Sun Oct 9 09:25:17 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 09:25:17 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 = 2683 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: 0.5914112 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): -80.61300 -32.94500 ymin,ymax (A): -33.12300 27.07200 zmin,zma (A): -52.14800 7.241000 x,y,z range (A): 47.66800 60.19500 59.38900 scale (grids/A): 0.5914112 object centre (A): -56.77900 -3.025500 -22.45350 number of atom coordinates read : 2683 total number of charged atoms : 2538 net assigned charge : -0.9999814 assigned positive charge : 397.0396 centred at (gu) : 89.44447 88.65705 88.39889 assigned negative charge : -398.0405 centred at (gu) : 89.42814 88.87790 88.47958 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6479 nv = 96 ne = 84 npr = 52210 no. pairs analyzed = 52210 no. exposed pairs = 3729 no. arc points = 26849 no. surface atoms = 1241 nbur = 1442 mkacc time = 8.9999996E-02 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 = 1.456000 m= 329 mr = 3213 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2665 ## 295 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7966 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6792824E-09 -1.9094382E-09 midg,1,midg; midg,igrid,midg 7.8015212E-09 -5.0477249E-09 1,midg,midg; igrid,midg,midg -1.0355111E-09 1.4097458E-11 gauss-seidel spectral radius is 0.9852287 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 09:25:18 rms-change max change #iterations 0.1012352 20.38288 at 10iterations 8.2333544E-03 1.909660 at 20iterations 6.7757088E-04 0.1095238 at 30iterations 5.6683300E-05 8.9507103E-03 at 40iterations 6.6250286E-06 1.3337135E-03 at 50iterations finished qdiffx linear iterations at : 09:25:21 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 6.6250286E-06 1.3337135E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 09:25:21 3.387u 0.173s 0:03.88 91.4% 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 Sun Oct 9 2011 at 09:25:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2683 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: 1.774234 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): -80.61300 -32.94500 ymin,ymax (A): -33.12300 27.07200 zmin,zma (A): -52.14800 7.241000 x,y,z range (A): 47.66800 60.19500 59.38900 scale (grids/A): 1.774234 object centre (A): -56.77900 -3.025500 -22.45350 number of atom coordinates read : 2683 total number of charged atoms : 2538 net assigned charge : -0.9999814 assigned positive charge : 397.0396 centred at (gu) : 88.33252 85.97073 85.19599 assigned negative charge : -398.0405 centred at (gu) : 88.28424 86.63345 85.43871 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 69736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26849 grid for indexing accessible points = 1.400000 m= 23489 mr = 45337 m= 3185 mr = 16387 m= 135 mr = 1656 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 140 time to turn everything in is 0.3400000 number of dielectric boundary points 33135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19817 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) : 0.5914112 object centre at (A) : -56.77900 -3.025500 -22.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0195874E-04 -4.5565399E-03 midg,1,midg; midg,igrid,midg 2.1548963E-03 -2.1233896E-02 1,midg,midg; igrid,midg,midg 9.4292937E-03 5.8616963E-03 gauss-seidel spectral radius is 0.9984555 estimated iterations to convergence 202 setup time was (sec) 0.5600000 now iterating at: 09:25:22 rms-change max change #iterations 3.720140 179.4462 at 10iterations 1.647156 61.71155 at 20iterations 0.7317216 25.94712 at 30iterations 0.3251610 13.08524 at 40iterations 0.1445802 4.783414 at 50iterations 6.4047039E-02 2.122987 at 60iterations 2.8618695E-02 0.9849167 at 70iterations 1.2768396E-02 0.4465113 at 80iterations 5.6806672E-03 0.2106743 at 90iterations 2.5217270E-03 8.8563919E-02 at 100iterations 1.1304575E-03 4.2333841E-02 at 110iterations 5.0343352E-04 1.9699097E-02 at 120iterations finished qdiffx linear iterations at : 09:25:29 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 5.0343352E-04 1.9699097E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 09:25:29 7.759u 0.217s 0:08.27 96.2% 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 09:25:29 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 = 2683 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: 2.661351 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): -80.61300 -32.94500 ymin,ymax (A): -33.12300 27.07200 zmin,zma (A): -52.14800 7.241000 x,y,z range (A): 47.66800 60.19500 59.38900 scale (grids/A): 2.661351 object centre (A): -56.77900 -3.025500 -22.45350 number of atom coordinates read : 2683 total number of charged atoms : 2538 net assigned charge : -0.9999814 assigned positive charge : 397.0396 centred at (gu) : 87.49862 83.95594 82.79380 assigned negative charge : -398.0405 centred at (gu) : 87.42625 84.95000 83.15800 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26849 grid for indexing accessible points = 1.400000 m= 77299 mr = 111053 m= 25942 mr = 60839 m= 5159 mr = 19741 m= 600 mr = 3475 m= 15 mr = 345 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 0.8700000 number of dielectric boundary points 74800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 20303 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) : 1.774234 object centre at (A) : -56.77900 -3.025500 -22.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0546094E-03 -8.0012120E-02 midg,1,midg; midg,igrid,midg -3.8566075E-02 8.0113309E-03 1,midg,midg; igrid,midg,midg 0.1320916 8.6385868E-02 gauss-seidel spectral radius is 0.9992178 estimated iterations to convergence 282 setup time was (sec) 1.110000 now iterating at: 09:25:31 rms-change max change #iterations 9.283588 293.1143 at 10iterations 5.419511 144.3353 at 20iterations 3.125980 70.03117 at 30iterations 1.792784 41.88797 at 40iterations 1.025698 23.82877 at 50iterations 0.5838984 14.08709 at 60iterations 0.3311101 7.301384 at 70iterations 0.1883396 3.955009 at 80iterations 0.1068993 2.160986 at 90iterations 6.0444281E-02 1.251762 at 100iterations 3.4246016E-02 0.6624550 at 110iterations 1.9387797E-02 0.3718834 at 120iterations 1.0950687E-02 0.2553711 at 130iterations 6.2012933E-03 0.1224909 at 140iterations 3.5018597E-03 6.7350388E-02 at 150iterations 1.9830917E-03 4.2968750E-02 at 160iterations 1.1235634E-03 2.4702072E-02 at 170iterations 6.3648820E-04 1.3485193E-02 at 180iterations finished qdiffx linear iterations at : 09:25:42 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 6.3648820E-04 1.3485193E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 09:25:43 12.664u 0.219s 0:13.15 97.8% 0+0k 0+0io 0pf+0w