iterations 0.2410101 3.923828 at 80iterations 0.1374137 2.524717 at 90iterations 7.8328498E-02 1.416321 at 100iterations 4.4982780E-02 0.8033218 at 110iterations 2.5958575E-02 0.4584656 at 120iterations 1.5234972E-02 0.2722931 at 130iterations 9.2052696E-03 0.1669579 at 140iterations 5.7957880E-03 0.1155701 at 150iterations 3.8819164E-03 8.5573196E-02 at 160iterations 2.7914732E-03 5.9310913E-02 at 170iterations 2.1166026E-03 4.7424316E-02 at 180iterations finished qdiffx linear iterations at : 20:46:04 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 2.1166026E-03 4.7424316E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 20:46:05 12.691u 0.188s 0:13.14 97.9% 0+0k 0+0io 0pf+0w